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Yuan H, Zhang R, Chen J, Wu J, Han Q, Li Q, Lu Q. Phosphorus resource partitioning underpins diversity patterns and assembly processes of microbial communities in plateau karst lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 952:175860. [PMID: 39214351 DOI: 10.1016/j.scitotenv.2024.175860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 08/09/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024]
Abstract
Eutrophication triggered by internal phosphorus (P) poses a substantial threat to the biodiversity of organisms in freshwater ecosystems. However, little is known about the linkages between P resource partitioning and microbial succession, especially in karst sediments. Here, we studied the diversity patterns and assembly processes of bacterial and archaeal communities in sediment cores from two historically hyper-eutrophicated karst lakes, Hongfeng Lake and Aha Lake, and investigated the relative contribution of P fractions to them. Our null and neutral models consistently indicated that bacterial and archaeal community assembly was judged to be deterministic rather than stochastic. We found a monotonically decreasing pattern for bacterial Shannon diversity toward deep sediments in Aha Lake, but U- or hump-shaped patterns for archaea in Hongfeng and Aha Lakes. Intriguingly, the community dissimilarity Bray-Curtis of bacteria and archaea consistently increased with increasing depth distance, with slopes of 0.0080 and 0.0069 in Hongfeng Lake and 0.0078 and 0.0087 in Aha Lake, respectively. Such cross-taxon congruence was well-supported by equivalent ecological processes (i.e., environmental selection). For bacteria and archaea, Shannon diversity was primarily affected by the total P (TP) fractions such as the loosely adsorbed TP or calcium-bound TP and sediment TP. Their community composition was significantly (P < 0.05) affected by calcium-bound inorganic P (Pi), loosely adsorbed Pi and reductant-soluble Pi. Although sediment properties were important, bacterial and archaeal diversity or community composition were well-explained by the Pi fractions, with high direct or indirect effects. In particular, Pi fractions exhibited stronger effects on bacterial and archaeal characteristics than organic P fractions. Taken together, our study provides novel insights into the ecological importance of P resource partitioning to microbial succession, which has crucial implications for disentangling the biogeochemical processes of P cycling in aquatic ecosystems.
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Affiliation(s)
- Haijun Yuan
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Runyu Zhang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China.
| | - Jingan Chen
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Jing Wu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiao Han
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiuxing Li
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; College of Earth Science, Chengdu University of Technology, Chengdu 610059, China
| | - Qiping Lu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
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Gong X, Xu L, Langwig MV, Chen Z, Huang S, Zhao D, Su L, Zhang Y, Francis CA, Liu J, Li J, Baker BJ. Globally distributed marine Gemmatimonadota have unique genomic potentials. MICROBIOME 2024; 12:149. [PMID: 39123272 PMCID: PMC11316326 DOI: 10.1186/s40168-024-01871-4] [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: 02/24/2024] [Accepted: 07/09/2024] [Indexed: 08/12/2024]
Abstract
BACKGROUND Gemmatimonadota bacteria are widely distributed in nature, but their metabolic potential and ecological roles in marine environments are poorly understood. RESULTS Here, we obtained 495 metagenome-assembled genomes (MAGs), and associated viruses, from coastal to deep-sea sediments around the world. We used this expanded genomic catalog to compare the protein composition and update the phylogeny of these bacteria. The marine Gemmatimonadota are phylogenetically different from those previously reported from terrestrial environments. Functional analyses of these genomes revealed these marine genotypes are capable of degradation of complex organic carbon, denitrification, sulfate reduction, and oxidizing sulfide and sulfite. Interestingly, there is widespread genetic potential for secondary metabolite biosynthesis across Gemmatimonadota, which may represent an unexplored source of novel natural products. Furthermore, viruses associated with Gemmatimonadota have the potential to "hijack" and manipulate host metabolism, including the assembly of the lipopolysaccharide in their hosts. CONCLUSIONS This expanded genomic diversity advances our understanding of these globally distributed bacteria across a variety of ecosystems and reveals genetic distinctions between those in terrestrial and marine communities. Video Abstract.
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Affiliation(s)
- Xianzhe Gong
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, Guangdong, China.
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Austin, TX, 78373, USA.
| | - Le Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China
| | - Marguerite V Langwig
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Austin, TX, 78373, USA
| | - Zhiyi Chen
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, China
| | - Shujie Huang
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China
| | - Duo Zhao
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China
| | - Lei Su
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Yan Zhang
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Christopher A Francis
- Departments of Earth System Science & Oceans, Stanford University, Stanford, CA, 94305, USA
| | - Jihua Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, Shandong, China.
| | - Jiangtao Li
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China.
| | - Brett J Baker
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Austin, TX, 78373, USA.
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA.
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Xie Z, Li W, Yang K, Wang X, Xiong S, Zhang X. Bacterial and Archaeal Communities in Erhai Lake Sediments: Abundance and Metabolic Insight into a Plateau Lake at the Edge of Eutrophication. Microorganisms 2024; 12:1617. [PMID: 39203459 PMCID: PMC11356345 DOI: 10.3390/microorganisms12081617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 07/31/2024] [Accepted: 08/02/2024] [Indexed: 09/03/2024] Open
Abstract
The littoral zones of lakes are potential hotspots for local algal blooms and biogeochemical cycles; however, the microbial communities within the littoral sediments of eutrophic plateau lakes remain poorly understood. Here, we investigated the taxonomic composition, co-occurrence networks, and potential functional roles of both abundant and rare taxa within bacterial and archaeal communities, as well as physicochemical parameters, in littoral sediments from Erhai Lake, a mesotrophic lake transitioning towards eutrophy located in the Yunnan-Guizhou Plateau. 16S rRNA gene sequencing revealed that bacterial communities were dominated by Proteobacteria, Bacteroidetes, and Chloroflexi, while Euryarchaeota was the main archaeal phylum. Co-occurrence network analysis revealed that keystone taxa mainly belonged to rare species in the bacterial domain, but in the archaeal domain, over half of keystone taxa were abundant species, demonstrating their fundamental roles in network persistence. The rare bacterial taxa contributed substantially to the overall abundance (81.52%), whereas a smaller subset of abundant archaeal taxa accounted for up to 82.70% of the overall abundance. Functional predictions highlighted a divergence in metabolic potentials, with abundant bacterial sub-communities enriched in pathways for nitrogen cycling, sulfur cycling, and chlorate reduction, while rare bacterial sub-communities were linked to carbon cycling processes such as methanotrophy. Abundant archaeal sub-communities exhibited a high potential for methanogenesis, chemoheterotrophy, and dark hydrogen oxidation. Spearman correlation analysis showed that genera such as Candidatus competibacter, Geobacter, Syntrophobacter, Methanocella, and Methanosarcina may serve as potential indicators of eutrophication. Overall, this study provides insight into the distinct roles that rare and abundant taxa play in the littoral sediments of mesotrophic plateau lakes.
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Affiliation(s)
- Zhen Xie
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (Z.X.); (K.Y.)
| | - Wei Li
- National Observation and Research Station of Erhai Lake Ecosystem in Yunnan, Dali 671000, China; (W.L.); (X.W.); (S.X.)
- Yunnan Dali Research Institute, Shanghai Jiao Tong University, Dali 671000, China
| | - Kaiwen Yang
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (Z.X.); (K.Y.)
| | - Xinze Wang
- National Observation and Research Station of Erhai Lake Ecosystem in Yunnan, Dali 671000, China; (W.L.); (X.W.); (S.X.)
- Yunnan Dali Research Institute, Shanghai Jiao Tong University, Dali 671000, China
| | - Shunzi Xiong
- National Observation and Research Station of Erhai Lake Ecosystem in Yunnan, Dali 671000, China; (W.L.); (X.W.); (S.X.)
- Yunnan Dali Research Institute, Shanghai Jiao Tong University, Dali 671000, China
| | - Xiaojun Zhang
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (Z.X.); (K.Y.)
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Wang P, Wu D, Su Y, Xie B. Mitigated dissemination of antibiotic resistance genes by nanoscale zero-valent iron and iron oxides during anaerobic digestion: Roles of microbial succession and regulation. JOURNAL OF HAZARDOUS MATERIALS 2024; 473:134636. [PMID: 38772111 DOI: 10.1016/j.jhazmat.2024.134636] [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: 10/21/2023] [Revised: 04/15/2024] [Accepted: 05/15/2024] [Indexed: 05/23/2024]
Abstract
Nanoscale zero-valent iron (ZVI) and the oxides have been documented as an effective approach for mitigating the dissemination of antibiotic resistance genes (ARGs) during anaerobic digestion (AD). However, the mechanism of ARGs dissemination mitigated by nanoscale ZVI and iron oxides remain unclear. Here, we investigated the influencing mechanisms of nanoscale ZVI and iron oxides on ARGs dissemination during AD. qPCR results indicated that nanoscale ZVI and iron oxides significantly declined the total ARGs abundances, and the strongest inhibiting effect was observed by 10 g/L nanoscale ZVI. Mantel test showed ARGs distribution was positively correlated with physiochemical properties, integrons and microbial community, among which microbial community primarily contributed to ARGs dissemination (39.74%). Furthermore, redundancy and null model analyses suggested the dominant and potential ARGs host was Fastidiosipila, and homogeneous selection in the determinism factors was the largest factor for driving Fastidiosipila variation, confirming the inhibition of Fastidiosipila was primary reason for mitigating ARGs dissemination by nanoscale ZVI and iron oxides. These results were related to the inhibition of ARGs transfer related functions. This work provides novel evidence for mitigating ARGs dissemination through regulating microbial succession and regulation induced by ZVI and iron oxides.
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Affiliation(s)
- Panliang Wang
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Sciences, Henan Normal University, Xinxiang, Henan 453007, PR China
| | - Dong Wu
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Yinglong Su
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China
| | - Bing Xie
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China.
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5
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Dash SP, Manu S, Kim JY, Rastogi G. Spatio-temporal structuring and assembly of abundant and rare bacteria in the benthic compartment of a marginally eutrophic lagoon. MARINE POLLUTION BULLETIN 2024; 200:116138. [PMID: 38359478 DOI: 10.1016/j.marpolbul.2024.116138] [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: 10/14/2023] [Revised: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 02/17/2024]
Abstract
The investigations on ecological processes that structure abundant and rare sub-communities are limited from the benthic compartments of tropical brackish lagoons. We examined the spatial and temporal patterns in benthic bacterial communities of a brackish lagoon; Chilika. Abundant and rare bacteria showed differences in niche specialization but exhibited similar distance-decay patterns. Abundant bacteria were mostly habitat generalists due to their broader niche breadth, environmental response thresholds, and greater functional redundancy. In contrast, rare bacteria were mostly habitat specialists due to their narrow niche breadth, lower environmental response thresholds, and functional redundancy. The spatial patterns in abundant bacteria were largely shaped by stochastic processes (88.7 %, mostly dispersal limitation). In contrast, rare bacteria were mostly structured by deterministic processes (56.4 %, mostly heterogeneous selection). These findings provided a quantitative assessment of the different forces namely spatial, environmental, and biotic that together structured bacterial communities in the benthic compartment of a marginally eutrophic lagoon.
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Affiliation(s)
- Stiti Prangya Dash
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon 752030, Odisha, India; KIIT School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar 751024, Odisha, India
| | - Shivakumara Manu
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500048, India
| | - Ji Yoon Kim
- Department of Biological Science, Kunsan National University, Gunsan 54150, Republic of Korea
| | - Gurdeep Rastogi
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon 752030, Odisha, India.
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Yuan Y, Zhang G, Fang H, Guo H, Li Y, Li Z, Peng S, Wang F. Diversity, composition, metabolic characteristics, and assembly process of the microbial community in sewer system at the early stage. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:13075-13088. [PMID: 38240967 DOI: 10.1007/s11356-024-31941-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: 07/17/2023] [Accepted: 01/05/2024] [Indexed: 02/23/2024]
Abstract
Sewer systems play vital roles in wastewater treatment facilities, and the microbial communities contribute significantly to the transformation of domestic wastewater. Therefore, this study conducted a 180-day experiment on a sewer system and utilized the high-throughput sequencing technology to characterize the microbial communities. Additionally, community assembly analysis was performed to understand the early-stage dynamics within the sewer system. The results demonstrated that the overall diversity of microbial communities exhibited fluctuations as the system progressed. The dominant phyla observed were Chloroflexi, Bacteroidetes, Firmicutes, and Proteobacteria, accounting for over 85.4% of the total relative abundances. At the genus level, bacteria associated with fermentation displayed a high relative abundance, particularly during days 75 to 180. A random-forest machine-learning model identified a group of microbes that confirmed the substantial contribution of fermentation. During the process of fermentation, microorganisms predominantly utilized propionate formation as the main pathway for acidogenesis, followed by acetate and butyrate formation. In terms of nitrogen and sulfur cycles, dissimilatory nitrate reduction and assimilatory sulfate reduction played significant roles. Furthermore, stochastic ecological processes had a dominant effect during the experiment. Dispersal limitation primarily governed the assembly process almost the entire experimental period, indicating the strong adaptability and metabolic plasticity of microorganisms in response to environmental variations. This experiment provides valuable insights into the metabolic mechanisms and microbial assembly associated with sewer systems.
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Affiliation(s)
- Yiming Yuan
- School of Water Conservancy and Transportation, Zhengzhou University, Kexue Road 100, Zhengzhou, 450001, Henan Province, China
- Yellow River Laboratory, Zhengzhou University, Zhengzhou, 450001, China
- National Local Joint Engineering Laboratory of Major Infrastructure Testing and Rehabilitation Technology, Zhengzhou, 450001, China
- Collaborative Innovation Center of Water Conservancy and Transportation Infrastructure Safety, Zhengzhou, 450001, Henan Province, China
| | - Guangyi Zhang
- School of Water Conservancy and Transportation, Zhengzhou University, Kexue Road 100, Zhengzhou, 450001, Henan Province, China.
| | - Hongyuan Fang
- School of Water Conservancy and Transportation, Zhengzhou University, Kexue Road 100, Zhengzhou, 450001, Henan Province, China
- Yellow River Laboratory, Zhengzhou University, Zhengzhou, 450001, China
- National Local Joint Engineering Laboratory of Major Infrastructure Testing and Rehabilitation Technology, Zhengzhou, 450001, China
- Collaborative Innovation Center of Water Conservancy and Transportation Infrastructure Safety, Zhengzhou, 450001, Henan Province, China
| | - Haifeng Guo
- School of Water Conservancy and Transportation, Zhengzhou University, Kexue Road 100, Zhengzhou, 450001, Henan Province, China
| | - Yongkang Li
- School of Water Conservancy and Transportation, Zhengzhou University, Kexue Road 100, Zhengzhou, 450001, Henan Province, China
| | - Zezhuang Li
- School of Water Conservancy and Transportation, Zhengzhou University, Kexue Road 100, Zhengzhou, 450001, Henan Province, China
| | - Siwei Peng
- School of Water Conservancy and Transportation, Zhengzhou University, Kexue Road 100, Zhengzhou, 450001, Henan Province, China
| | - Fuming Wang
- School of Water Conservancy and Transportation, Zhengzhou University, Kexue Road 100, Zhengzhou, 450001, Henan Province, China
- Yellow River Laboratory, Zhengzhou University, Zhengzhou, 450001, China
- National Local Joint Engineering Laboratory of Major Infrastructure Testing and Rehabilitation Technology, Zhengzhou, 450001, China
- Collaborative Innovation Center of Water Conservancy and Transportation Infrastructure Safety, Zhengzhou, 450001, Henan Province, China
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Sun C, Zhang S, Yang J, Zhou H, Cheng H, Chen Z, Yu L, Wang Y, Chen X. Discrepant assembly processes of prokaryotic communities between the abyssal and hadal sediments in Yap Trench. ENVIRONMENTAL RESEARCH 2024; 241:117602. [PMID: 37951379 DOI: 10.1016/j.envres.2023.117602] [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: 08/05/2023] [Revised: 10/17/2023] [Accepted: 11/03/2023] [Indexed: 11/14/2023]
Abstract
Abyssal and hadal sediments represent two of the most type ecosystems on Earth and have the potential interactions with geochemistry. However, little is known about the prokaryotic community assembly and the response of prokaryotic communities to metal(loid)s in trench sediments due to the lack of adequate and appropriate samples. In this study, a systematic investigation combined the assembly mechanisms and co-occurrence patterns of prokaryotic communities between the hadal and abyssal sediments across the Yap Trench. The results revealed that the hadal prokaryotes had less species diversity, but more abundant function than the abyssal prokaryotes. The prokaryotic communities in the abyssal sediments had more core taxa than the hadal sediments. Twenty-one biomarkers mostly affiliated with Nitrosopumilaceae were detected using Random-Forests machine learning algorithm. Furthermore, stochasticity was dominant in the prokaryotic community assembly processes of the Yap Trench sediments. Meanwhile, homogeneous selection (32.6%-52.9%) belonging to deterministic processes governed the prokaryotic community assembly in hadal sediments with increasing of sediment depth. In addition to total nitrogen and total organic carbon, more metal(loid)s were significantly correlated with the prokaryotic community in the hadal sediments than that in the abyssal sediments. The hadal prokaryotic communities was most positively related to bismuth (r = 0.31, p < 0.01), followed by calcium, chromium, cerium, potassium, plumbum, scandium, titanium, and vanadium. Finally, co-occurrence networks revealed two potential dominant prokaryotic modules in Yap Trench sediments covaried across oceanographic zonation. By contrast, the hadal network had relatively more complexity, more bacterial taxa, and more associations among prokaryotic taxa, relative to the abyssal network. This study reveals potentially metal variables and community assembly mechanisms of the prokaryotic community in abyssal and hadal sediments and provides a better understanding on the prokaryotic diversity and ecology in trench sediment ecosystems.
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Affiliation(s)
- Chongran Sun
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China
| | - Shuangfei Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China
| | - Jichao Yang
- College of Marine Science and Engineering, Shandong University of Science and Technology, Qingdao, 266590, Shandong, China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, Hunan, China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, Hunan, China
| | - Zhu Chen
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, Hunan, China
| | - Libo Yu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Fujian, China
| | - Yuguang Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, Hunan, China.
| | - Xinhua Chen
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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Che Y, Lin C, Li S, Liu J, Zhu L, Yu S, Wang N, Li H, Bao M, Zhou Y, Si T, Bao R. Influences of hydrodynamics on microbial community assembly and organic carbon composition of resuspended sediments in shallow marginal seas. WATER RESEARCH 2024; 248:120882. [PMID: 38006834 DOI: 10.1016/j.watres.2023.120882] [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: 07/25/2023] [Revised: 10/25/2023] [Accepted: 11/14/2023] [Indexed: 11/27/2023]
Abstract
Hydrodynamic processes play a crucial role in driving the transmission of sediments, likely harboring diverse microbes and heterogeneous organic carbon (OC) in the ocean. Here we conducted continuous micro-erosion experiments on surface sediments retrieved from shallow marginal seas, and analyzed the microbial community structures, OC content, and isotope compositions (δ13C and Δ14C) of resuspended sediments to investigate the effects of hydrodynamics on microbial assembly and OC composition in marginal seas. Our results showed that gene abundance and major microbial compositions in resuspended sediments changed with varying benthic shear stresses, which evolved towards diversification after continuous hydrodynamic erosion. Aerobic bacteria were more likely to be eroded out from sediments under lower shear stresses compared with anaerobic bacteria. Our study provides evidence that hydrodynamic disturbances shape the assembly of microbial communities with different metabolic functions, especially for bacteria, which may spatially influence the microbial-mediated biogeochemical transformation in marginal seas. Isotopic results revealed that more terrestrial OC was resuspended under initial erosion, while more marine OC was eroded out with increasing shear stresses, suggesting that hydrodynamics may control the redistribution of different sourced OC and contribute to the dispersion and degradation of terrestrial OC during transport process. Our findings further suggest that the nature of resuspended OC may influence the assembly of sediment-attached microbes due to their metabolic preference for carbon sources, as evidenced by correlations between OC compositions and microbial diversity and abundance. We thus suggest that hydrodynamic disturbance is an extrinsic physical driver of OC redistribution and microbial reassembly, whereas OC may be an intrinsic factor influencing microbial colonization, helping to interpret the spatial heterogeneity of microbes and OC compositions observed in marginal sea sediments. Our study underscores the significant roles of hydrodynamic-driven sediment resuspension in shaping diverse microbial communities and redistributing OC in aquatic systems, and highlights the importance of this process in biogeochemical cycles and ecological environment evolution in shallow marginal sea systems.
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Affiliation(s)
- Yangli Che
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Chaoran Lin
- College of Marine Geosciences, Ocean University of China, Qingdao, China
| | - Shen Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Jiao Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Longhai Zhu
- College of Marine Geosciences, Ocean University of China, Qingdao, China
| | - Shilei Yu
- College of Marine Geosciences, Ocean University of China, Qingdao, China
| | - Nan Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Key Lab of Submarine Geosciences and Prospecting Techniques, Ministry of Education and College of Marine Geosciences, Ocean University of China, Qingdao, China
| | - Haoshuai Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Mutai Bao
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Yang Zhou
- Guangzhou Marine Geological Survey, Guangzhou, China
| | - Tonghao Si
- College of Marine Geosciences, Ocean University of China, Qingdao, China
| | - Rui Bao
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China.
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Yu B, Zeng Q, Li J, Li J, Tan X, Gao X, Huang P, Wu S. Vertical variation in prokaryotic community composition and co-occurrence patterns in sediments of the Three Gorges Reservoir, China. ENVIRONMENTAL RESEARCH 2023; 237:116927. [PMID: 37604225 DOI: 10.1016/j.envres.2023.116927] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/17/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023]
Abstract
Archaea and bacteria are distributed throughout the sediment; however, our understanding of their biodiversity patterns, community composition, and interactions is primarily limited to the surface horizons (0-20 cm). In this research, sediment samples were collected from three vertical sediment profiles (depths of 0-295 cm) in the Three Gorges Reservoir (TGR), one of the largest reservoirs in the world. Through 16S rRNA sequencing, it was shown that sediment microbial diversity did not significantly vary across the sediment. Nevertheless, a decline in the similarity of archaeal and bacterial communities over distance along sediment vertical profiles was noted. Nonmetric multidimensional scaling (NMDS) analysis revealed that archaeal and bacterial communities could be clearly separated into two groups, located in the upper sediments (0-135 cm) and deep sediments (155-295 cm). Meanwhile, at the fine-scale of the vertical section, noteworthy variations were observed in the relative abundance of prominent archaea (e.g., Euryarchaeota) and bacteria (e.g., Proteobacteria). The linear discriminant analysis effect size (LEfSe) demonstrated that twenty-four bacterial and twenty-six archaeal biomarker microbes exist in the upper and deep sediment layers. Each layer exhibited distinctive microbial divisions, suggesting that microbes with diverse biological functions are capable of thriving and propagating along the sediment profile. Co-occurrence network analysis further indicated that the microbial network in the upper sediments was more complex than that in the deep sediments. Additionally, the newly discovered anaerobic methanotrophic archaeon Candidatus Methanoperedens was identified as the most abundant keystone archaeal taxon in both sediment layers, highlighting the significance of methane oxidation in material cycling within the TGR ecosystem. In summary, our study examined the biodiversity and coexistence patterns of benthic microbial communities throughout the vertical sediment profile, providing detailed insights into the vertical geography of archaeal and bacterial communities in typical deep-water reservoir ecosystems.
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Affiliation(s)
- Baohong Yu
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, PR China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, PR China
| | - Quanchao Zeng
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, PR China.
| | - Jinlin Li
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, PR China
| | - Jun Li
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, PR China
| | - Xun Tan
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, PR China
| | - Xin Gao
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, PR China
| | - Ping Huang
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, PR China
| | - Shengjun Wu
- Key Laboratory of Reservoir Aquatic Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, PR China
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Zou K, Zhu Y, Jiang Y, Ma S, Li M, Zhao W, Wang J. Distinct stochastic processes drive bacterial community assembly and co-occurrence patterns with common antibiotic resistance genes in two highly urbanised coastal ecosystems of the Pearl River Estuary. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132161. [PMID: 37523960 DOI: 10.1016/j.jhazmat.2023.132161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/15/2023] [Accepted: 07/25/2023] [Indexed: 08/02/2023]
Abstract
To comprehensively elucidate the ecology of the bacterial community and antibiotic resistance genes (ARGs) in urbanised coastal ecosystems, this study investigated the variations of bacterial community and five common types of ARGs, the impacting factors and assembly of bacterial community, as well as their co-occurrence relationships in two ecosystems of the Pearl River Estuary (PRE). The bacterial community composition and structure of the nearshore ecosystem (NSE) and the eight mouths of the PRE (EPR) markedly differed, with 38 phyla shared between these two ecosystems. The abundances of 10 ARGs and bacterial community diversity were significantly higher in the EPR than NSE. Moreover, 67.82% and 27.82% of the variation in the bacterial community was explained by spatial (44.42%/8.63%) and environmental (23.40%/19.19%) variables in the NSE and EPR, respectively. Significant distance-decay patterns were observed, and distinct stochastic processes (undominated processes or dispersal limitation) dominated bacterial community assembly in the NSE and EPR. Furthermore, co-occurrence patterns showed significant positive correlations between 48/182 ASVs belonging to 6/15 bacterial phyla and 8/11 ARGs in the NSE/EPR, with six common dominant hosts. These results clarify the drivers and mechanism shaping the bacterial community, providing further proof for potential ARG bacterial hosts in urbanised estuarine ecosystems.
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Affiliation(s)
- Keshu Zou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China.
| | - Yiyi Zhu
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Yun Jiang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Shanshan Ma
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Min Li
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300 Guangzhou, China; Scientific Observation and Research Field Station of Pearl River Estuary Ecosystem, Guangzhou 510300, Guangdong Province, China
| | - Wencheng Zhao
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China
| | - Jun Wang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, 510642 Guangzhou, China.
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11
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Sun J, Zhang A, Zhang Z, Liu Y, Zhou H, Cheng H, Chen Z, Li H, Zhang R, Wang Y. Distinct assembly processes and environmental adaptation of abundant and rare archaea in Arctic marine sediments. MARINE ENVIRONMENTAL RESEARCH 2023; 190:106082. [PMID: 37429213 DOI: 10.1016/j.marenvres.2023.106082] [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: 01/09/2023] [Revised: 06/23/2023] [Accepted: 07/05/2023] [Indexed: 07/12/2023]
Abstract
Revealing the ecological processes and environmental adaptation of abundant and rare archaea is a central, but poorly understood, topic in ecology. Here, abundant and rare archaeal diversity, community assembly processes and co-occurrence patterns were comparatively analyzed in Arctic marine sediments. Our findings revealed that the rare taxa exhibited significantly higher diversity compared to the abundant taxa. Additionally, the abundant taxa displayed stronger environmental adaptation than the rare taxa. The co-occurrence network analysis demonstrated that the rare taxa developed more interspecies interactions and modules in response to environmental disturbance. Furthermore, the community assembly of abundant and rare taxa in sediments was primarily controlled by stochastic and deterministic processes, respectively. These findings provide valuable insights into the archaeal community assembly processes and significantly contribute to a deeper understanding of the environmental adaptability of abundant and rare taxa in Arctic marine sediments.
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Affiliation(s)
- Jianxing Sun
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China
| | - Aoqi Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China
| | - Zhongxian Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China
| | - Yang Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China
| | - Haina Cheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China
| | - Zhu Chen
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China
| | - Hai Li
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Hunan, PR China
| | - Ran Zhang
- Laboratory of Marine Biodiversity Research, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, Hunan, PR China
| | - Yuguang Wang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, PR China; Key Laboratory of Biohydrometallurgy of Ministry of Education, Changsha, 410083, Hunan, PR China.
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12
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Carlton JD, Langwig MV, Gong X, Aguilar-Pine EJ, Vázquez-Rosas-Landa M, Seitz KW, Baker BJ, De Anda V. Expansion of Armatimonadota through marine sediment sequencing describes two classes with unique ecological roles. ISME COMMUNICATIONS 2023; 3:64. [PMID: 37355707 PMCID: PMC10290634 DOI: 10.1038/s43705-023-00269-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/22/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023]
Abstract
Marine sediments comprise one of the largest environments on the planet, and their microbial inhabitants are significant players in global carbon and nutrient cycles. Recent studies using metagenomic techniques have shown the complexity of these communities and identified novel microorganisms from the ocean floor. Here, we obtained 77 metagenome-assembled genomes (MAGs) from the bacterial phylum Armatimonadota in the Guaymas Basin, Gulf of California, and the Bohai Sea, China. These MAGs comprise two previously undescribed classes within Armatimonadota, which we propose naming Hebobacteria and Zipacnadia. They are globally distributed in hypoxic and anoxic environments and are dominant members of deep-sea sediments (up to 1.95% of metagenomic raw reads). The classes described here also have unique metabolic capabilities, possessing pathways to reduce carbon dioxide to acetate via the Wood-Ljungdahl pathway (WLP) and generating energy through the oxidative branch of glycolysis using carbon dioxide as an electron sink, maintaining the redox balance using the WLP. Hebobacteria may also be autotrophic, not previously identified in Armatimonadota. Furthermore, these Armatimonadota may play a role in sulfur and nitrogen cycling, using the intermediate compounds hydroxylamine and sulfite. Description of these MAGs enhances our understanding of diversity and metabolic potential within anoxic habitats worldwide.
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Affiliation(s)
- John D Carlton
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA
| | - Marguerite V Langwig
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Xianzhe Gong
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Emily J Aguilar-Pine
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Mirna Vázquez-Rosas-Landa
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA
- Unidad Académica de Ecologia y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnologia, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Kiley W Seitz
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA
- EMBL Heidelberg, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Brett J Baker
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA.
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
| | - Valerie De Anda
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA.
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
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13
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Zelenina D, Kuzmenkova N, Sobolev D, Boldyrev K, Namsaraev Z, Artemiev G, Samylina O, Popova N, Safonov A. Biogeochemical Factors of Cs, Sr, U, Pu Immobilization in Bottom Sediments of the Upa River, Located in the Zone of Chernobyl Accident. BIOLOGY 2022; 12:biology12010010. [PMID: 36671703 PMCID: PMC9854679 DOI: 10.3390/biology12010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/14/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
Laboratory modeling of Cs, Sr, U, Pu immobilization by phytoplankton of the river Upa, affected after the Chernobyl accident, has been carried out. Certain conditions are selected for strong fixation of radionuclides in bottom sediments due to biogeochemical processes. The process of radionuclide removal from the water phase via precipitation was based on their accumulation by phytoplankton, stimulated by nitrogen and phosphorus sources. After eight days of stimulation, planktonic phototrophic biomass, dominated by cyanobacteria of the genus Planktothrix, appears in the water sample. The effectiveness of U, Pu and Sr purification via their transfer to bottom sediment was observed within one month. The addition of ammonium sulfate and phosphate (Ammophos) led to the activation of sulfate- and iron-reducing bacteria of the genera Desulfobacterota, Desulfotomaculum, Desulfosporomusa, Desulfosporosinus, Thermodesulfobium, Thiomonas, Thiobacillus, Sulfuritallea, Pseudomonas, which form sulphide ferrous precipitates such as pyrite, wurtzite, hydrotroillite, etc., in anaerobic bottom sediments. The biogenic mineral composition of the sediments obtained under laboratory conditions was verified via thermodynamic modeling.
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Affiliation(s)
- Darya Zelenina
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, RAS, Obrucheva Str. 40, Moscow 117342, Russia
| | - Natalia Kuzmenkova
- Radiochemistry Division, Faculty of Chemistry, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
- V. Vernadsky Institute of Geochemistry and Analytical Chemistry, RAS, Kosygina Str. 19, Moscow 119991, Russia
| | - Denis Sobolev
- Nuclear Safety Institute, RAS, Bolshaya Tulskaya St. 52, Moscow 115191, Russia
| | - Kirill Boldyrev
- Nuclear Safety Institute, RAS, Bolshaya Tulskaya St. 52, Moscow 115191, Russia
| | - Zorigto Namsaraev
- Kurchatov Centre for Genome Research, NRC Kurchatov Institute, Akad. Kurchatov Sq., 2, Moscow 123098, Russia
| | - Grigoriy Artemiev
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, RAS, Obrucheva Str. 40, Moscow 117342, Russia
| | - Olga Samylina
- Winogradsky Institute of Microbiology, Research Centre for Biotechnology, Russian Academy of Sciences, Prospect 60-Letiya Oktyabrya 7/2, Moscow 117312, Russia
| | - Nadezhda Popova
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, RAS, Obrucheva Str. 40, Moscow 117342, Russia
| | - Alexey Safonov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, RAS, Obrucheva Str. 40, Moscow 117342, Russia
- Correspondence:
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14
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Gong X, Del Río ÁR, Xu L, Chen Z, Langwig MV, Su L, Sun M, Huerta-Cepas J, De Anda V, Baker BJ. New globally distributed bacterial phyla within the FCB superphylum. Nat Commun 2022; 13:7516. [PMID: 36473838 PMCID: PMC9727166 DOI: 10.1038/s41467-022-34388-1] [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: 05/10/2022] [Accepted: 10/24/2022] [Indexed: 12/12/2022] Open
Abstract
Microbes in marine sediments play crucial roles in global carbon and nutrient cycling. However, our understanding of microbial diversity and physiology on the ocean floor is limited. Here, we use phylogenomic analyses of thousands of metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments to identify 55 MAGs that are phylogenetically distinct from previously described bacterial phyla. We propose that these MAGs belong to 4 novel bacterial phyla (Blakebacterota, Orphanbacterota, Arandabacterota, and Joyebacterota) and a previously proposed phylum (AABM5-125-24), all of them within the FCB superphylum. Comparison of their rRNA genes with public databases reveals that these phyla are globally distributed in different habitats, including marine, freshwater, and terrestrial environments. Genomic analyses suggest these organisms are capable of mediating key steps in sedimentary biogeochemistry, including anaerobic degradation of polysaccharides and proteins, and respiration of sulfur and nitrogen. Interestingly, these genomes code for an unusually high proportion (~9% on average, up to 20% per genome) of protein families lacking representatives in public databases. Genes encoding hundreds of these protein families colocalize with genes predicted to be involved in sulfur reduction, nitrogen cycling, energy conservation, and degradation of organic compounds. Our findings advance our understanding of bacterial diversity, the ecological roles of these bacteria, and potential links between novel gene families and metabolic processes in the oceans.
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Affiliation(s)
- Xianzhe Gong
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong, 266237, China.
- Department of Marine Science, University of Texas at Austin, Port Aransas, TX, 78373, USA.
| | - Álvaro Rodríguez Del Río
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Le Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Zhiyi Chen
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong, 266237, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Marguerite V Langwig
- Department of Marine Science, University of Texas at Austin, Port Aransas, TX, 78373, USA
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Lei Su
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Mingxue Sun
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, China
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Valerie De Anda
- Department of Marine Science, University of Texas at Austin, Port Aransas, TX, 78373, USA.
| | - Brett J Baker
- Department of Marine Science, University of Texas at Austin, Port Aransas, TX, 78373, USA.
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78701, USA.
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