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Adebayo O, Bhatnagar S, Webb J, Campbell C, Fowler M, MacAdam NM, Macdonald A, Li C, Hubert CRJ. Hydrocarbon-degrading microbial populations in permanently cold deep-sea sediments in the NW Atlantic. MARINE POLLUTION BULLETIN 2024; 208:117052. [PMID: 39357372 DOI: 10.1016/j.marpolbul.2024.117052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 07/19/2024] [Accepted: 09/24/2024] [Indexed: 10/04/2024]
Abstract
Permanently cold deep-sea sediments (2500-3500 m water depth) with and without indications of thermogenic hydrocarbon seepage were exposed to naphtha to examine the presence and potential of cold-adapted aerobic hydrocarbon-degrading microbial populations. Monitoring these microcosms for volatile hydrocarbons by GC-MS revealed sediments without in situ hydrocarbons responded more rapidly to naphtha amendment than hydrocarbon seep sediments overall, but seep sediments removed aromatic hydrocarbons benzene, toluene, ethylbenzene and xylene (BTEX) more readily. Naphtha-driven aerobic respiration was more evident in surface sediment (0-20 cmbsf) than deeper anoxic layers (>130 cmbsf) that responded less rapidly. In all cases, enrichment of Gammaproteobacteria included lineages of Oleispira, Pseudomonas, and Alteromonas known to be associated with marine oil spills. On the other hand, taxa known to be prevalent in situ and diagnostic for thermogenic hydrocarbon seepage in deep sea sediment, did not respond to naphtha amendment. This suggests a limited role for these prevalent seep-associated populations in the context of aerobic hydrocarbon biodegradation.
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Affiliation(s)
- Oyeboade Adebayo
- Department of Biological Sciences, University of Calgary, AB T2N 1N4, Canada.
| | - Srijak Bhatnagar
- Department of Biological Sciences, University of Calgary, AB T2N 1N4, Canada; Faculty of Science and Technology, Athabasca University, Athabasca, AB T9S 3A3, Canada
| | - Jamie Webb
- Applied Petroleum Technology (Canada), Calgary, AB T2N 1Z6, Canada
| | - Calvin Campbell
- Geological Survey of Canada-Atlantic, Dartmouth, NS B3B 1A6, Canada
| | - Martin Fowler
- Applied Petroleum Technology (Canada), Calgary, AB T2N 1Z6, Canada
| | - Natasha M MacAdam
- Nova Scotia Department of Natural Resources and Renewables, Halifax, NS B2H 4G8, Canada
| | - Adam Macdonald
- Nova Scotia Department of Natural Resources and Renewables, Halifax, NS B2H 4G8, Canada
| | - Carmen Li
- Department of Biological Sciences, University of Calgary, AB T2N 1N4, Canada
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, AB T2N 1N4, Canada.
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Góngora E, Lirette AO, Freyria NJ, Greer CW, Whyte LG. Metagenomic survey reveals hydrocarbon biodegradation potential of Canadian high Arctic beaches. ENVIRONMENTAL MICROBIOME 2024; 19:72. [PMID: 39294752 PMCID: PMC11411865 DOI: 10.1186/s40793-024-00616-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 09/03/2024] [Indexed: 09/21/2024]
Abstract
BACKGROUND Decreasing sea ice coverage across the Arctic Ocean due to climate change is expected to increase shipping activity through previously inaccessible shipping routes, including the Northwest Passage (NWP). Changing weather conditions typically encountered in the Arctic will still pose a risk for ships which could lead to an accident and the uncontrolled release of hydrocarbons onto NWP shorelines. We performed a metagenomic survey to characterize the microbial communities of various NWP shorelines and to determine whether there is a metabolic potential for hydrocarbon degradation in these microbiomes. RESULTS We observed taxonomic and functional gene evidence supporting the potential of NWP beach microbes to degrade various types of hydrocarbons. The metagenomic and metagenome-assembled genome (MAG) taxonomy showed that known hydrocarbon-degrading taxa are present in these beaches. Additionally, we detected the presence of biomarker genes of aerobic and anaerobic degradation pathways of alkane and aromatic hydrocarbons along with complete degradation pathways for aerobic alkane degradation. Alkane degradation genes were present in all samples and were also more abundant (33.8 ± 34.5 hits per million genes, HPM) than their aromatic hydrocarbon counterparts (11.7 ± 12.3 HPM). Due to the ubiquity of MAGs from the genus Rhodococcus (23.8% of the MAGs), we compared our MAGs with Rhodococcus genomes from NWP isolates obtained using hydrocarbons as the carbon source to corroborate our results and to develop a pangenome of Arctic Rhodococcus. Our analysis revealed that the biodegradation of alkanes is part of the core pangenome of this genus. We also detected nitrogen and sulfur pathways as additional energy sources and electron donors as well as carbon pathways providing alternative carbon sources. These pathways occur in the absence of hydrocarbons allowing microbes to survive in these nutrient-poor beaches. CONCLUSIONS Our metagenomic analyses detected the genetic potential for hydrocarbon biodegradation in these NWP shoreline microbiomes. Alkane metabolism was the most prevalent type of hydrocarbon degradation observed in these tidal beach ecosystems. Our results indicate that bioremediation could be used as a cleanup strategy, but the addition of adequate amounts of N and P fertilizers, should be considered to help bacteria overcome the oligotrophic nature of NWP shorelines.
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Affiliation(s)
- Esteban Góngora
- Natural Resource Sciences, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC, Canada.
| | - Antoine-O Lirette
- Natural Resource Sciences, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC, Canada
| | - Nastasia J Freyria
- Natural Resource Sciences, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC, Canada
| | - Charles W Greer
- Natural Resource Sciences, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC, Canada
- Energy, Mining and Environment Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, Canada
| | - Lyle G Whyte
- Natural Resource Sciences, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC, Canada
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Chen J, Deng L, Wang X, Zhong C, Xia X, Liu H. Chemosynthetic alphaproteobacterial diazotrophs reside in deep-sea cold-seep bottom waters. mSystems 2024; 9:e0017624. [PMID: 39105582 PMCID: PMC11406894 DOI: 10.1128/msystems.00176-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 07/07/2024] [Indexed: 08/07/2024] Open
Abstract
Nitrogen (N)-fixing organisms, also known as diazotrophs, play a crucial role in N-limited ecosystems by controlling the production of bioavailable N. The carbon-dominated cold-seep ecosystems are inherently N-limited, making them hotspots of N fixation. However, the knowledge of diazotrophs in cold-seep ecosystems is limited compared to other marine ecosystems. In this study, we used multi-omics to investigate the diversity and catabolism of diazotrophs in deep-sea cold-seep bottom waters. Our findings showed that the relative abundance of diazotrophs in the bacterial community reached its highest level in the cold-seep bottom waters compared to the cold-seep upper waters and non-seep bottom waters. Remarkably, more than 98% of metatranscriptomic reads aligned on diazotrophs in cold-seep bottom waters belonged to the genus Sagittula, an alphaproteobacterium. Its metagenome-assembled genome, named Seep-BW-D1, contained catalytic genes (nifHDK) for nitrogen fixation, and the nifH gene was actively transcribed in situ. Seep-BW-D1 also exhibited chemosynthetic capability to oxidize C1 compounds (methanol, formaldehyde, and formate) and thiosulfate (S2O32-). In addition, we observed abundant transcripts mapped to genes involved in the transport systems for acetate, spermidine/putrescine, and pectin oligomers, suggesting that Seep-BW-D1 can utilize organics from the intermediates synthesized by methane-oxidizing microorganisms, decaying tissues from cold-seep benthic animals, and refractory pectin derived from upper photosynthetic ecosystems. Overall, our study corroborates that carbon-dominated cold-seep bottom waters select for diazotrophs and reveals the catabolism of a novel chemosynthetic alphaproteobacterial diazotroph in cold-seep bottom waters. IMPORTANCE Bioavailable nitrogen (N) is a crucial element for cellular growth and division, and its production is controlled by diazotrophs. Marine diazotrophs contribute to nearly half of the global fixed N and perform N fixation in various marine ecosystems. While previous studies mainly focused on diazotrophs in the sunlit ocean and oxygen minimum zones, recent research has recognized cold-seep ecosystems as overlooked N-fixing hotspots because the seeping fluids in cold-seep ecosystems introduce abundant bioavailable carbon but little bioavailable N, making most cold seeps inherently N-limited. With thousands of cold-seep ecosystems detected at continental margins worldwide in the past decades, the significant role of cold seeps in marine N biogeochemical cycling is emphasized. However, the diazotrophs in cold-seep bottom waters remain poorly understood. Through multi-omics, this study identified a novel alphaproteobacterial chemoheterotroph belonging to Sagittula as one of the most active diazotrophs residing in cold-seep bottom waters and revealed its catabolism.
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Affiliation(s)
- Jiawei Chen
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Lixia Deng
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Xiao Wang
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Cheng Zhong
- College of Chemistry and Chemical Engineering, Southwest Petroleum University, Chengdu, Sichuan, China
| | - Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Innovation Research Center for Carbon Neutralization, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Hongbin Liu
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong, China
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Yin X, Chen H, Jiang K, Zhang B, Li R, Zhu X, Sun L, Ng ZL, Su M. Distribution Characteristics of Nitrogen-Cycling Microorganisms in Deep-Sea Surface Sediments of Western South China Sea. Microorganisms 2024; 12:1901. [PMID: 39338575 PMCID: PMC11434414 DOI: 10.3390/microorganisms12091901] [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: 08/19/2024] [Revised: 09/11/2024] [Accepted: 09/11/2024] [Indexed: 09/30/2024] Open
Abstract
Nitrogen-cycling processes in the deep sea remain understudied. This study investigates the distribution of nitrogen-cycling microbial communities in the deep-sea surface sediments of the western South China Sea, using metagenomic sequencing and real-time fluorescent quantitative PCR techniques to analyze their composition and abundance, and the effects of 11 environmental parameters, including NH4+-N, NO3--N, NO2--N, PO43--P, total nitrogen (TN), total organic carbon (TOC), C/N ratio, pH, electrical conductivity (EC), SO42-, and Cl-. The phylum- and species-level microbial community compositions show that five sites can be grouped as a major cluster, with sites S1 and S9 forming a sub-cluster, and sites S13, S19, and S26 forming the other; whereas sites S3 and S5 constitute a separate cluster. This is also evident for nitrogen-cycling functional genes, where their abundance is influenced by distinct environmental conditions, including water depths (shallower at sites S1 and S9 against deeper at sites S13, S19, and S26) and unique geological features (sites S3 and S5), whereas the vertical distribution of nitrogen-cycling gene abundance generally shows a decreasing trend against sediment depth. Redundancy analysis (RDA) exploring the correlation between the 11 environmental parameters and microbial communities revealed that the NO2--N, C/N ratio, and TN significantly affect microbial community composition (p < 0.05). This study assesses the survival strategies of microorganisms within deep-sea surface sediments and their role in the marine nitrogen cycle.
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Affiliation(s)
- Xingjia Yin
- School of Marine Sciences, Sun Yat-Sen University & Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; (X.Y.); (H.C.); (K.J.); (B.Z.); (Z.L.N.)
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai 519082, China
- College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Hui Chen
- School of Marine Sciences, Sun Yat-Sen University & Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; (X.Y.); (H.C.); (K.J.); (B.Z.); (Z.L.N.)
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai 519082, China
| | - Kaixi Jiang
- School of Marine Sciences, Sun Yat-Sen University & Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; (X.Y.); (H.C.); (K.J.); (B.Z.); (Z.L.N.)
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai 519082, China
- Office of Laboratory Safety and Equipment Management, Beijing Normal University, Zhuhai 519087, China
| | - Boda Zhang
- School of Marine Sciences, Sun Yat-Sen University & Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; (X.Y.); (H.C.); (K.J.); (B.Z.); (Z.L.N.)
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai 519082, China
- Center for Environmental Monitoring of Geology, Shenzhen 518034, China
| | - Ruohong Li
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China; (R.L.); (X.Z.); (L.S.)
| | - Xinzhe Zhu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China; (R.L.); (X.Z.); (L.S.)
| | - Lianpeng Sun
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China; (R.L.); (X.Z.); (L.S.)
| | - Zhi Lin Ng
- School of Marine Sciences, Sun Yat-Sen University & Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; (X.Y.); (H.C.); (K.J.); (B.Z.); (Z.L.N.)
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai 519082, China
| | - Ming Su
- School of Marine Sciences, Sun Yat-Sen University & Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; (X.Y.); (H.C.); (K.J.); (B.Z.); (Z.L.N.)
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai 519082, China
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Su L, Marshall IPG, Teske AP, Yao H, Li J. Genomic characterization of the bacterial phylum Candidatus Effluviviacota, a cosmopolitan member of the global seep microbiome. mBio 2024; 15:e0099224. [PMID: 38980039 PMCID: PMC11323493 DOI: 10.1128/mbio.00992-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 06/17/2024] [Indexed: 07/10/2024] Open
Abstract
The microbial communities of marine seep sediments contain unexplored physiological and phylogenetic diversity. Here, we examined 30 bacterial metagenome-assembled genomes (MAGs) from cold seeps in the South China Sea, the Indian Ocean, the Scotian Basin, and the Gulf of Mexico, as well as from deep-sea hydrothermal sediments in the Guaymas Basin, Gulf of California. Phylogenetic analyses of these MAGs indicate that they form a distinct phylum-level bacterial lineage, which we propose as a new phylum, Candidatus Effluviviacota, in reference to its preferential occurrence at diverse seep areas. Based on tightly clustered high-quality MAGs, we propose two new genus-level candidatus taxa, Candidatus Effluvivivax and Candidatus Effluvibates. Genomic content analyses indicate that Candidatus Effluviviacota are chemoheterotrophs that harbor the Embden-Meyerhof-Parnas glycolysis pathway. They gain energy by fermenting organic substrates. Additionally, they display potential capabilities for the degradation of cellulose, hemicellulose, starch, xylan, and various peptides. Extracellular anaerobic respiration appears to rely on metals as electron acceptors, with electron transfer primarily mediated by multiheme cytochromes and by a flavin-based extracellular electron transfer (EET) mechanism that involves NADH-quinone oxidoreductase-demethylmenaquinone-synthesizing enzymes, uncharacterized membrane proteins, and flavin-binding proteins, also known as the NUO-DMK-EET-FMN complex. The heterogeneity within the Ca. Effluviviacota phylum suggests varying roles in energy metabolism among different genera. While NUO-DMK-EET-FMN electron transfer has been reported predominantly in Gram-positive bacteria, it is now identified in Ca. Effluviviacota as well. We detected the presence of genes associated with bacterial microcompartments in Ca. Effluviviacota, which can promote specific metabolic processes and protect the cytosol from toxic intermediates. IMPORTANCE The newly discovered bacterial phylum Candidatus Effluviviacota is widespread across diverse seepage ecosystems, marine environments, and freshwater environments, with a notable preference for cold seeps. While maintaining an average abundance of approximately 1% in the global gene catalog of cold seep habitats, it has not hitherto been characterized. The metabolic versatility of Ca. Effluviviacota in anaerobic carbon, hydrogen, and metal cycling aligns with its prevalence in anoxic niches, with a preference for cold seep environments. Variations in metabolic potential between Ca. Effluvivivax and Ca. Effluvibates may contribute to shaping their respective habitat distributions.
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Affiliation(s)
- Lei Su
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
- Department of Biology, Center for Electromicrobiology (CEM), Section for Microbiology, Aarhus University, Aarhus, Denmark
| | - Ian P. G. Marshall
- Department of Biology, Center for Electromicrobiology (CEM), Section for Microbiology, Aarhus University, Aarhus, Denmark
| | - Andreas P. Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Huiqiang Yao
- MLR Key Laboratory of Marine Mineral Resources, Guangzhou Marine Geological Survey, Guangzhou, China
| | - Jiangtao Li
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
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Yan W, Wang D, Wang Y, Wang C, Chen X, Liu L, Wang Y, Li YY, Kamagata Y, Nobu MK, Zhang T. Metatranscriptomics-guided genome-scale metabolic reconstruction reveals the carbon flux and trophic interaction in methanogenic communities. MICROBIOME 2024; 12:121. [PMID: 38970122 PMCID: PMC11225162 DOI: 10.1186/s40168-024-01830-z] [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: 12/16/2023] [Accepted: 05/06/2024] [Indexed: 07/07/2024]
Abstract
BACKGROUND Despite rapid advances in genomic-resolved metagenomics and remarkable explosion of metagenome-assembled genomes (MAGs), the function of uncultivated anaerobic lineages and their interactions in carbon mineralization remain largely uncertain, which has profound implications in biotechnology and biogeochemistry. RESULTS In this study, we combined long-read sequencing and metatranscriptomics-guided metabolic reconstruction to provide a genome-wide perspective of carbon mineralization flow from polymers to methane in an anaerobic bioreactor. Our results showed that incorporating long reads resulted in a substantial improvement in the quality of metagenomic assemblies, enabling the effective recovery of 132 high-quality genomes meeting stringent criteria of minimum information about a metagenome-assembled genome (MIMAG). In addition, hybrid assembly obtained 51% more prokaryotic genes in comparison to the short-read-only assembly. Metatranscriptomics-guided metabolic reconstruction unveiled the remarkable metabolic flexibility of several novel Bacteroidales-affiliated bacteria and populations from Mesotoga sp. in scavenging amino acids and sugars. In addition to recovering two circular genomes of previously known but fragmented syntrophic bacteria, two newly identified bacteria within Syntrophales were found to be highly engaged in fatty acid oxidation through syntrophic relationships with dominant methanogens Methanoregulaceae bin.74 and Methanothrix sp. bin.206. The activity of bin.206 preferring acetate as substrate exceeded that of bin.74 with increasing loading, reinforcing the substrate determinantal role. CONCLUSION Overall, our study uncovered some key active anaerobic lineages and their metabolic functions in this complex anaerobic ecosystem, offering a framework for understanding carbon transformations in anaerobic digestion. These findings advance the understanding of metabolic activities and trophic interactions between anaerobic guilds, providing foundational insights into carbon flux within both engineered and natural ecosystems. Video Abstract.
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Affiliation(s)
- Weifu Yan
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Dou Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yubo Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Chunxiao Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xi Chen
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yu-You Li
- Laboratory of Environmental Protection Engineering, Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi, 980-8579, Japan
| | - Yoichi Kamagata
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Masaru K Nobu
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, 237-0061, Japan
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China.
- School of Public Health, The University of Hong Kong, Hong Kong SAR, China.
- Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macao SAR, China.
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Wang C, Zheng R, Sun C. Multi-omics analyses provide insights into the sulfur metabolism of a novel deep-sea sulfate-reducing bacterium. iScience 2024; 27:110095. [PMID: 38947506 PMCID: PMC11214288 DOI: 10.1016/j.isci.2024.110095] [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: 01/24/2024] [Revised: 04/02/2024] [Accepted: 05/21/2024] [Indexed: 07/02/2024] Open
Abstract
Sulfate-reducing bacteria (SRB) are ubiquitously distributed across various biospheres and play key roles in global sulfur and carbon cycles. However, few deep-sea SRB have been cultivated and studied in situ, limiting our understanding of the true metabolism of deep-sea SRB. Here, we firstly clarified the high abundance of SRB in deep-sea sediments and successfully isolated a sulfate-reducing bacterium (zrk46) from a cold seep sediment. Our genomic, physiological, and phylogenetic analyses indicate that strain zrk46 is a novel species, which we propose as Pseudodesulfovibrio serpens. We found that supplementation with sulfate, thiosulfate, or sulfite promoted strain zrk46 growth by facilitating energy production through the dissimilatory sulfate reduction, which was coupled to the oxidation of organic matter in both laboratory and deep-sea conditions. Moreover, in situ metatranscriptomic results confirmed that other deep-sea SRB also performed the dissimilatory sulfate reduction, strongly suggesting that SRB may play undocumented roles in deep-sea sulfur cycling.
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Affiliation(s)
- Chong Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Rikuan Zheng
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Chaomin Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
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8
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Chen Y, Dong X, Sun Z, Xu C, Zhang X, Qin S, Geng W, Cao H, Zhai B, Li X, Wu N. Potential coupling of microbial methane, nitrogen, and sulphur cycling in the Okinawa Trough cold seep sediments. Microbiol Spectr 2024; 12:e0349023. [PMID: 38690913 PMCID: PMC11237511 DOI: 10.1128/spectrum.03490-23] [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: 09/28/2023] [Accepted: 03/13/2024] [Indexed: 05/03/2024] Open
Abstract
The Okinawa Trough (OT) is a back-arc basin with a wide distribution of active cold seep systems. However, our understanding of the metabolic function of microbial communities in the cold seep sediments of the OT remains limited. In this study, we investigated the vertical profiles of functional genes involved in methane, nitrogen, and sulphur cycling in the cold seep sediments of the OT. Furthermore, we explored the possible coupling mechanisms between these biogeochemical cycles. The study revealed that the majority of genes associated with the nitrogen and sulphur cycles were most abundant in the surface sediment layers. However, only the key genes responsible for sulphur disproportionation (sor), nitrogen fixation (nifDKH), and methane metabolism (mcrABG) were more prevalent within sulfate-methane transition zone (SMTZ). Significant positive correlations (P < 0.05) were observed between functional genes involved in sulphur oxidation, thiosulphate disproportionation with denitrification, and dissimilatory nitrate reduction to ammonium (DNRA), as well as between AOM/methanogenesis and nitrogen fixation, and between sulphur disproportionation and AOM. A genome of Filomicrobium (class Alphaproteobacteria) has demonstrated potential in chemoautotrophic activities, particularly in coupling DNRA and denitrification with sulphur oxidation. Additionally, the characterized sulfate reducers such as Syntrophobacterales have been found to be capable of utilizing nitrate as an electron acceptor. The predominant methanogenic/methanotrophic groups in the OT sediments were identified as H2-dependent methylotrophic methanogens (Methanomassiliicoccales and Methanofastidiosales) and ANME-1a. This study offered a thorough understanding of microbial ecosystems in the OT cold seep sediments, emphasizing their contribution to nutrient cycling.IMPORTANCEThe Okinawa Trough (OT) is a back-arc basin formed by extension within the continental lithosphere behind the Ryukyu Trench arc system. Cold seeps are widespread in the OT. While some studies have explored microbial communities in OT cold seep sediments, their metabolic potential remains largely unknown. In this study, we used metagenomic analysis to enhance comprehension of the microbial community's role in nutrient cycling and proposed hypotheses on the coupling process and mechanisms involved in biogeochemical cycles. It was revealed that multiple metabolic pathways can be performed by a single organism or microbes that interact with each other to carry out various biogeochemical cycling. This data set provided a genomic road map on microbial nutrient cycling in OT sediment microbial communities.
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Affiliation(s)
- Ye Chen
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Zhilei Sun
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Cuiling Xu
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Xilin Zhang
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Shuangshuang Qin
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, China
| | - Wei Geng
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Hong Cao
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Bin Zhai
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Xuecheng Li
- China Offshore Fugro Geosolutions (Shenzhen)Co.Ltd., Shenzhen, China
| | - Nengyou Wu
- Key Laboratory of Gas Hydrate, Qingdao Institute of Marine Geology, Ministry of Natural Resources, Qingdao, China
- Laboratory for Marine Mineral Resources, Qingdao Marine Science and Technology Center, Qingdao, China
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9
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Zhang Y, Chen H, Lian C, Cao L, Guo Y, Wang M, Zhong Z, Li M, Zhang H, Li C. Insights into phage-bacteria interaction in cold seep Gigantidas platifrons through metagenomics and transcriptome analyses. Sci Rep 2024; 14:10540. [PMID: 38719945 PMCID: PMC11078923 DOI: 10.1038/s41598-024-61272-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 05/03/2024] [Indexed: 05/12/2024] Open
Abstract
Viruses are crucial for regulating deep-sea microbial communities and biogeochemical cycles. However, their roles are still less characterized in deep-sea holobionts. Bathymodioline mussels are endemic species inhabiting cold seeps and harboring endosymbionts in gill epithelial cells for nutrition. This study unveiled a diverse array of viruses in the gill tissues of Gigantidas platifrons mussels and analyzed the viral metagenome and transcriptome from the gill tissues of Gigantidas platifrons mussels collected from a cold seep in the South Sea. The mussel gills contained various viruses including Baculoviridae, Rountreeviridae, Myoviridae and Siphovirdae, but the active viromes were Myoviridae, Siphoviridae, and Podoviridae belonging to the order Caudovirales. The overall viral community structure showed significant variation among environments with different methane concentrations. Transcriptome analysis indicated high expression of viral structural genes, integrase, and restriction endonuclease genes in a high methane concentration environment, suggesting frequent virus infection and replication. Furthermore, two viruses (GP-phage-contig14 and GP-phage-contig72) interacted with Gigantidas platifrons methanotrophic gill symbionts (bathymodiolin mussels host intracellular methanotrophic Gammaproteobacteria in their gills), showing high expression levels, and have huge different expression in different methane concentrations. Additionally, single-stranded DNA viruses may play a potential auxiliary role in the virus-host interaction using indirect bioinformatics methods. Moreover, the Cro and DNA methylase genes had phylogenetic similarity between the virus and Gigantidas platifrons methanotrophic gill symbionts. This study also explored a variety of viruses in the gill tissues of Gigantidas platifrons and revealed that bacteria interacted with the viruses during the symbiosis with Gigantidas platifrons. This study provides fundamental insights into the interplay of microorganisms within Gigantidas platifrons mussels in deep sea.
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Affiliation(s)
- Yan Zhang
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Hao Chen
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Chao Lian
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Lei Cao
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yang Guo
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Minxiao Wang
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Zhaoshan Zhong
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Mengna Li
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- National Deep Sea Center, Qingdao, 266071, China
| | - Huan Zhang
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- National Deep Sea Center, Qingdao, 266071, China
| | - Chaolun Li
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China.
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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10
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Dong X, Zhang T, Wu W, Peng Y, Liu X, Han Y, Chen X, Gao Z, Xia J, Shao Z, Greening C. A vast repertoire of secondary metabolites potentially influences community dynamics and biogeochemical processes in cold seeps. SCIENCE ADVANCES 2024; 10:eadl2281. [PMID: 38669328 PMCID: PMC11051675 DOI: 10.1126/sciadv.adl2281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 03/27/2024] [Indexed: 04/28/2024]
Abstract
In deep-sea cold seeps, microbial communities thrive on the geological seepage of hydrocarbons and inorganic compounds, differing from photosynthetically driven ecosystems. However, their biosynthetic capabilities remain largely unexplored. Here, we analyzed 81 metagenomes, 33 metatranscriptomes, and 7 metabolomes derived from nine different cold seep areas to investigate their secondary metabolites. Cold seep microbiomes encode diverse and abundant biosynthetic gene clusters (BGCs). Most BGCs are affiliated with understudied bacteria and archaea, including key mediators of methane and sulfur cycling. The BGCs encode diverse antimicrobial compounds that potentially shape community dynamics and various metabolites predicted to influence biogeochemical cycling. BGCs from key players are widely distributed and highly expressed, with their abundance and expression levels varying with sediment depth. Sediment metabolomics reveals unique natural products, highlighting uncharted chemical potential and confirming BGC activity in these sediments. Overall, these results demonstrate that cold seep sediments serve as a reservoir of hidden natural products and sheds light on microbial adaptation in chemosynthetically driven ecosystems.
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Affiliation(s)
- Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
| | - Tianxueyu Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, China
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310005, China
| | - Weichao Wu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Science, Shanghai Ocean University, Shanghai 201306, China
| | - Yongyi Peng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
| | - Xinyue Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Yingchun Han
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Xiangwei Chen
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Zhizeng Gao
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
| | - Jinmei Xia
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
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11
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Chowdhury A, Ventura GT, Owino Y, Lalk EJ, MacAdam N, Dooma JM, Ono S, Fowler M, MacDonald A, Bennett R, MacRae RA, Hubert CRJ, Bentley JN, Kerr MJ. Cold seep formation from salt diapir-controlled deep biosphere oases. Proc Natl Acad Sci U S A 2024; 121:e2316878121. [PMID: 38466851 PMCID: PMC10963010 DOI: 10.1073/pnas.2316878121] [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: 09/29/2023] [Accepted: 01/24/2024] [Indexed: 03/13/2024] Open
Abstract
Deep sea cold seeps are sites where hydrogen sulfide, methane, and other hydrocarbon-rich fluids vent from the ocean floor. They are an important component of Earth's carbon cycle in which subsurface hydrocarbons form the energy source for highly diverse benthic micro- and macro-fauna in what is otherwise vast and spartan sea scape. Passive continental margin cold seeps are typically attributed to the migration of hydrocarbons generated from deeply buried source rocks. Many of these seeps occur over salt tectonic provinces, where the movement of salt generates complex fault systems that can enable fluid migration or create seals and traps associated with reservoir formation. The elevated advective heat transport of the salt also produces a chimney effect directly over these structures. Here, we provide geophysical and geochemical evidence that the salt chimney effect in conjunction with diapiric faulting drives a subsurface groundwater circulation system that brings dissolved inorganic carbon, nutrient-rich deep basinal fluids, and potentially overlying seawater onto the crests of deeply buried salt diapirs. The mobilized fluids fuel methanogenic archaea locally enhancing the deep biosphere. The resulting elevated biogenic methane production, alongside the upward heat-driven fluid transport, represents a previously unrecognized mechanism of cold seep formation and regulation.
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Affiliation(s)
- Anirban Chowdhury
- Department of Geology, Saint Mary’s University, Halifax, NSB3H 3C3, Canada
| | - Gregory T. Ventura
- Department of Geology, Saint Mary’s University, Halifax, NSB3H 3C3, Canada
| | - Yaisa Owino
- Department of Geology, Saint Mary’s University, Halifax, NSB3H 3C3, Canada
| | - Ellen J. Lalk
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Natasha MacAdam
- Nova Scotia Department of Natural Resources and Renewables, Halifax, NSB3J 3J9, Canada
| | - John M. Dooma
- Department of Geology, Saint Mary’s University, Halifax, NSB3H 3C3, Canada
| | - Shuhei Ono
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Martin Fowler
- Applied Petroleum Technology (Canada) Ltd., Calgary, ABT3A 2M3, Canada
| | - Adam MacDonald
- Nova Scotia Department of Natural Resources and Renewables, Halifax, NSB3J 3J9, Canada
| | - Robbie Bennett
- Natural Resources Canada, Geological Survey of Canada-Atlantic, Dartmouth, NSB2Y 4A2, Canada
| | - R. Andrew MacRae
- Department of Geology, Saint Mary’s University, Halifax, NSB3H 3C3, Canada
| | - Casey R. J. Hubert
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, ABT2N 1N4, Canada
| | - Jeremy N. Bentley
- Department of Geology, Saint Mary’s University, Halifax, NSB3H 3C3, Canada
| | - Mitchell J. Kerr
- Department of Geology, Saint Mary’s University, Halifax, NSB3H 3C3, Canada
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12
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Wu Z, Yu X, Ji Y, Liu G, Gao P, Xia L, Li P, Liang B, Freilich S, Gu L, Qiao W, Jiang J. Flexible catabolism of monoaromatic hydrocarbons by anaerobic microbiota adapting to oxygen exposure. JOURNAL OF HAZARDOUS MATERIALS 2024; 462:132762. [PMID: 37837778 DOI: 10.1016/j.jhazmat.2023.132762] [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: 07/17/2023] [Revised: 09/26/2023] [Accepted: 10/10/2023] [Indexed: 10/16/2023]
Abstract
Microbe-mediated anaerobic degradation is a practical method for remediation of the hazardous monoaromatic hydrocarbons (BTEX, including benzene, toluene, ethylbenzene and xylenes) under electron-deficient contaminated sites. However, how do the anaerobic functional microbes adapt to oxygen exposure and flexibly catabolize BTEX remain poorly understood. We investigated the switches of substrate spectrum and bacterial community upon oxygen perturbation in a nitrate-amended anaerobic toluene-degrading microbiota which was dominated by Aromatoleum species. DNA-stable isotope probing demonstrated that Aromatoleum species was involved in anaerobic mineralization of toluene. Metagenome-assembled genome of Aromatoleum species harbored both the nirBD-type genes for nitrate reduction to ammonium coupled with toluene oxidation and the additional meta-cleavage pathway for aerobic benzene catabolism. Once the anaerobic microbiota was fully exposed to oxygen and benzene, 1.05 ± 0.06% of Diaphorobacter species rapidly replaced Aromatoleum species and flourished to 96.72 ± 0.01%. Diaphorobacter sp. ZM was isolated, which was not only able to utilize benzene as the sole carbon source for aerobic growth and but also innovatively reduce nitrate to ammonium with citrate/lactate/glucose as the carbon source under anaerobic conditions. This study expands our understanding of the adaptive mechanism of microbiota for environmental redox disturbance and provides theoretical guidance for the bioremediation of BTEX-contaminated sites.
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Affiliation(s)
- Zhiming Wu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Yu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanhan Ji
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Guiping Liu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ping Gao
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lei Xia
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Pengfa Li
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Bin Liang
- State Key Laboratory of Urban Water Resource and Environment, School of Civil & Environmental Engineering, Harbin Institute of Technology Shenzhen, Shenzhen 518055, China
| | - Shiri Freilich
- Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Lifeng Gu
- ChangXing AISHENG Environmental Technology Co., Ltd, Zhejiang 313199, China
| | - Wenjing Qiao
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jiandong Jiang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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13
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Benito Merino D, Lipp JS, Borrel G, Boetius A, Wegener G. Anaerobic hexadecane degradation by a thermophilic Hadarchaeon from Guaymas Basin. THE ISME JOURNAL 2024; 18:wrad004. [PMID: 38365230 PMCID: PMC10811742 DOI: 10.1093/ismejo/wrad004] [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: 10/25/2023] [Accepted: 11/06/2023] [Indexed: 02/18/2024]
Abstract
Hadarchaeota inhabit subsurface and hydrothermally heated environments, but previous to this study, they had not been cultured. Based on metagenome-assembled genomes, most Hadarchaeota are heterotrophs that grow on sugars and amino acids, or oxidize carbon monoxide or reduce nitrite to ammonium. A few other metagenome-assembled genomes encode alkyl-coenzyme M reductases (Acrs), β-oxidation, and Wood-Ljungdahl pathways, pointing toward multicarbon alkane metabolism. To identify the organisms involved in thermophilic oil degradation, we established anaerobic sulfate-reducing hexadecane-degrading cultures from hydrothermally heated sediments of the Guaymas Basin. Cultures at 70°C were enriched in one Hadarchaeon that we propose as Candidatus Cerberiarchaeum oleivorans. Genomic and chemical analyses indicate that Ca. C. oleivorans uses an Acr to activate hexadecane to hexadecyl-coenzyme M. A β-oxidation pathway and a tetrahydromethanopterin methyl branch Wood-Ljungdahl (mWL) pathway allow the complete oxidation of hexadecane to CO2. Our results suggest a syntrophic lifestyle with sulfate reducers, as Ca. C. oleivorans lacks a sulfate respiration pathway. Comparative genomics show that Acr, mWL, and β-oxidation are restricted to one family of Hadarchaeota, which we propose as Ca. Cerberiarchaeaceae. Phylogenetic analyses further indicate that the mWL pathway is basal to all Hadarchaeota. By contrast, the carbon monoxide dehydrogenase/acetyl-coenzyme A synthase complex in Ca. Cerberiarchaeaceae was horizontally acquired from Bathyarchaeia. The Acr and β-oxidation genes of Ca. Cerberiarchaeaceae are highly similar to those of other alkane-oxidizing archaea such as Ca. Methanoliparia and Ca. Helarchaeales. Our results support the use of Acrs in the degradation of petroleum alkanes and suggest a role of Hadarchaeota in oil-rich environments.
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Affiliation(s)
- David Benito Merino
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Klagenfurter Straße 2, 428359, Bremen, Germany
| | - Julius S Lipp
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, 28359, Bremen, Germany
| | - Guillaume Borrel
- Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, 25 rue du Dr Roux, 75015, Paris, France
| | - Antje Boetius
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, 28359, Bremen, Germany
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, 28359, Bremen, Germany
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14
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Liu Z, Huang Y, Chen H, Liu C, Wang M, Bian C, Wang L, Song L. Chromosome-level genome assembly of the deep-sea snail Phymorhynchus buccinoides provides insights into the adaptation to the cold seep habitat. BMC Genomics 2023; 24:679. [PMID: 37950158 PMCID: PMC10638732 DOI: 10.1186/s12864-023-09760-0] [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: 02/09/2023] [Accepted: 10/22/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND The deep-sea snail Phymorhynchus buccinoides belongs to the genus Phymorhynchus (Neogastropoda: Raphitomidae), and it is a dominant specie in the cold seep habitat. As the environment of the cold seep is characterized by darkness, hypoxia and high concentrations of toxic substances such as hydrogen sulfide (H2S), exploration of the diverse fauna living around cold seeps will help to uncover the adaptive mechanisms to this unique habitat. In the present study, a chromosome-level genome of P. buccinoides was constructed and a series of genomic and transcriptomic analyses were conducted to explore its molecular adaptation mechanisms to the cold seep environments. RESULTS The assembled genome size of the P. buccinoides was approximately 2.1 Gb, which is larger than most of the reported snail genomes, possibly due to the high proportion of repetitive elements. About 92.0% of the assembled base pairs of contigs were anchored to 34 pseudo-chromosomes with a scaffold N50 size of 60.0 Mb. Compared with relative specie in the shallow water, the glutamate regulative and related genes were expanded in P. buccinoides, which contributes to the acclimation to hypoxia and coldness. Besides, the relatively high mRNA expression levels of the olfactory/chemosensory genes in osphradium indicate that P. buccinoides might have evolved a highly developed and sensitive olfactory organ for its orientation and predation. Moreover, the genome and transcriptome analyses demonstrate that P. buccinoides has evolved a sulfite-tolerance mechanism by performing H2S detoxification. Many genes involved in H2S detoxification were highly expressed in ctenidium and hepatopancreas, suggesting that these tissues might be critical for H2S detoxification and sulfite tolerance. CONCLUSIONS In summary, our report of this chromosome-level deep-sea snail genome provides a comprehensive genomic basis for the understanding of the adaptation strategy of P. buccinoides to the extreme environment at the deep-sea cold seeps.
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Affiliation(s)
- Zhaoqun Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China
- Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
- Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Yuting Huang
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Chen
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Chang Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China
- Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
- Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Minxiao Wang
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Chao Bian
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China.
- Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China.
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China.
- Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China.
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China.
- Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China.
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China.
- Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China.
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15
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Peng Y, Lu Z, Pan D, Shi LD, Zhao Z, Liu Q, Zhang C, Jia K, Li J, Hubert CRJ, Dong X. Viruses in deep-sea cold seep sediments harbor diverse survival mechanisms and remain genetically conserved within species. THE ISME JOURNAL 2023; 17:1774-1784. [PMID: 37573455 PMCID: PMC10504277 DOI: 10.1038/s41396-023-01491-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 08/14/2023]
Abstract
Deep sea cold seep sediments have been discovered to harbor novel, abundant, and diverse bacterial and archaeal viruses. However, little is known about viral genetic features and evolutionary patterns in these environments. Here, we examined the evolutionary ecology of viruses across active and extinct seep stages in the area of Haima cold seeps in the South China Sea. A total of 338 viral operational taxonomic units are identified and linked to 36 bacterial and archaeal phyla. The dynamics of host-virus interactions are informed by diverse antiviral defense systems across 43 families found in 487 microbial genomes. Cold seep viruses are predicted to harbor diverse adaptive strategies to persist in this environment, including counter-defense systems, auxiliary metabolic genes, reverse transcriptases, and alternative genetic code assignments. Extremely low nucleotide diversity is observed in cold seep viral populations, being influenced by factors including microbial host, sediment depth, and cold seep stage. Most cold seep viral genes are under strong purifying selection with trajectories that differ depending on whether cold seeps are active or extinct. This work sheds light on the understanding of environmental adaptation mechanisms and evolutionary patterns of viruses in the sub-seafloor biosphere.
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Affiliation(s)
- Yongyi Peng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Zijian Lu
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Donald Pan
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Ling-Dong Shi
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhao Zhao
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
| | - Qing Liu
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Chuwen Zhang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Kuntong Jia
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Jiwei Li
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
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16
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Liu WW, Pan P, Zhou NY. The presence of benzene ring activating CoA ligases for aromatics degradation in the ANaerobic MEthanotrophic (ANME) archaea. Microbiol Spectr 2023; 11:e0176623. [PMID: 37754561 PMCID: PMC10581246 DOI: 10.1128/spectrum.01766-23] [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: 04/27/2023] [Accepted: 08/03/2023] [Indexed: 09/28/2023] Open
Abstract
Petroleum-source and black carbon-source aromatic compounds are present in the cold seep environments, where ANaerobic MEthanotrophic (ANME) archaea as the dominant microbial community mediates the anaerobic oxidation of methane to produce inorganic and organic carbon. Here, by predicting the aromatics catabolic pathways in ANME metagenome-assembled genomes, we provide genomic and biochemical evidences that ANME have the potential of metabolizing aromatics via the strategy of CoA activation of the benzene ring using phenylacetic acid and benzoate as the substrates. Two ring-activating enzymes phenylacetate-CoA ligase (PaaKANME) and benzoate-CoA ligase (BadAANME) are able to convert phenylacetate to phenylacetyl-CoA and benzoate to benzoyl-CoA in vitro, respectively. They are mesophilic, alkali resistance, and with broad substrate spectra showing different affinity with various substrates. An exploration of the relative gene abundance in ANME genomes and cold seep environments indicates that about 50% of ANME genomes contain PCL genes, and various bacteria and archaea contain PCL and BCL genes. The results provide evidences for the capability of heterotrophic metabolism of aromatic compounds by ANME. This has not only enhanced our understanding of the nutrient range of ANME but also helped to explore the additional ecological and biogeochemical significance of this ubiquitous sedimentary archaea in the carbon flow in the cold seep environments. IMPORTANCE ANaerobic MEthanotrophic (ANME) archaea is the dominant microbial community mediating the anaerobic oxidation of methane in the cold seep environments, where aromatic compounds are present. Then it is hypothesized that ANME may be involved in the metabolism of aromatics. Here, we provide genomic and biochemical evidences for the heterotrophic metabolism of aromatic compounds by ANME, enhancing our understanding of their nutrient range and also shedding light on the ecological and biogeochemical significance of these ubiquitous sedimentary archaea in carbon flow within cold seep environments. Overall, this study offers valuable insights into the metabolic capabilities of ANME and their potential contributions to the global carbon cycle.
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Affiliation(s)
- Wei-Wei Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Piaopiao Pan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Han Y, Zhang C, Zhao Z, Peng Y, Liao J, Jiang Q, Liu Q, Shao Z, Dong X. A comprehensive genomic catalog from global cold seeps. Sci Data 2023; 10:596. [PMID: 37684262 PMCID: PMC10491686 DOI: 10.1038/s41597-023-02521-4] [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: 04/12/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
Cold seeps harbor abundant and diverse microbes with tremendous potential for biological applications and that have a significant influence on biogeochemical cycles. Although recent metagenomic studies have expanded our understanding of the community and function of seep microorganisms, knowledge of the diversity and genetic repertoire of global seep microbes is lacking. Here, we collected a compilation of 165 metagenomic datasets from 16 cold seep sites across the globe to construct a comprehensive gene and genome catalog. The non-redundant gene catalog comprised 147 million genes, and 36% of them could not be assigned to a function with the currently available databases. A total of 3,164 species-level representative metagenome-assembled genomes (MAGs) were obtained, most of which (94%) belonged to novel species. Of them, 81 ANME species were identified that cover all subclades except ANME-2d, and 23 syntrophic SRB species spanned the Seep-SRB1a, Seep-SRB1g, and Seep-SRB2 clades. The non-redundant gene and MAG catalog is a valuable resource that will aid in deepening our understanding of the functions of cold seep microbiomes.
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Affiliation(s)
- Yingchun Han
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Chuwen Zhang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Zhuoming Zhao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Yongyi Peng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Jing Liao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Qiuyun Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Qing Liu
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
| | - Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
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18
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Liu Y, Chen S, Wang J, Shao B, Fang J, Cao J. The Phylogeny, Metabolic Potentials, and Environmental Adaptation of an Anaerobe, Abyssisolibacter sp. M8S5, Isolated from Cold Seep Sediments of the South China Sea. Microorganisms 2023; 11:2156. [PMID: 37764000 PMCID: PMC10536192 DOI: 10.3390/microorganisms11092156] [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: 08/08/2023] [Revised: 08/17/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Bacillota are widely distributed in various environments, owing to their versatile metabolic capabilities and remarkable adaptation strategies. Recent studies reported that Bacillota species were highly enriched in cold seep sediments, but their metabolic capabilities, ecological functions, and adaption mechanisms in the cold seep habitats remained obscure. In this study, we conducted a systematic analysis of the complete genome of a novel Bacillota bacterium strain M8S5, which we isolated from cold seep sediments of the South China Sea at a depth of 1151 m. Phylogenetically, strain M8S5 was affiliated with the genus Abyssisolibacter within the phylum Bacillota. Metabolically, M8S5 is predicted to utilize various carbon and nitrogen sources, including chitin, cellulose, peptide/oligopeptide, amino acids, ethanolamine, and spermidine/putrescine. The pathways of histidine and proline biosynthesis were largely incomplete in strain M8S5, implying that its survival strictly depends on histidine- and proline-related organic matter enriched in the cold seep ecosystems. On the other hand, strain M8S5 contained the genes encoding a variety of extracellular peptidases, e.g., the S8, S11, and C25 families, suggesting its capabilities for extracellular protein degradation. Moreover, we identified a series of anaerobic respiratory genes, such as glycine reductase genes, in strain M8S5, which may allow it to survive in the anaerobic sediments of cold seep environments. Many genes associated with osmoprotectants (e.g., glycine betaine, proline, and trehalose), transporters, molecular chaperones, and reactive oxygen species-scavenging proteins as well as spore formation may contribute to its high-pressure and low-temperature adaptations. These findings regarding the versatile metabolic potentials and multiple adaptation strategies of strain M8S5 will expand our understanding of the Bacillota species in cold seep sediments and their potential roles in the biogeochemical cycling of deep marine ecosystems.
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Affiliation(s)
- Ying Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (Y.L.); (J.W.); (B.S.)
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535000, China
| | - Songze Chen
- Shenzhen Ecological and Environmental Monitoring Center of Guangdong Province, Shenzhen 518049, China;
| | - Jiahua Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (Y.L.); (J.W.); (B.S.)
| | - Baoying Shao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (Y.L.); (J.W.); (B.S.)
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (Y.L.); (J.W.); (B.S.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
| | - Junwei Cao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (Y.L.); (J.W.); (B.S.)
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Zhang ZF, Liu LR, Pan YP, Pan J, Li M. Long-read assembled metagenomic approaches improve our understanding on metabolic potentials of microbial community in mangrove sediments. MICROBIOME 2023; 11:188. [PMID: 37612768 PMCID: PMC10464287 DOI: 10.1186/s40168-023-01630-x] [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: 04/15/2023] [Accepted: 07/21/2023] [Indexed: 08/25/2023]
Abstract
BACKGROUND Mangrove wetlands are coastal ecosystems with important ecological features and provide habitats for diverse microorganisms with key roles in nutrient and biogeochemical cycling. However, the overall metabolic potentials and ecological roles of microbial community in mangrove sediment are remained unanswered. In current study, the microbial and metabolic profiles of prokaryotic and fungal communities in mangrove sediments were investigated using metagenomic analysis based on PacBio single-molecule real time (SMRT) and Illumina sequencing techniques. RESULTS Comparing to Illumina short reads, the incorporation of PacBio long reads significantly contributed to more contiguous assemblies, yielded more than doubled high-quality metagenome-assembled genomes (MAGs), and improved the novelty of the MAGs. Further metabolic reconstruction for recovered MAGs showed that prokaryotes potentially played an essential role in carbon cycling in mangrove sediment, displaying versatile metabolic potential for degrading organic carbons, fermentation, autotrophy, and carbon fixation. Mangrove fungi also functioned as a player in carbon cycling, potentially involved in the degradation of various carbohydrate and peptide substrates. Notably, a new candidate bacterial phylum named as Candidatus Cosmopoliota with a ubiquitous distribution is proposed. Genomic analysis revealed that this new phylum is capable of utilizing various types of organic substrates, anaerobic fermentation, and carbon fixation with the Wood-Ljungdahl (WL) pathway and the reverse tricarboxylic acid (rTCA) cycle. CONCLUSIONS The study not only highlights the advantages of HiSeq-PacBio Hybrid assembly for a more complete profiling of environmental microbiomes but also expands our understanding of the microbial diversity and potential roles of distinct microbial groups in biogeochemical cycling in mangrove sediment. Video Abstract.
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Affiliation(s)
- Zhi-Feng Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Present Address: Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Li-Rui Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yue-Ping Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China.
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China.
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20
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Chen Y, Dai T, Li N, Li Q, Lyu Y, Di P, Lyu L, Zhang S, Li J. Environmental heterogeneity shapes the C and S cycling-associated microbial community in Haima's cold seeps. Front Microbiol 2023; 14:1199853. [PMID: 37502402 PMCID: PMC10370420 DOI: 10.3389/fmicb.2023.1199853] [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: 04/04/2023] [Accepted: 06/07/2023] [Indexed: 07/29/2023] Open
Abstract
Environmental heterogeneity in cold seeps is usually reflected by different faunal aggregates. The sediment microbiome, especially the geochemical cycling-associated communities, sustains the ecosystem through chemosynthesis. To date, few studies have paid attention to the structuring and functioning of geochemical cycling-associated communities relating to environmental heterogeneity in different faunal aggregates of cold seeps. In this study, we profiled the microbial community of four faunal aggregates in the Haima cold seep, South China Sea. Through a combination of geochemical and meta-omics approaches, we have found that geochemical variables, such as sulfate and calcium, exhibited a significant variation between different aggregates, indicating changes in the methane flux. Anaerobic methanotrophic archaea (ANME), sulfate-reducing, and sulfide-oxidizing bacteria (SRB and SOB) dominated the microbial community but varied in composition among the four aggregates. The diversity of archaea and bacteria exhibited a strong correlation between sulfate, calcium, and silicate. Interspecies co-exclusion inferred by molecular ecological network analysis increased from non-seep to clam aggregates and peaked at the mussel aggregate. The networked geochemical cycling-associated species showed an obvious aggregate-specific distribution pattern. Notably, hydrocarbon oxidation and sulfate reduction by ANME and SRB produced carbonate and sulfide, driving the alkalization of the sediment environment, which may impact the microbial communities. Collectively, these results highlighted that geofluid and microbial metabolism together resulted in environmental heterogeneity, which shaped the C and S cycling-associated microbial community.
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Affiliation(s)
- Yu Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Tianjiao Dai
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, China
| | - Niu Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Qiqi Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Yuanjiao Lyu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Pengfei Di
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Lina Lyu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Si Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Jie Li
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
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21
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Vigneron A, Cruaud P, Lovejoy C, Vincent WF. Genomic insights into cryptic cycles of microbial hydrocarbon production and degradation in contiguous freshwater and marine microbiomes. MICROBIOME 2023; 11:104. [PMID: 37173775 PMCID: PMC10176705 DOI: 10.1186/s40168-023-01537-7] [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: 01/20/2023] [Accepted: 03/29/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND Cyanobacteria and eukaryotic phytoplankton produce long-chain alkanes and generate around 100 times greater quantities of hydrocarbons in the ocean compared to natural seeps and anthropogenic sources. Yet, these compounds do not accumulate in the water column, suggesting rapid biodegradation by co-localized microbial populations. Despite their ecological importance, the identities of microbes involved in this cryptic hydrocarbon cycle are mostly unknown. Here, we identified genes encoding enzymes involved in the hydrocarbon cycle across the salinity gradient of a remote, vertically stratified, seawater-containing High Arctic lake that is isolated from anthropogenic petroleum sources and natural seeps. Metagenomic analysis revealed diverse hydrocarbon cycling genes and populations, with patterns of variation along gradients of light, salinity, oxygen, and sulfur that are relevant to freshwater, oceanic, hadal, and anoxic deep sea ecosystems. RESULTS Analyzing genes and metagenome-assembled genomes down the water column of Lake A in the Canadian High Arctic, we detected microbial hydrocarbon production and degradation pathways at all depths, from surface freshwaters to dark, saline, anoxic waters. In addition to Cyanobacteria, members of the phyla Flavobacteria, Nitrospina, Deltaproteobacteria, Planctomycetes, and Verrucomicrobia had pathways for alkane and alkene production, providing additional sources of biogenic hydrocarbons. Known oil-degrading microorganisms were poorly represented in the system, while long-chain hydrocarbon degradation genes were identified in various freshwater and marine lineages such as Actinobacteria, Schleiferiaceae, and Marinimicrobia. Genes involved in sulfur and nitrogen compound transformations were abundant in hydrocarbon producing and degrading lineages, suggesting strong interconnections with nitrogen and sulfur cycles and a potential for widespread distribution in the ocean. CONCLUSIONS Our detailed metagenomic analyses across water column gradients in a remote petroleum-free lake derived from the Arctic Ocean suggest that the current estimation of bacterial hydrocarbon production in the ocean could be substantially underestimated by neglecting non-phototrophic production and by not taking low oxygen zones into account. Our findings also suggest that biogenic hydrocarbons may sustain a large fraction of freshwater and oceanic microbiomes, with global biogeochemical implications for carbon, sulfur, and nitrogen cycles. Video Abstract.
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Affiliation(s)
- Adrien Vigneron
- Département de Biologie, Université Laval, Québec, QC, Canada.
- Centre d'études nordiques (CEN), Université Laval, Québec, QC, Canada.
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada.
- Takuvik Joint International Laboratory, CNRS / Université Laval, Québec, QC, Canada.
| | - Perrine Cruaud
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC, Canada
| | - Connie Lovejoy
- Département de Biologie, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Takuvik Joint International Laboratory, CNRS / Université Laval, Québec, QC, Canada
- Québec Océan, Université Laval, Québec, QC, Canada
| | - Warwick F Vincent
- Département de Biologie, Université Laval, Québec, QC, Canada
- Centre d'études nordiques (CEN), Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Takuvik Joint International Laboratory, CNRS / Université Laval, Québec, QC, Canada
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22
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Zorz J, Li C, Chakraborty A, Gittins DA, Surcon T, Morrison N, Bennett R, MacDonald A, Hubert CRJ. SituSeq: an offline protocol for rapid and remote Nanopore 16S rRNA amplicon sequence analysis. ISME COMMUNICATIONS 2023; 3:33. [PMID: 37081077 PMCID: PMC10119094 DOI: 10.1038/s43705-023-00239-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/27/2023] [Accepted: 04/04/2023] [Indexed: 04/22/2023]
Abstract
Microbiome analysis through 16S rRNA gene sequencing is a crucial tool for understanding the microbial ecology of any habitat or ecosystem. However, workflows require large equipment, stable internet, and extensive computing power such that most of the work is performed far away from sample collection in both space and time. Performing amplicon sequencing and analysis at sample collection would have positive implications in many instances including remote fieldwork and point-of-care medical diagnoses. Here we present SituSeq, an offline and portable workflow for the sequencing and analysis of 16S rRNA gene amplicons using Nanopore sequencing and a standard laptop computer. SituSeq was validated by comparing Nanopore 16S rRNA gene amplicons, Illumina 16S rRNA gene amplicons, and Illumina metagenomes, sequenced using the same environmental DNA. Comparisons revealed consistent community composition, ecological trends, and sequence identity across platforms. Correlation between the abundance of taxa in each taxonomic level in Illumina and Nanopore data sets was high (Pearson's r > 0.9), and over 70% of Illumina 16S rRNA gene sequences matched a Nanopore sequence with greater than 97% sequence identity. On board a research vessel on the open ocean, SituSeq was used to analyze amplicon sequences from deep sea sediments less than 2 h after sequencing, and 8 h after sample collection. The rapidly available results informed decisions about subsequent sampling in near real-time while the offshore expedition was still underway. SituSeq is a portable and user-friendly workflow that helps to bring the power of microbial genomics and diagnostics to many more researchers and situations.
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Affiliation(s)
- Jackie Zorz
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada.
| | - Carmen Li
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Anirban Chakraborty
- Department of Biological Sciences, Idaho State University, Pocatello, ID, USA
| | - Daniel A Gittins
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Taylor Surcon
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Natasha Morrison
- Department of Natural Resources and Renewables, Government of Nova Scotia, Halifax, NS, Canada
| | - Robbie Bennett
- Natural Resources Canada, Geological Survey of Canada-Atlantic, Dartmouth, NS, Canada
| | - Adam MacDonald
- Department of Natural Resources and Renewables, Government of Nova Scotia, Halifax, NS, Canada
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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23
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Raman M, Vishnubhotla R, Ramay HR, Gonçalves MCB, Shin AS, Pawale D, Subramaniam B, Sadhasivam S. Isha yoga practices, vegan diet, and participation in Samyama meditation retreat: impact on the gut microbiome & metabolome - a non-randomized trial. BMC Complement Med Ther 2023; 23:107. [PMID: 37020274 PMCID: PMC10074366 DOI: 10.1186/s12906-023-03935-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/22/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUND Growing evidence suggests a role for gut bacteria and their metabolites in host-signaling responses along the gut-brain axis which may impact mental health. Meditation is increasingly utilized to combat stress, anxiety, and depression symptoms. However, its impact on the microbiome remains unclear. This study observes the effects of preparation and participation in an advanced meditation program (Samyama) implemented with a vegan diet including 50% raw foods, on gut microbiome and metabolites profiles. METHODS There were 288 subjects for this study. Stool samples were collected at 3-time points for meditators and household controls. Meditators prepared for 2 months for the Samyama, incorporating daily yoga and meditation practices with a vegan diet including 50% raw foods. Subjects were requested to submit stool samples for 3 time points - 2 months before Samyama (T1), right before Samyama (T2), and 3 months following Samyama (T3). 16 s rRNA sequencing was used to study participants' microbiome. Alpha and beta diversities along with short-chain fatty acid (SCFA) were assessed. Metabolomics were performed on a mass spectrometer coupled to a UHLPC system and analyzed by El-MAVEN software. RESULTS Alpha diversity showed no significant differences between meditators and controls, while beta diversity showed significant changes (padj = 0.001) after Samyama in meditators' microbiota composition. After the preparation phase, changes in branched short-chain fatty acids, higher levels of iso-valerate (padj = 0.02) and iso-buytrate (padj = 0.019) were observed at T2 in meditators. Other metabolites were also observed to have changed in meditators at timepoint T2. CONCLUSION This study examined the impact of an advanced meditation program combined with a vegan diet on the gut microbiome. There was an increase in beneficial bacteria even three months after the completion of the Samyama program. Further study is warranted to validate current observations and investigate the significance and mechanisms of action related to diet, meditation, and microbial composition and function, on psychological processes, including mood. TRIAL REGISTRATION Registration number: NCT04366544 ; Registered on 29/04/2020.
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Affiliation(s)
- Maitreyi Raman
- Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Ramana Vishnubhotla
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Hena R Ramay
- International Microbiome Centre, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Maria C B Gonçalves
- Department of Anesthesia, Critical Care and Pain Medicine, Sadhguru Center for a Conscious Planet, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Andrea S Shin
- Division of Gastroenterology and Hepatology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Dhanashri Pawale
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Balachundhar Subramaniam
- Department of Anesthesia, Critical Care and Pain Medicine, Sadhguru Center for a Conscious Planet, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Senthilkumar Sadhasivam
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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24
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Zhang C, Liu X, Shi LD, Li J, Xiao X, Shao Z, Dong X. Unexpected genetic and microbial diversity for arsenic cycling in deep sea cold seep sediments. NPJ Biofilms Microbiomes 2023; 9:13. [PMID: 36991068 PMCID: PMC10060404 DOI: 10.1038/s41522-023-00382-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 03/13/2023] [Indexed: 03/31/2023] Open
Abstract
Cold seeps, where cold hydrocarbon-rich fluid escapes from the seafloor, show strong enrichment of toxic metalloid arsenic (As). The toxicity and mobility of As can be greatly altered by microbial processes that play an important role in global As biogeochemical cycling. However, a global overview of genes and microbes involved in As transformation at seeps remains to be fully unveiled. Using 87 sediment metagenomes and 33 metatranscriptomes derived from 13 globally distributed cold seeps, we show that As detoxification genes (arsM, arsP, arsC1/arsC2, acr3) were prevalent at seeps and more phylogenetically diverse than previously expected. Asgardarchaeota and a variety of unidentified bacterial phyla (e.g. 4484-113, AABM5-125-24 and RBG-13-66-14) may also function as the key players in As transformation. The abundances of As cycling genes and the compositions of As-associated microbiome shifted across different sediment depths or types of cold seep. The energy-conserving arsenate reduction or arsenite oxidation could impact biogeochemical cycling of carbon and nitrogen, via supporting carbon fixation, hydrocarbon degradation and nitrogen fixation. Overall, this study provides a comprehensive overview of As cycling genes and microbes at As-enriched cold seeps, laying a solid foundation for further studies of As cycling in deep sea microbiome at the enzymatic and processual levels.
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Affiliation(s)
- Chuwen Zhang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Xinyue Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Ling-Dong Shi
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Jiwei Li
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Xi Xiao
- Key Laboratory of Marine Mineral Resources, Ministry of Natural Resources, Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
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Genomic Insights into Niche Partitioning across Sediment Depth among Anaerobic Methane-Oxidizing Archaea in Global Methane Seeps. mSystems 2023; 8:e0117922. [PMID: 36927099 PMCID: PMC10134854 DOI: 10.1128/msystems.01179-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
Marine sediments are important methane reservoirs. Methane efflux from the seabed is significantly restricted by anaerobic methanotrophic (ANME) archaea through a process known as anaerobic oxidation of methane (AOM). Different clades of ANME archaea occupy distinct niches in methane seeps, but their underlying molecular mechanisms still need to be fully understood. To provide genetic explanations for the niche partitioning of ANME archaea, we applied comparative genomic analysis to ANME archaeal genomes retrieved from global methane seeps. Our results showed that ANME-2 archaea are more prevalent than ANME-1 archaea in shallow sediments because they carry genes that encode a significantly higher number of outer membrane multiheme c-type cytochromes and flagellar proteins. These features make ANME-2 archaea perform direct interspecies electron transfer better and benefit more from electron acceptors in AOM. Besides, ANME-2 archaea carry genes that encode extra peroxidase compared to ANME-1 archaea, which may lead to ANME-2 archaea better tolerating oxygen toxicity. In contrast, ANME-1 archaea are more competitive in deep layers than ANME-2 archaea because they carry extra genes (mtb and mtt) for methylotrophic methanogenesis and a significantly higher number of frh and mvh genes for hydrogenotrophic methanogenesis. Additionally, ANME-1 archaea carry exclusive genes (sqr, TST, and mddA) involved in sulfide detoxification compared to ANME-2 archaea, leading to stronger sulfide tolerance. Overall, this study reveals the genomic mechanisms shaping the niche partitioning among ANME archaea in global methane seeps. IMPORTANCE Anaerobic methanotrophic (ANME) archaea are important methanotrophs in marine sediment, controlling the flux of biologically generated methane, which plays an essential role in the marine carbon cycle and climate change. So far, no strain of this lineage has been isolated in pure culture, which makes metagenomics one of the fundamental approaches to reveal their metabolic potential. Although the niche partitioning of ANME archaea was frequently reported in different studies, whether this pattern was consistent in global methane seeps had yet to be verified, and little was known about the genetic mechanisms underlying it. Here, we reviewed and analyzed the community structure of ANME archaea in global methane seeps and indicated that the niche partitioning of ANME archaea was statistically supported. Our comparative genomic analysis indicated that the capabilities of interspecies electron transfer, methanogenesis, and the resistance of oxygen and hydrogen sulfide could be critical in defining the distribution of ANME archaea in methane seep sediment.
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Shekarriz E, Chen J, Xu Z, Liu H. Disentangling the Functional Role of Fungi in Cold Seep Sediment. Microbiol Spectr 2023; 11:e0197822. [PMID: 36912690 PMCID: PMC10100914 DOI: 10.1128/spectrum.01978-22] [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: 05/27/2022] [Accepted: 12/22/2022] [Indexed: 03/14/2023] Open
Abstract
Cold seeps are biological oases of the deep sea fueled by methane, sulfates, nitrates, and other inorganic sources of energy. Chemolithoautotrophic bacteria and archaea dominate seep sediment, and their diversity and biogeochemical functions are well established. Fungi are likewise diverse, metabolically versatile, and known for their ability to capture and oxidize methane. Still, no study has ever explored the functional role of the mycobiota in the cold seep biome. To assess the complex role of fungi and fill in the gaps, we performed network analysis on 147 samples to disentangle fungal-prokaryotic interactions (fungal 18S and prokaryotic 16S) in the Haima cold seep region. We demonstrated that fungi are central species with high connectivity at the epicenter of prokaryotic networks, reduce their random-attack vulnerability by 60%, and enhance information transfer efficiency by 15%. We then scavenged a global metagenomic and metatranscriptomic data set from 10 cold seep regions for fungal genes of interest (hydrophobins, cytochrome P450s, and ligninolytic family of enzymes); this is the first study to report active transcription of 2,500+ fungal genes in the cold seep sediment. The genera Fusarium and Moniliella were of notable importance and directly correlated with high methane abundance in the sulfate-methane transition zone (SMTZ), likely due to their ability to degrade and solubilize methane and oils. Overall, our results highlight the essential yet overlooked contribution of fungi to cold seep biological networks and the role of fungi in regulating cold seep biogeochemistry. IMPORTANCE The challenges we face when analyzing eukaryotic metagenomic and metatranscriptomic data sets have hindered our understanding of cold seep fungi and microbial eukaryotes. This fact does not make the mycobiota any less critical in mediating cold seep biogeochemistry. On the contrary, many fungal genera can oxidize and solubilize methane, produce methane, and play a unique role in nutrient recycling via saprotrophic enzymatic activity. In this study, we used network analysis to uncover key fungal-prokaryotic interactions that can mediate methane biogeochemistry and metagenomics and metatranscriptomics to report that fungi are transcriptionally active in the cold seep sediment. With concerns over rising methane levels and cold seeps being a pivotal source of global methane input, our holistic understanding of methane biogeochemistry with all domains of life is essential. We ultimately encourage scientists to utilize state-of-the-art tools and multifaceted approaches to uncover the role of microeukaryotic organisms in understudied systems.
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Affiliation(s)
- Erfan Shekarriz
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jiawei Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhimeng Xu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hongbin Liu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
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Zhang C, Fang YX, Yin X, Lai H, Kuang Z, Zhang T, Xu XP, Wegener G, Wang JH, Dong X. The majority of microorganisms in gas hydrate-bearing subseafloor sediments ferment macromolecules. MICROBIOME 2023; 11:37. [PMID: 36864529 PMCID: PMC9979476 DOI: 10.1186/s40168-023-01482-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/30/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND Gas hydrate-bearing subseafloor sediments harbor a large number of microorganisms. Within these sediments, organic matter and upward-migrating methane are important carbon and energy sources fueling a light-independent biosphere. However, the type of metabolism that dominates the deep subseafloor of the gas hydrate zone is poorly constrained. Here we studied the microbial communities in gas hydrate-rich sediments up to 49 m below the seafloor recovered by drilling in the South China Sea. We focused on distinct geochemical conditions and performed metagenomic and metatranscriptomic analyses to characterize microbial communities and their role in carbon mineralization. RESULTS Comparative microbial community analysis revealed that samples above and in sulfate-methane interface (SMI) zones were clearly distinguished from those below the SMI. Chloroflexota were most abundant above the SMI, whereas Caldatribacteriota dominated below the SMI. Verrucomicrobiota, Bathyarchaeia, and Hadarchaeota were similarly present in both types of sediment. The genomic inventory and transcriptional activity suggest an important role in the fermentation of macromolecules. In contrast, sulfate reducers and methanogens that catalyze the consumption or production of commonly observed chemical compounds in sediments are rare. Methanotrophs and alkanotrophs that anaerobically grow on alkanes were also identified to be at low abundances. The ANME-1 group actively thrived in or slightly below the current SMI. Members from Heimdallarchaeia were found to encode the potential for anaerobic oxidation of short-chain hydrocarbons. CONCLUSIONS These findings indicate that the fermentation of macromolecules is the predominant energy source for microorganisms in deep subseafloor sediments that are experiencing upward methane fluxes. Video Abstract.
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Affiliation(s)
- Chuwen Zhang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Yun-Xin Fang
- Guangzhou Marine Geological Survey, China Geological Survey, Ministry of Natural Resources, Guangzhou, China
| | - Xiuran Yin
- Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Hongfei Lai
- Guangzhou Marine Geological Survey, China Geological Survey, Ministry of Natural Resources, Guangzhou, China
| | - Zenggui Kuang
- Guangzhou Marine Geological Survey, China Geological Survey, Ministry of Natural Resources, Guangzhou, China
| | - Tianxueyu Zhang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Xiang-Po Xu
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Gunter Wegener
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jiang-Hai Wang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China.
| | - Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
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28
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Dong X, Peng Y, Wang M, Woods L, Wu W, Wang Y, Xiao X, Li J, Jia K, Greening C, Shao Z, Hubert CRJ. Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps. Nat Commun 2023; 14:1127. [PMID: 36854684 PMCID: PMC9974965 DOI: 10.1038/s41467-023-36877-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 02/21/2023] [Indexed: 03/02/2023] Open
Abstract
Deep sea cold seep sediments host abundant and diverse microbial populations that significantly influence biogeochemical cycles. While numerous studies have revealed their community structure and functional capabilities, little is known about genetic heterogeneity within species. Here, we examine intraspecies diversity patterns of 39 abundant species identified in sediment layers down to 430 cm below the sea floor across six cold seep sites. These populations are grouped as aerobic methane-oxidizing bacteria, anaerobic methanotrophic archaea and sulfate-reducing bacteria. Different evolutionary trajectories are observed at the genomic level among these physiologically and phylogenetically diverse populations, with generally low rates of homologous recombination and strong purifying selection. Functional genes related to methane (pmoA and mcrA) and sulfate (dsrA) metabolisms are under strong purifying selection in most species investigated. These genes differ in evolutionary trajectories across phylogenetic clades but are functionally conserved across sites. Intrapopulation diversification of genomes and their mcrA and dsrA genes is depth-dependent and subject to different selection pressure throughout the sediment column redox zones at different sites. These results highlight the interplay between ecological processes and the evolution of key bacteria and archaea in deep sea cold seep extreme environments, shedding light on microbial adaptation in the subseafloor biosphere.
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Affiliation(s)
- Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
| | - Yongyi Peng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Muhua Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Laura Woods
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Wenxue Wu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Yong Wang
- Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Xi Xiao
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, 510075, China
| | - Jiwei Li
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Kuntong Jia
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
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Chen Y, Lyu Y, Zhang J, Li Q, Lyu L, Zhou Y, Kong J, Zeng X, Zhang S, Li J. Riddles of Lost City: Chemotrophic Prokaryotes Drives Carbon, Sulfur, and Nitrogen Cycling at an Extinct Cold Seep, South China Sea. Microbiol Spectr 2023; 11:e0333822. [PMID: 36511717 PMCID: PMC9927161 DOI: 10.1128/spectrum.03338-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022] Open
Abstract
Deep-sea cold seeps are one of the most productive ecosystems that sustained by hydrocarbons carried by the fluid. Once the seep fluid ceases, the thriving autotrophic communities die out, terming as the extinct seep. But heterotrophic fauna can still survive even for thousands of years. The critical role of prokaryotes in active seeps are well defined, but their functions in extinct seeps are poorly understood to date. Here, we clarified the diversity, taxonomic specificity, interspecies correlation, and metabolic profiles of sediment prokaryotes at an extinct seep site of Haima cold seep, South China Sea. Alpha diversity of archaea significantly increased, while that of bacteria remained unchanged in extinct seep compared to active seep. However, archaea composition did not differ significantly at extinct seep from active or nonseep sites based on weighted-unifrac dissimilarity, while bacteria composition exhibited significant difference. Distribution of archaea and bacteria showed clear specificity to extinct seeps, indicating the unique life strategies here. Prokaryotes might live chemolithoautotrophically on cycling of inorganic carbon, sulfur, and nitrogen, or chemoorganotrophically on recycling of hydrocarbons. Notably, many of the extinct seep specific species and networked keystone lineages are classified as Proteobacteria. Regarding the functional diversity and metabolic flexibility of this clade, Proteobacteria is supposed to integrate the geochemical cycles and play a critical role in energy and resource supplement for microbiome in extinct seep. Collectively, our findings shed lights on the microbial ecology and functional diversity in extinct seeps, providing new understanding of biogeochemical cycling after fluid cessation. IMPORTANCE This research paper uncovered the potential mechanisms for microbiota mediated geochemical cycling in extinct cold seep, advancing our understanding in deep sea microbiology ecology.
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Affiliation(s)
- Yu Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, People’s Republic of China
| | - Yuanjiao Lyu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, People’s Republic of China
| | - Jian Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, People’s Republic of China
| | - Qiqi Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, People’s Republic of China
| | - Lina Lyu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, People’s Republic of China
| | - Yingli Zhou
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, People’s Republic of China
| | - Jie Kong
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, People’s Republic of China
| | - Xinyang Zeng
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, People’s Republic of China
| | - Si Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, People’s Republic of China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, People’s Republic of China
| | - Jie Li
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, People’s Republic of China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, People’s Republic of China
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30
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Frequent Occurrence and Metabolic Versatility of Marinifilaceae Bacteria as Key Players in Organic Matter Mineralization in Global Deep Seas. mSystems 2022; 7:e0086422. [PMID: 36342154 PMCID: PMC9765461 DOI: 10.1128/msystems.00864-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Transfer of animal and plant detritus of both terrestrial and marine origins to the deep sea occurs on a global scale. Microorganisms play an important role in mineralizing them therein, but these are yet to be identified in situ. To observe key bacteria involved, we conducted long-term in situ incubation and found that members of the family Marinifilaceae (MF) occurred as some of the most predominant bacteria thriving on the new inputs of plant and animal biomasses in the deep sea in both marginal and oceanic areas. This taxon is diverse and ubiquitous in marine environments. A total of 11 MAGs belonging to MF were retrieved from metagenomic data and diverged into four subgroups in the phylogenomic tree. Based on metagenomic and metatranscriptomic analyses, we described the metabolic features and in situ metabolizing activities of different subgroups. The MF-2 subgroup, which dominates plant detritus-enriched cultures, specializes in polysaccharide degradation and lignin oxidation and has high transcriptional activities of related genes in situ. Intriguingly, members of this subgroup encode a nitrogen fixation pathway to compensate for the shortage of nitrogen sources inside the plant detritus. In contrast, other subgroups dominating the animal tissue-supported microbiomes are distinguished from MF-2 with regard to carbon and nitrogen metabolism and exhibit high transcriptional activity for proteolysis in situ. Despite these metabolic divergences of MF lineages, they show high in situ transcriptional activities for organic fermentation and anaerobic respiration (reductions of metal and/or dimethyl sulfoxide). These results highlight the role of previously unrecognized Marinifilaceae bacteria in organic matter mineralization in marine environments by coupling carbon and nitrogen cycling with metal and sulfur. IMPORTANCE Microbial mineralization of organic matter has a significant impact on the global biogeochemical cycle. This report confirms the role of Marinifilaceae in organic degradation in the oceans, with a contribution to ocean carbon cycling that has previously been underestimated. It was the dominant taxon thriving on plant and animal biomasses in our in situ incubator, as well as in whale falls and wood falls. At least 9 subgroups were revealed, and they were widely distributed in oceans globally but predominant in organic-matter-rich environments, with an average relative abundance of 8.3%. Different subgroups display a preference for the degradation of different macromolecules (polysaccharides, lignin, and protein) and adapt to their environments via special metabolic mechanisms.
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31
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Silva JB, Centurion VB, Duarte AWF, Galazzi RM, Arruda MAZ, Sartoratto A, Rosa LH, Oliveira VM. Unravelling the genetic potential for hydrocarbon degradation in the sediment microbiome of Antarctic islands. FEMS Microbiol Ecol 2022; 99:6847214. [PMID: 36427064 DOI: 10.1093/femsec/fiac143] [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: 07/04/2022] [Revised: 10/08/2022] [Accepted: 11/23/2022] [Indexed: 11/27/2022] Open
Abstract
Hydrocarbons may have a natural or anthropogenic origin and serve as a source of carbon and energy for microorganisms in Antarctic soils. Herein, 16S rRNA gene and shotgun sequencing were employed to characterize taxonomic diversity and genetic potential for hydrocarbon degradation of the microbiome from sediments of sites located in two Antarctic islands subjected to different temperatures, geochemical compositions, and levels of presumed anthropogenic impact, named: Crater Lake/Deception Island (pristine area), Whalers Bay and Fumarole Bay/Deception Island (anthropogenic-impacted area), and Hannah Point/Livingston Island (anthropogenic-impacted area). Hydrocarbon concentrations were measured for further correlation analyses with biological data. The majority of the hydrocarbon-degrading genes were affiliated to the most abundant bacterial groups of the microbiome: Proteobacteria and Actinobacteria. KEGG annotation revealed 125 catabolic genes related to aromatic hydrocarbon (styrene, toluene, ethylbenzene, xylene, naphthalene, and polycyclic hydrocarbons) and aliphatic (alkanes and cycloalkanes) pathways. Only aliphatic hydrocarbons, in low concentrations, were detected in all areas, thus not characterizing the areas under study as anthropogenically impacted or nonimpacted. The high richness and abundance of hydrocarbon-degrading genes suggest that the genetic potential of the microbiome from Antarctic sediments for hydrocarbon degradation is driven by natural hydrocarbon occurrence.
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Affiliation(s)
- Jéssica B Silva
- Research Center for Chemistry, Biology and Agriculture (CPQBA), UNICAMP, Division of Microbial Resources, Zip code 13148-218, Paulínia, São Paulo, Brazil.,Institute of Biology, UNICAMP, Zip code 13083-862, Campinas, São Paulo, Brazil
| | - Victor B Centurion
- Research Center for Chemistry, Biology and Agriculture (CPQBA), UNICAMP, Division of Microbial Resources, Zip code 13148-218, Paulínia, São Paulo, Brazil.,Institute of Biology, UNICAMP, Zip code 13083-862, Campinas, São Paulo, Brazil
| | - Alysson W F Duarte
- Federal University of Alagoas, Campus Arapiraca (UFAL), Zip code 57309-005, Araparica, Alagoas, Brazil
| | - Rodrigo M Galazzi
- Spectrometry, Sample Preparation and Mechanization Group (GEPAM), Institute of Chemistry (UNICAMP), Zip code 13083-970, Campinas São Paulo, Brazil.,National Institute of Science and Technology for Bioanalytics (INCTBio), Institute of Chemistry (UNICAMP), Zip code 13083-970, Campinas, São Paulo, Brazil
| | - Marco A Z Arruda
- Spectrometry, Sample Preparation and Mechanization Group (GEPAM), Institute of Chemistry (UNICAMP), Zip code 13083-970, Campinas São Paulo, Brazil.,National Institute of Science and Technology for Bioanalytics (INCTBio), Institute of Chemistry (UNICAMP), Zip code 13083-970, Campinas, São Paulo, Brazil
| | - Adilson Sartoratto
- Organic Chemistry and Pharmaceutical Division, Pluridisciplinary Research Center for Chemistry, Biology, and Agriculture (CPQBA), UNICAMP, Zip code 13081-970, Paulínia, São Paulo, Brazil
| | - Luiz H Rosa
- Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Zip code 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Valéria M Oliveira
- Research Center for Chemistry, Biology and Agriculture (CPQBA), UNICAMP, Division of Microbial Resources, Zip code 13148-218, Paulínia, São Paulo, Brazil
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32
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Mining of novel secondary metabolite biosynthetic gene clusters from acid mine drainage. Sci Data 2022; 9:760. [PMID: 36494363 PMCID: PMC9734747 DOI: 10.1038/s41597-022-01866-6] [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: 05/19/2021] [Accepted: 11/23/2022] [Indexed: 12/13/2022] Open
Abstract
Acid mine drainage (AMD) is usually acidic (pH < 4) and contains high concentrations of dissolved metals and metalloids, making AMD a typical representative of extreme environments. Recent studies have shown that microbes play a key role in AMD bioremediation, and secondary metabolite biosynthetic gene clusters (smBGCs) from AMD microbes are important resources for the synthesis of antibacterial and anticancer drugs. Here, 179 samples from 13 mineral types were used to analyze the putative novel microorganisms and secondary metabolites in AMD environments. Among 7,007 qualified metagenome-assembled genomes (MAGs) mined from these datasets, 6,340 MAGs could not be assigned to any GTDB species representative. Overall, 11,856 smBGCs in eight categories were obtained from 7,007 qualified MAGs, and 10,899 smBGCs were identified as putative novel smBGCs. We anticipate that these datasets will accelerate research in the field of AMD bioremediation, aid in the discovery of novel secondary metabolites, and facilitate investigation into gene functions, metabolic pathways, and CNPS cycles in AMD.
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John J A, Samuel MS, Govarthanan M, Selvarajan E. A comprehensive review on strategic study of cellulase producing marine actinobacteria for biofuel applications. ENVIRONMENTAL RESEARCH 2022; 214:114018. [PMID: 35961544 DOI: 10.1016/j.envres.2022.114018] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/12/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Every year, 180 billion tonnes of cellulose are produced by plants as waste biomass after the cultivation of the desired product. One of the smart and effective ways to utilize this biomass rather than burn it is to utilize the biomass to adequately meet the energy needs with the help of microbial cellulase that can catalytically convert the cellulose into simple sugar units. Marine actinobacteria is one of the plentiful gram-positive bacteria known for its industrial application as it can produce multienzyme cellulase with high thermal tolerance, pH stability and high resistant towards metal ions and salt concentration, along with other antimicrobial properties. Highly stable cellulase obtained from marine actinobacteria will convert the cellulose biomass into glucose, which is the precursor for biofuel production. This review will provide a comprehensive outlook of various strategic applications of cellulase from marine actinobacteria which can facilitate the breakdown of lignocellulosic biomass to bioenergy with respect to its characteristics based on the location/environment that the organism was collected and its screening strategies followed by adopted methodologies to mine the novel cellulase genome and enhance the production, thereby increasing the activity of cellulase continued by effective immobilization on novel substrates for the multiple usage of cellulase along with the industrial applications.
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Affiliation(s)
- Ashwini John J
- Department of Genetic Engineering, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, 603 203, Tamil Nadu, India
| | - Melvin S Samuel
- Department of Material Science and Engineering, University of Winsconsin-Milwaukee, Milwaukee, WI, USA
| | - Muthusamy Govarthanan
- Department of Environmental Engineering, Kyungpook National University, Daegu, South Korea; Departrment of Biomaterials, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, 600 077, India
| | - Ethiraj Selvarajan
- Department of Genetic Engineering, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, 603 203, Tamil Nadu, India.
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Liu S, Yu S, Lu X, Yang H, Li Y, Xu X, Lu H, Fang Y. Microbial communities associated with thermogenic gas hydrate-bearing marine sediments in Qiongdongnan Basin, South China Sea. Front Microbiol 2022; 13:1032851. [PMID: 36386663 PMCID: PMC9640435 DOI: 10.3389/fmicb.2022.1032851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/10/2022] [Indexed: 11/29/2022] Open
Abstract
Biogenic and thermogenic gas are two major contributors to gas hydrate formation. Methane hydrates from both origins may have critical impacts on the ecological properties of marine sediments. However, research on microbial diversity in thermogenic hydrate-containing sediments is limited. This study examined the prokaryotic diversity and distributions along a sediment core with a vertical distribution of thermogenic gas hydrates with different occurrences obtained from the Qiongdongnan Basin by Illumina sequencing of 16S rRNA genes as well as molecular and geochemical techniques. Here, we show that gas hydrate occurrence has substantial impacts on both microbial diversity and community composition. Compared to the hydrate-free zone, distinct microbiomes with significantly higher abundance and lower diversity were observed within the gas hydrate-containing layers. Gammaproteobacteria and Actinobacterota dominated the bacterial taxa in all collected samples, while archaeal communities shifted sharply along the vertical profile of sediment layers. A notable stratified distribution of anaerobic methanotrophs shaped by both geophysical and geochemical parameters was also determined. In addition, the hydrate-free zone hosted a large number of rare taxa that might perform a fermentative breakdown of proteins in the deep biosphere and probably respond to the hydrate formation.
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Affiliation(s)
- Siwei Liu
- School of Earth and Space Sciences, Peking University, Beijing, China
| | - Shan Yu
- Beijing International Center for Gas Hydrate, School of Earth and Space Sciences, Peking University, Beijing, China
- *Correspondence: Shan Yu,
| | - Xindi Lu
- Beijing International Center for Gas Hydrate, School of Earth and Space Sciences, Peking University, Beijing, China
| | - Hailin Yang
- Beijing International Center for Gas Hydrate, School of Earth and Space Sciences, Peking University, Beijing, China
| | - Yuanyuan Li
- School of Earth and Space Sciences, Peking University, Beijing, China
| | - Xuemin Xu
- School of Earth and Space Sciences, Peking University, Beijing, China
- National Research Center for Geoanalysis, Beijing, China
| | - Hailong Lu
- Beijing International Center for Gas Hydrate, School of Earth and Space Sciences, Peking University, Beijing, China
| | - Yunxin Fang
- Guangzhou Marine Geological Survey, Guangzhou, China
- Yunxin Fang,
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35
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Vulcano F, Hahn CJ, Roerdink D, Dahle H, Reeves EP, Wegener G, Steen IH, Stokke R. Phylogenetic and functional diverse ANME-1 thrive in Arctic hydrothermal vents. FEMS Microbiol Ecol 2022; 98:fiac117. [PMID: 36190327 PMCID: PMC9576274 DOI: 10.1093/femsec/fiac117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 09/15/2022] [Accepted: 09/29/2022] [Indexed: 01/21/2023] Open
Abstract
The methane-rich areas, the Loki's Castle vent field and the Jan Mayen vent field at the Arctic Mid Ocean Ridge (AMOR), host abundant niches for anaerobic methane-oxidizers, which are predominantly filled by members of the ANME-1. In this study, we used a metagenomic-based approach that revealed the presence of phylogenetic and functional different ANME-1 subgroups at AMOR, with heterogeneous distribution. Based on a common analysis of ANME-1 genomes from AMOR and other geographic locations, we observed that AMOR subgroups clustered with a vent-specific ANME-1 group that occurs solely at vents, and with a generalist ANME-1 group, with a mixed environmental origin. Generalist ANME-1 are enriched in genes coding for stress response and defense strategies, suggesting functional diversity among AMOR subgroups. ANME-1 encode a conserved energy metabolism, indicating strong adaptation to sulfate-methane-rich sediments in marine systems, which does not however prevent global dispersion. A deep branching family named Ca. Veteromethanophagaceae was identified. The basal position of vent-related ANME-1 in phylogenomic trees suggests that ANME-1 originated at hydrothermal vents. The heterogeneous and variable physicochemical conditions present in diffuse venting areas of hydrothermal fields could have favored the diversification of ANME-1 into lineages that can tolerate geochemical and environmental variations.
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Affiliation(s)
- F Vulcano
- Department of Biological Sciences, Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - C J Hahn
- Max-Plank Institute for Marine Microbiology, HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Bremen, 28359, Germany
| | - D Roerdink
- Department of Earth Science, Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - H Dahle
- Computational Biological Unit, Department of Informatics, Department of Biological Sciences, Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - E P Reeves
- Department of Earth Science, Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - G Wegener
- Max-Plank Institute for Marine Microbiology, HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Bremen, 28359, Germany
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, 28359, Germany
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, 27570, Germany
| | - I H Steen
- Department of Biological Sciences, Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - R Stokke
- Department of Biological Sciences, Center for Deep Sea Research, University of Bergen, Bergen, Norway
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36
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Tan X, Nie WB, Xie GJ, Dang CC, Wang XW, Xing D, Liu BF, Ding J, Ren N. Deciphering the Inhibition of Ethane on Anaerobic Ammonium Oxidation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:13419-13427. [PMID: 35917334 DOI: 10.1021/acs.est.2c01527] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Anaerobic ammonium oxidation (anammox) and nitrification, two common biological ammonium oxidation pathways, are critical for the microbial nitrogen cycle. Short chain alkanes (C2-C8) have been well-known as inhibitors for nitrification through interaction with the ammonia monooxygenase, while whether these alkanes affect anammox is an open question. Here, this work demonstrated significant inhibition of ethane on anammox and revealed the inhibitory mechanism. The acute inhibition of ethane on anammox was concentration-dependent and reversible; 0.86 mM dissolved ethane caused 50% inhibition (IC50), and 1.72 mM ethane almost completely inhibited anammox. After long-term exposure to 0.09 mM ethane for 30 days, the ammonium (nitrite) removal rate dropped from 202 (267) mg N L-1 d-1 to 1 (1) mg N L-1 d-1, and the abundance of anammox bacteria decreased from 61.9% to 9.5%. The intercellular ammonium concentration of anammox bacteria decreased after ethane exposure, while metatranscriptome analysis showed significant upregulation of genes for ammonium transport of anammox bacteria. Thus, ethane could suppress ammonium uptake resulting in the inhibition of anammox activities. As ethane is the second most prevalent alkane after methane in various anoxic environments, ethane may have an important effect on the nitrogen cycle driven by anammox that should be investigated in future research.
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Affiliation(s)
- Xin Tan
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Wen-Bo Nie
- Key Laboratory of the Three Gorges Region's Eco-Environment, Ministry of Education, College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Cheng-Cheng Dang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Xiao-Wei Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Defeng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Bing-Feng Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jie Ding
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
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37
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Dong X, Zhang C, Peng Y, Zhang HX, Shi LD, Wei G, Hubert CRJ, Wang Y, Greening C. Phylogenetically and catabolically diverse diazotrophs reside in deep-sea cold seep sediments. Nat Commun 2022; 13:4885. [PMID: 35985998 PMCID: PMC9391474 DOI: 10.1038/s41467-022-32503-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
Microbially mediated nitrogen cycling in carbon-dominated cold seep environments remains poorly understood. So far anaerobic methanotrophic archaea (ANME-2) and their sulfate-reducing bacterial partners (SEEP-SRB1 clade) have been identified as diazotrophs in deep sea cold seep sediments. However, it is unclear whether other microbial groups can perform nitrogen fixation in such ecosystems. To fill this gap, we analyzed 61 metagenomes, 1428 metagenome-assembled genomes, and six metatranscriptomes derived from 11 globally distributed cold seeps. These sediments contain phylogenetically diverse nitrogenase genes corresponding to an expanded diversity of diazotrophic lineages. Diverse catabolic pathways were predicted to provide ATP for nitrogen fixation, suggesting diazotrophy in cold seeps is not necessarily associated with sulfate-dependent anaerobic oxidation of methane. Nitrogen fixation genes among various diazotrophic groups in cold seeps were inferred to be genetically mobile and subject to purifying selection. Our findings extend the capacity for diazotrophy to five candidate phyla (Altarchaeia, Omnitrophota, FCPU426, Caldatribacteriota and UBA6262), and suggest that cold seep diazotrophs might contribute substantially to the global nitrogen balance.
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Affiliation(s)
- Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
| | - Chuwen Zhang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Yongyi Peng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Hong-Xi Zhang
- Institute for Marine Engineering, Shenzhen International Graduate School, Tsinghua University, University Town, Shenzhen, China
- Department of Life Science, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Ling-Dong Shi
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Guangshan Wei
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Yong Wang
- Institute for Marine Engineering, Shenzhen International Graduate School, Tsinghua University, University Town, Shenzhen, China.
- Department of Life Science, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Clayton, VIC, Australia
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38
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Wegener G, Laso-Pérez R, Orphan VJ, Boetius A. Anaerobic Degradation of Alkanes by Marine Archaea. Annu Rev Microbiol 2022; 76:553-577. [PMID: 35917471 DOI: 10.1146/annurev-micro-111021-045911] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alkanes are saturated apolar hydrocarbons that range from its simplest form, methane, to high-molecular-weight compounds. Although alkanes were once considered biologically recalcitrant under anaerobic conditions, microbiological investigations have now identified several microbial taxa that can anaerobically degrade alkanes. Here we review recent discoveries in the anaerobic oxidation of alkanes with a specific focus on archaea that use specific methyl coenzyme M reductases to activate their substrates. Our understanding of the diversity of uncultured alkane-oxidizing archaea has expanded through the use of environmental metagenomics and enrichment cultures of syntrophic methane-, ethane-, propane-, and butane-oxidizing marine archaea with sulfate-reducing bacteria. A recently cultured group of archaea directly couples long-chain alkane degradation with methane formation, expanding the range of substrates used for methanogenesis. This article summarizes the rapidly growing knowledge of the diversity, physiology, and habitat distribution of alkane-degrading archaea. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Gunter Wegener
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rafael Laso-Pérez
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Max Planck Institute for Marine Microbiology, Bremen, Germany.,Current affiliation: Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Victoria J Orphan
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Division of Geological and Planetary Sciences and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA;
| | - Antje Boetius
- MARUM, Center for Marine Environmental Sciences, University Bremen, Bremen, Germany; , .,Max Planck Institute for Marine Microbiology, Bremen, Germany.,Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany;
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39
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Lemaire O, Wagner T. A Structural View of Alkyl-Coenzyme M Reductases, the First Step of Alkane Anaerobic Oxidation Catalyzed by Archaea. Biochemistry 2022; 61:805-821. [PMID: 35500274 PMCID: PMC9118554 DOI: 10.1021/acs.biochem.2c00135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/14/2022] [Indexed: 11/28/2022]
Abstract
Microbial anaerobic oxidation of alkanes intrigues the scientific community by way of its impact on the global carbon cycle, and its biotechnological applications. Archaea are proposed to degrade short- and long-chain alkanes to CO2 by reversing methanogenesis, a theoretically reversible process. The pathway would start with alkane activation, an endergonic step catalyzed by methyl-coenzyme M reductase (MCR) homologues that would generate alkyl-thiols carried by coenzyme M. While the methane-generating MCR found in methanogens has been well characterized, the enzymatic activity of the putative alkane-fixing counterparts has not been validated so far. Such an absence of biochemical investigations contrasts with the current explosion of metagenomics data, which draws new potential alkane-oxidizing pathways in various archaeal phyla. Therefore, validating the physiological function of these putative alkane-fixing machines and investigating how their structures, catalytic mechanisms, and cofactors vary depending on the targeted alkane have become urgent needs. The first structural insights into the methane- and ethane-capturing MCRs highlighted unsuspected differences and proposed some explanations for their substrate specificity. This Perspective reviews the current physiological, biochemical, and structural knowledge of alkyl-CoM reductases and offers fresh ideas about the expected mechanistic and chemical differences among members of this broad family. We conclude with the challenges of the investigation of these particular enzymes, which might one day generate biofuels for our modern society.
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Affiliation(s)
- Olivier
N. Lemaire
- Max Planck Institute for
Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Tristan Wagner
- Max Planck Institute for
Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
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40
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Khot V, Zorz J, Gittins DA, Chakraborty A, Bell E, Bautista MA, Paquette AJ, Hawley AK, Novotnik B, Hubert CRJ, Strous M, Bhatnagar S. CANT-HYD: A Curated Database of Phylogeny-Derived Hidden Markov Models for Annotation of Marker Genes Involved in Hydrocarbon Degradation. Front Microbiol 2022; 12:764058. [PMID: 35069469 PMCID: PMC8767102 DOI: 10.3389/fmicb.2021.764058] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/08/2021] [Indexed: 02/04/2023] Open
Abstract
Many pathways for hydrocarbon degradation have been discovered, yet there are no dedicated tools to identify and predict the hydrocarbon degradation potential of microbial genomes and metagenomes. Here we present the Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD), a database of 37 HMMs of marker genes involved in anaerobic and aerobic degradation pathways of aliphatic and aromatic hydrocarbons. Using this database, we identify understudied or overlooked hydrocarbon degradation potential in many phyla. We also demonstrate its application in analyzing high-throughput sequence data by predicting hydrocarbon utilization in large metagenomic datasets from diverse environments. CANT-HYD is available at https://github.com/dgittins/CANT-HYD-HydrocarbonBiodegradation.
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Affiliation(s)
- Varada Khot
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Jackie Zorz
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Daniel A Gittins
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Anirban Chakraborty
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Emma Bell
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - María A Bautista
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Alexandre J Paquette
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Alyse K Hawley
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Breda Novotnik
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Casey R J Hubert
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Marc Strous
- Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Srijak Bhatnagar
- Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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41
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Li WL, Dong X, Lu R, Zhou YL, Zheng PF, Feng D, Wang Y. Microbial ecology of sulfur cycling near the sulfate-methane transition of deep-sea cold seep sediments. Environ Microbiol 2021; 23:6844-6858. [PMID: 34622529 DOI: 10.1111/1462-2920.15796] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 11/27/2022]
Abstract
Microbial sulfate reduction is largely associated with anaerobic methane oxidation and alkane degradation in sulfate-methane transition zone (SMTZ) of deep-sea cold seeps. How the sulfur cycling is mediated by microbes near SMTZ has not been fully understood. In this study, we detected a shallow SMTZ in three of eight sediment cores sampled from two cold seep areas in the South China Sea. One hundred ten genomes representing sulfur-oxidizing bacteria (SOB) and sulfur-reducing bacteria (SRB) strains were identified from three SMTZ-bearing cores. In the layers above SMTZ, SOB were mostly constituted by Campylobacterota, Gammaproteobacteria and Alphaproteobacteria that probably depended on nitrogen oxides and/or oxygen for oxidation of sulfide and thiosulfate in near-surface sediment layers. In the layers below the SMTZ, the deltaproteobacterial SRB genomes and metatranscriptomes revealed CO2 fixation by Wood-Ljungdahl pathway, sulfate reduction and nitrogen fixation for syntrophic or fermentative lifestyle. A total of 68% of the metagenome assembled genomes were not adjacent to known species in a phylogenomic tree, indicating a high diversity of bacteria involved in sulfur cycling. With the large number of genomes for SOB and SRB, our study uncovers the microbial populations that potentially mediate sulfur metabolism and associated carbon and nitrogen cycles, which sheds light on complex biogeochemical processes in deep-sea environments.
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Affiliation(s)
- Wen-Li Li
- Department of Life Science, Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, 572000, China
| | - Xiyang Dong
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
| | - Rui Lu
- Department of Life Science, Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, 572000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying-Li Zhou
- Department of Life Science, Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, 572000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peng-Fei Zheng
- Department of Life Science, Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, 572000, China
| | - Dong Feng
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Yong Wang
- Department of Life Science, Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, 572000, China
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42
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Wu JY, Gu L, Hua ZL, Liang ZY, Chu KJ, He XX. Per-, poly-fluoroalkyl substances (PFASs) pollution in benthic riverine ecosystem: Integrating microbial community coalescence and biogeochemistry with sediment distribution. CHEMOSPHERE 2021; 281:130977. [PMID: 34289625 DOI: 10.1016/j.chemosphere.2021.130977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/17/2021] [Accepted: 05/22/2021] [Indexed: 06/13/2023]
Abstract
Per-, Poly-fluoroalkyl substances (PFASs) accumulation in benthic environments is mainly determined by material mixing and represents a significant challenge to river remediation. However, less attention has been paid to the effects of sediment distribution on PFASs accumulation, and how PFASs influence microbial community coalescence and biogeochemical processes. In order to identify correlations between PFASs distribution and benthic microbial community functions, we conducted a field study and quantified the ecological constrains of material transportation on benthic microorganisms. Perfluorohexanoic acid (PFHxA) contributed most to the taxonomic heterogeneity of both archaeal (12.199%) and bacterial (13.675%) communities. Genera Methanoregula (R2 = 0.292) and Bacillus (R2 = 0.791) were identified as indicators that respond to PFASs. Phylogenetic null modeling indicated that deterministic processes (50.0-82.2%) dominated in spatial assembly of archaea, while stochasticity (94.4-97.8%) dominated in bacteria. Furthermore, spatial mixing of PFASs influenced broadly in nitrogen cycling of archaeal genomes, and phosphorus mineralization of bacterial genomes (p < 0.05). Overall, we quantified the effect of PFASs on community assembly and highlighted the constrains of PFASs influence on benthic geochemical potentials, which may provide new insights into riverine remediation.
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Affiliation(s)
- Jian-Yi Wu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; Yangtze Institute for Conservation and Development, Hohai University, Jiangsu, 210098, China
| | - Li Gu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; Yangtze Institute for Conservation and Development, Hohai University, Jiangsu, 210098, China.
| | - Zu-Lin Hua
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; Yangtze Institute for Conservation and Development, Hohai University, Jiangsu, 210098, China
| | - Zhong-Yan Liang
- Nanjing Guohuan Science and Technology Co., Ltd., Nanjing, 210001, China
| | - Ke-Jian Chu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Xin-Xin He
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
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43
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Zhao Y, Wang J, Liu Y, Zheng P, Hu B. Microbial interaction promotes desulfurization efficiency under high pH condition. ENVIRONMENTAL RESEARCH 2021; 200:111423. [PMID: 34118244 DOI: 10.1016/j.envres.2021.111423] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/22/2021] [Accepted: 05/25/2021] [Indexed: 06/12/2023]
Abstract
The existence of H2S in biogas may cause equipment corrosion and considerable SO2 emission. Commonly used biotrickling filters may cause biogas dilution or generation of explosive mixtures. Compared with biotrickling filters, two-step process such as bioscrubber filters can overcome these shortages. However, its removal efficiency was still limited due to low microbial activity under high pH condition. Here, a bioreactor filter was carried out under pH 9.0. Removal efficiency higher than 99% was achieved under sulfide loading rate reaching 4.24 kg S m-3d-1. Results of network and high throughput sequencing showed that Thiobacillus acted as both dominant species (accounting for 75%) and unique kinless hub in this bioreactor. Other bacteria (accounting for 25%) contributed 75% to the network, which implied the intensive interaction between Thiobacillus and others. Sulfide removal ability and pH tolerance of pure bacteria and mixed culture were considered to verify how microbial interaction influenced them. Compared with pure bacteria, mixed culture had better performance under high pH condition, which confirmed that microbial interaction promoted desulfurization efficiency under high pH condition. These results showed that intensive microbial interaction might be the key to enhance sulfide removal efficiency under high pH condition.
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Affiliation(s)
- Yuxiang Zhao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Yan Liu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China.
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44
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Li Z, Pan D, Wei G, Pi W, Zhang C, Wang JH, Peng Y, Zhang L, Wang Y, Hubert CRJ, Dong X. Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity. THE ISME JOURNAL 2021; 15:2366-2378. [PMID: 33649554 PMCID: PMC8319345 DOI: 10.1038/s41396-021-00932-y] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 12/11/2022]
Abstract
In marine ecosystems, viruses exert control on the composition and metabolism of microbial communities, influencing overall biogeochemical cycling. Deep sea sediments associated with cold seeps are known to host taxonomically diverse microbial communities, but little is known about viruses infecting these microorganisms. Here, we probed metagenomes from seven geographically diverse cold seeps across global oceans to assess viral diversity, virus-host interaction, and virus-encoded auxiliary metabolic genes (AMGs). Gene-sharing network comparisons with viruses inhabiting other ecosystems reveal that cold seep sediments harbour considerable unexplored viral diversity. Most cold seep viruses display high degrees of endemism with seep fluid flux being one of the main drivers of viral community composition. In silico predictions linked 14.2% of the viruses to microbial host populations with many belonging to poorly understood candidate bacterial and archaeal phyla. Lysis was predicted to be a predominant viral lifestyle based on lineage-specific virus/host abundance ratios. Metabolic predictions of prokaryotic host genomes and viral AMGs suggest that viruses influence microbial hydrocarbon biodegradation at cold seeps, as well as other carbon, sulfur and nitrogen cycling via virus-induced mortality and/or metabolic augmentation. Overall, these findings reveal the global diversity and biogeography of cold seep viruses and indicate how viruses may manipulate seep microbial ecology and biogeochemistry.
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Affiliation(s)
- Zexin Li
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Donald Pan
- Department of Ecology and Environmental Studies, The Water School, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Guangshan Wei
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Weiling Pi
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Chuwen Zhang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Jiang-Hai Wang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Yongyi Peng
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Lu Zhang
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Yong Wang
- Department of Life Science, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Xiyang Dong
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China.
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45
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Hughes ER, Winter MG, Alves da Silva L, Muramatsu MK, Jimenez AG, Gillis CC, Spiga L, Chanin RB, Santos RL, Zhu W, Winter SE. Reshaping of bacterial molecular hydrogen metabolism contributes to the outgrowth of commensal E. coli during gut inflammation. eLife 2021; 10:e58609. [PMID: 34085924 PMCID: PMC8177889 DOI: 10.7554/elife.58609] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 05/20/2021] [Indexed: 12/24/2022] Open
Abstract
The composition of gut-associated microbial communities changes during intestinal inflammation, including an expansion of Enterobacteriaceae populations. The mechanisms underlying microbiota changes during inflammation are incompletely understood. Here, we analyzed previously published metagenomic datasets with a focus on microbial hydrogen metabolism. The bacterial genomes in the inflamed murine gut and in patients with inflammatory bowel disease contained more genes encoding predicted hydrogen-utilizing hydrogenases compared to communities found under non-inflamed conditions. To validate these findings, we investigated hydrogen metabolism of Escherichia coli, a representative Enterobacteriaceae, in mouse models of colitis. E. coli mutants lacking hydrogenase-1 and hydrogenase-2 displayed decreased fitness during colonization of the inflamed cecum and colon. Utilization of molecular hydrogen was in part dependent on respiration of inflammation-derived electron acceptors. This work highlights the contribution of hydrogenases to alterations of the gut microbiota in the context of non-infectious colitis.
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Affiliation(s)
| | - Maria G Winter
- Department of Microbiology, UT SouthwesternDallasUnited States
| | - Laice Alves da Silva
- Departamento de Clinica e Cirurgia Veterinarias, Escola de Veterinaria, Universidade Federal de Minas GeraisBelo HorizonteBrazil
| | | | - Angel G Jimenez
- Department of Microbiology, UT SouthwesternDallasUnited States
| | | | - Luisella Spiga
- Department of Microbiology, UT SouthwesternDallasUnited States
| | | | - Renato L Santos
- Departamento de Clinica e Cirurgia Veterinarias, Escola de Veterinaria, Universidade Federal de Minas GeraisBelo HorizonteBrazil
| | - Wenhan Zhu
- Department of Microbiology, UT SouthwesternDallasUnited States
| | - Sebastian E Winter
- Department of Microbiology, UT SouthwesternDallasUnited States
- Department of Immunology, UT SouthwesternDallasUnited States
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46
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Zhang C, Meckenstock RU, Weng S, Wei G, Hubert CRJ, Wang JH, Dong X. Marine sediments harbor diverse archaea and bacteria with the potential for anaerobic hydrocarbon degradation via fumarate addition. FEMS Microbiol Ecol 2021; 97:6171024. [PMID: 33720296 DOI: 10.1093/femsec/fiab045] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/12/2021] [Indexed: 11/13/2022] Open
Abstract
Marine sediments can contain large amounts of alkanes and methylated aromatic hydrocarbons that are introduced by natural processes or anthropogenic activities. These compounds can be biodegraded by anaerobic microorganisms via enzymatic addition of fumarate. However, the identity and ecological roles of a significant fraction of hydrocarbon degraders containing fumarate-adding enzymes (FAE) in various marine sediments remains unknown. By combining phylogenetic reconstructions, protein homolog modelling, and functional profiling of publicly available metagenomes and genomes, 61 draft bacterial and archaeal genomes encoding anaerobic hydrocarbon degradation via fumarate addition were obtained. Besides Desulfobacterota (previously known as Deltaproteobacteria) that are well-known to catalyze these reactions, Chloroflexi are dominant FAE-encoding bacteria in hydrocarbon-impacted sediments, potentially coupling sulfate reduction or fermentation to anaerobic hydrocarbon degradation. Among Archaea, besides Archaeoglobi previously shown to have this capability, genomes of Heimdallarchaeota, Lokiarchaeota, Thorarchaeota and Thermoplasmata also suggest fermentative hydrocarbon degradation using archaea-type FAE. These bacterial and archaeal hydrocarbon degraders occur in a wide range of marine sediments, including high abundances of FAE-encoding Asgard archaea associated with natural seeps and subseafloor ecosystems. Our results expand the knowledge of diverse archaeal and bacterial lineages engaged in anaerobic degradation of alkanes and methylated aromatic hydrocarbons.
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Affiliation(s)
- Chuwen Zhang
- School of Marine Sciences, Sun Yat-Sen University, 2 Daxue Road, Xiangzhou District, Zhuhai 519082, China
| | - Rainer U Meckenstock
- Environmental Microbiology and Biotechnology, University Duisburg-Essen, Universitätsstrasse 5, Essen 45141, Germany
| | - Shengze Weng
- School of Marine Sciences, Sun Yat-Sen University, 2 Daxue Road, Xiangzhou District, Zhuhai 519082, China
| | - Guangshan Wei
- School of Marine Sciences, Sun Yat-Sen University, 2 Daxue Road, Xiangzhou District, Zhuhai 519082, China.,Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184 Daxue Road, Siming District, Xiamen 361005, China
| | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, AB T2N1N4, Canada
| | - Jiang-Hai Wang
- School of Marine Sciences, Sun Yat-Sen University, 2 Daxue Road, Xiangzhou District, Zhuhai 519082, China
| | - Xiyang Dong
- School of Marine Sciences, Sun Yat-Sen University, 2 Daxue Road, Xiangzhou District, Zhuhai 519082, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), 2 Daxue Road, XiangZhou District, Zhuhai 519000, China
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