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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] [MESH Headings] [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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Zhang J, Chen J, Wang C, Wang P, Gao H, Feng B, Fu J. Vertical variation of antibiotic resistance genes and their interaction with environmental nutrients in sediments of Taihu lake. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 370:122661. [PMID: 39332305 DOI: 10.1016/j.jenvman.2024.122661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 09/22/2024] [Accepted: 09/23/2024] [Indexed: 09/29/2024]
Abstract
Antibiotic resistance is a growing environmental issue. As a sink for antibiotic resistance genes (ARGs), lake surface sediments are well known for the spread of ARGs. However, the distribution pattern of ARGs and their relationship with environmental factors in vertical sediment layers are unclear. In this study, we investigated the resistome distribution in sediment cores from Taihu Lake using metagenomic analysis. The results showed that the abundance of total ARGs increased by 153% as the sediment depth rose from 0 to 50 cm, and the ARG Shannon index significantly increased. Among all the ARG types, efflux pump genes (e.g., mexT and mexW) were dominant, especially in 40-50 cm sediment. The variation in ARG with depth described above was related to the changes in bacterial adaptation to environmental gradients. Specifically, sulfate and nitrate concentrations decreased with depth, and random forest analysis showed that they were the main factors affecting the changes in ARG abundance. Environmental factors were also found to indirectly impact the distribution of ARGs by affecting the bacterial community. Potential sulfate-reducing gene/nitrate-reducing gene-ARG co-hosts were annotated through metagenomic assembly. The dominant co-hosts, Curvibacter, and Comamonas, which were enriched in deeper sediments, may have contributed to the enrichment of ARGs in deep sediments. Overall, our findings demonstrated that bacterial-mediated sulfate and nitrate reduction was closely related to sediment resistance, which provided new insights into the control of antibiotic resistance.
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Affiliation(s)
- Jingjing Zhang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing, 210098, PR China
| | - Juan Chen
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing, 210098, PR China.
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing, 210098, PR China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing, 210098, PR China
| | - Han Gao
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing, 210098, PR China
| | - Bingbing Feng
- Key Laboratory of Integrated Regulation and Resource Department on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, 1 Xikang Road, Nanjing, 210098, PR China
| | - Jingjing Fu
- PowerChina Huadong Engineering Corporation Limited, No.201, Gaojiao Road, Yuhang District, Hangzhou, Zhejiang, 311122, PR China
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Pu W, Wang M, Song D, Zhao W, Sheng X, Huo T, Du X, Sui X. Bacterial Diversity in Sediments from Lianhuan Lake, Northeast China. Microorganisms 2024; 12:1914. [PMID: 39338588 PMCID: PMC11433699 DOI: 10.3390/microorganisms12091914] [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: 08/20/2024] [Revised: 09/16/2024] [Accepted: 09/18/2024] [Indexed: 09/30/2024] Open
Abstract
Lake microbiota play a crucial role in geochemical cycles, influencing both energy flow and material production. However, the distribution patterns of bacterial communities in lake sediments remain largely unclear. In this study, we used 16S rRNA high-throughput sequencing technology to investigate the bacterial structure and diversity in sediments across different locations (six independent lakes) within Lianhuan Lake and analyzed their relationship with environmental factors. Our findings revealed that both the alpha and beta diversity of sediment bacterial communities varied significantly among the six independent lakes. Furthermore, changes between lakes had a significant impact on the relative abundance of bacterial phyla, such as Pseudomonadota and Chloroflexota. The relative abundance of Pseudomonadota was highest in Habuta Lake and lowest in Xihulu Lake, while Chloroflexota abundance was lowest in Habuta Lake and highest in Tiehala Lake. At the genus level, the relative abundance of Luteitalea was highest in Xihulu Lake compared to the other five lakes, whereas the relative abundances of Clostridium, Thiobacillus, and Ilumatobacter were highest in Habuta Lake. Mantel tests and heatmaps revealed that the relative abundance of Pseudomonadota was significantly negatively correlated with pH, while the abundance of Chloroflexota was significantly positively correlated with total phosphorus and total nitrogen in water, and negatively correlated with electrical conductivity. In conclusion, this study significantly enhances our understanding of bacterial communities in the different lakes within the Lianhuan Lake watershed.
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Affiliation(s)
- Wenmiao Pu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Science, Heilongjiang University, Harbin 150080, China
- Heilongjiang River Basin Fishery Ecological Environment Monitoring Center, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150010, China
| | - Mingyu Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Science, Heilongjiang University, Harbin 150080, China
| | - Dan Song
- Heilongjiang River Basin Fishery Ecological Environment Monitoring Center, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150010, China
| | - Wei Zhao
- Heilongjiang River Basin Fishery Ecological Environment Monitoring Center, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150010, China
- College of Marine Science and Environment, Dalian Ocean University, No. 52, Heishijiao Street, Shahekou District, Dalian 116023, China
| | - Xuran Sheng
- Heilongjiang River Basin Fishery Ecological Environment Monitoring Center, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150010, China
| | - Tangbin Huo
- Heilongjiang River Basin Fishery Ecological Environment Monitoring Center, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150010, China
| | - Xue Du
- Heilongjiang River Basin Fishery Ecological Environment Monitoring Center, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150010, China
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xin Sui
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Science, Heilongjiang University, Harbin 150080, China
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Zhou W, Shen X, Xu Z, Yang Q, Jiao M, Li H, Zhang L, Ling J, Liu H, Dong J, Suo A. Specialists regulate microbial network and community assembly in subtropical seagrass sediments under differing land use conditions. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 370:122486. [PMID: 39278015 DOI: 10.1016/j.jenvman.2024.122486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 09/03/2024] [Accepted: 09/10/2024] [Indexed: 09/17/2024]
Abstract
Microorganisms in the sediment play a pivotal role in the functioning and stability of seagrass ecosystems and their dynamics are influenced by the nutrient acquisition strategies of host plants. While the distinct impacts of microbial generalists and specialists on community dynamics are recognized, their distribution patterns and ecological roles within seagrass ecosystems remain largely unexplored. To address this issue, we conducted an analysis of community assembly processes and co-occurrence relationships of both microbial generalists and specialists within sediment profiles (0-100 cm) from seagrass habitats subjected to differing land use conditions. The results revealed that seagrasses in Yifeng Estuary experienced the large proportion of cultivated land and exhibited higher organic carbon content in the 0-20 cm surface sediment layer. Nitrogen-cycling bacteria were predominantly associated with seagrasses from Yifeng Estuary, whereas Vibrio spp. was more prevalent in seagrasses from Liusha Bay. Notably, seagrass Halophia beccarii (YHB) in Yifeng Estuary harbored higher niche breadths for both microbial generalist and specialist compared to Halodule uninervis (LHU) and Halophia ovalis (LHO) from Liusha Bay. Stochastic processes were pivotal in shaping seagrass sediment microbial communities, with a higher immigration rate observed in YHB, suggesting greater microbial turnover in this area. Additionally, YHB sediment presented lower drift and higher dispersal limitation among generalists compared to LHU and LHO, whereas the pattern was reversed among specialists. Specialists were found to play a crucial role in shaping microbial interactions within YHB sediment, with genera Halioglobus identified as keystone species in the network. The specialists were further found to significantly influence microbial β-diversity in seagrass sediment directly. Overall, our findings illustrated how microbial generalists and specialists were distributed in seagrass sediments in response to land use changes and provided new insights into the potential roles of microbial regulation in degraded seagrass ecosystems.
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Affiliation(s)
- Weiguo Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Xiaomei Shen
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Zhimeng Xu
- Haide college, Ocean University of China, Qingdao, 266003, China
| | - Qingsong Yang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Mengyu Jiao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Hanying Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Li Zhang
- Marine Environmental Engineering Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Juan Ling
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
| | - Hongbin Liu
- The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Junde Dong
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Anning Suo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Marine Environmental Engineering Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
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Zhang L, Bai J, Zhai Y, Zhang K, Wang Y, Tang R, Xiao R, Jorquera MA. Multimedia distribution, partitioning, sources, comprehensive toxicity risk and co-occurrence network characteristics of trace elements in a typical Chinese shallow lake with high antibiotic risk. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133436. [PMID: 38190795 DOI: 10.1016/j.jhazmat.2024.133436] [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: 12/06/2023] [Revised: 12/31/2023] [Accepted: 01/02/2024] [Indexed: 01/10/2024]
Abstract
Although the combined pollution of trace elements and antibiotics has received extensive attention, the fate and toxicity risk of trace elements with high antibiotic risk are still unclear. The multimedia distributions, partitioning, sources, toxicity risks and co-occurrence network characteristics of trace elements in surface water (SW), overlying water (OW), pore water (PW) and sediment (Sedi) samples of 61 sites from Baiyangdian (BYD) Lake were investigated. The trace elements in the SW and OW are derived mainly from traffic and agricultural sources, and those in PW and Sedi samples are primarily from lithogenic and industrial sources. The total toxicity risk index (TRI) of nine trace elements (ΣTRI) in Sedi samples showed a very high toxicity risk (18.35 ± 8.84), and a high combined pollution toxicity risk (ΣΣTRI) was observed in PW (149.17 ± 97.52) and Sedi samples (46.37 ± 24.00). The co-occurrence network from SW to PW became more vulnerable. Generally, total antibiotics and TP may be keystones of trace elements in water and sediment. The high antibiotic risk significantly influenced ΣΣTRI in water samples but not in Sedi samples. The findings provide new implications for the monitoring and control of combined antibiotic-trace element pollution in shallow lakes.
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Affiliation(s)
- Ling Zhang
- School of Environment, Beijing Normal University, Beijing 100875, China; School of Chemistry and Chemical Engineering, Qinghai Normal University, Xining 810008, China
| | - Junhong Bai
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Yujia Zhai
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Kegang Zhang
- Department of Environmental Engineering and Science, North China Electric Power University, Baoding, China
| | - Yaqi Wang
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Ruoxuan Tang
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Rong Xiao
- College of Environment & Safety Engineering, FuZhou University, Fuzhou, China
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile
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Li J, Fu N, Wang M, Gao C, Gao B, Ren L, Tao J, Luo Y. Functional and Compositional Changes in Sirex noctilio Gut Microbiome in Different Habitats: Unraveling the Complexity of Invasive Adaptation. Int J Mol Sci 2024; 25:2526. [PMID: 38473774 DOI: 10.3390/ijms25052526] [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: 12/28/2023] [Revised: 02/04/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024] Open
Abstract
The mutualistic symbiosis relationship between the gut microbiome and their insect hosts has attracted much scientific attention. The native woodwasp, Sirex nitobei, and the invasive European woodwasp, Sirex noctilio, are two pests that infest pines in northeastern China. Following its encounter with the native species, however, there is a lack of research on whether the gut microbiome of S. noctilio changed, what causes contributed to these alterations, and whether these changes were more conducive to invasive colonization. We used high-throughput and metatranscriptomic sequencing to investigate S. noctilio larval gut and frass from four sites where only S. noctilio and both two Sirex species and investigated the effects of environmental factors, biological interactions, and ecological processes on S. noctilio gut microbial community assembly. Amplicon sequencing of two Sirex species revealed differential patterns of bacterial and fungal composition and functional prediction. S. noctilio larval gut bacterial and fungal diversity was essentially higher in coexistence sites than in separate existence sites, and most of the larval gut bacterial and fungal community functional predictions were significantly different as well. Moreover, temperature and precipitation positively correlate with most of the highly abundant bacterial and fungal genera. Source-tracking analysis showed that S. noctilio larvae at coexistence sites remain dependent on adult gut transmission (vertical transmission) or recruitment to frass (horizontal transmission). Meanwhile, stochastic processes of drift and dispersal limitation also have important impacts on the assembly of S. noctilio larval gut microbiome, especially at coexistence sites. In summary, our results reveal the potential role of changes in S. noctilio larval gut microbiome in the successful colonization and better adaptation of the environment.
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Affiliation(s)
- Jiale Li
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China
- Sino-France Joint Laboratory for Invasive Forest Pests in Eurasia, Beijing Forestry University, Beijing 100083, China
| | - Ningning Fu
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China
- Department of Forest Protection, College of Forestry, Hebei Agricultural University, Baoding 071033, China
| | - Ming Wang
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Chenglong Gao
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Bingtao Gao
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China
| | - Lili Ren
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China
- Sino-France Joint Laboratory for Invasive Forest Pests in Eurasia, Beijing Forestry University, Beijing 100083, China
| | - Jing Tao
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China
- Sino-France Joint Laboratory for Invasive Forest Pests in Eurasia, Beijing Forestry University, Beijing 100083, China
| | - Youqing Luo
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China
- Sino-France Joint Laboratory for Invasive Forest Pests in Eurasia, Beijing Forestry University, Beijing 100083, China
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Yu B, Zeng Q, Li J, Li J, Tan X, Gao X, Mao Z, Huang P, Wu S. Sediment depth-related variations of comammox Nitrospira: Evidence in the Three Gorges Reservoir, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167055. [PMID: 37709074 DOI: 10.1016/j.scitotenv.2023.167055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 09/04/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
The recent discovery of comammox Nitrospira as complete ammonia-oxidizing microorganism has fundamentally revolutionized our understanding of nitrogen cycling in sediment environments. However, knowledge regarding their abundance, biodiversity, community structure, and interactions is predominantly limited to the upper layers (0-20 cm). To address this gap, we collected sediment samples along profiles ranging from 0 to 300 cm in depth at three locations within the middle segment of the Three Gorges Reservoir (TGR), China. Quantitative real-time PCR (qPCR) analyses suggested that comammox bacteria were not only ubiquitous in deep sediments but also more abundant than ammonia-oxidizing bacteria (AOB). Ammonia monooxygenases subunit A (amoA) gene amplicon sequencing illuminated that comammox bacteria were more sensitive to sedimental depth compared to AOB and ammonia-oxidizing archaea (AOA), as evidenced by a more significant decline in community diversity and similarity over distance along sediment vertical profiles. Notably, we discovered that the amoA gene abundance, alpha- and beta-diversity of comammox bacteria exerted an essential contribution to potential nitrification rates according to random forest model. Phylogenetic analysis indicted that most comammox bacteria within sediment samples belonged to clade A.2. Intriguingly, the average relative abundance of comammox clade A.2 displayed a noteworthy rise with sediment depth, whereas clade A.1 demonstrated a converse pattern, unveiling distinct ecological niche adaptations of these two clades along the sediment profile. Ecological network analysis further revealed closer interactions between comammox bacteria and canonical ammonia oxidizers in the superficial layer (0-40 cm), with the network structure gradually simplifying from superficial to deep sediment (200-300 cm). Overall, these findings broaden the current recognition of the geographic distribution and niche segregation of comammox bacteria at the fine scale of the sediments ecosystems and provide insights into sediment depth-related variations of their coexistence network patterns in large freshwater reservoirs.
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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
| | - Ziqiang Mao
- 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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