1
|
Li H, Liu J, Zhang L, Che X, Zhang M, Zhang T. A pilot restoration of Enhalus acoroides by transplanting dislodged rhizome fragments and its effect on the microbial diversity of submarine sediments. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 359:120996. [PMID: 38669885 DOI: 10.1016/j.jenvman.2024.120996] [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: 10/19/2023] [Revised: 04/18/2024] [Accepted: 04/20/2024] [Indexed: 04/28/2024]
Abstract
Enhalus acoroides, the largest seagrass species in terms of morphology, has been observed to be declining significantly. In an effort to restore seagrass meadows, we conducted a transplantion utilizing dislodged rhizome fragments of E. acoroides as the donor materials. The growth of transplanted seagrass was monitored over a period of three years, and the impact of seagrass recolonization on sedimentary environment was assessed through analysis of sediment microbial diversity. The transplanted plants displayed notable growth, resulting in the successful recolonization of experimental plots by seagrass. The 3-year data also revealed the following findings: 1) the new shoot recruitment rate (per year) (NSR) of transplanted seagrass was 2.33 in the first year, 1.36 in the second year, and 0.83 in the third year, indicating a rapid initial growth rate of E. acoroides that subsequently slowed down; 2) the numbers of shoots and aboveground biomass of transplanted seagrass had increased by 13.0 and 15.9-fold, respectively, whereas only 3.3 and 5.3-fold increases of the natural seagrass were observed, suggesting that the transplantation of seagrass leads to a significantly accelerated recovery compared to its natural regeneration process. Furthermore, the restoration of E. acoroides resulted in a higher microbial diversity in the submarine sediments within the restoration area, as compared to the adjacent unvegetated area. This suggests that the re-vegetation of E. acoroides has a positive influence on the overall health of the sedimentary environment. This study strongly advocates for the active transplantation of dislodged E. acoroides plants resulting from human activities as a potential approach for future coastal management, specifically for the restoration of E. acoroides meadows.
Collapse
Affiliation(s)
- Hu Li
- CAS and Shandong Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, 168 Wenhai Road, Aoshanwei Town, Jimo, Qingdao, 266237, China
| | - Jianguo Liu
- CAS and Shandong Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, 168 Wenhai Road, Aoshanwei Town, Jimo, Qingdao, 266237, China.
| | - Litao Zhang
- CAS and Shandong Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, 168 Wenhai Road, Aoshanwei Town, Jimo, Qingdao, 266237, China
| | - Xingkai Che
- CAS and Shandong Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, 168 Wenhai Road, Aoshanwei Town, Jimo, Qingdao, 266237, China
| | - Mengjie Zhang
- CAS and Shandong Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, 168 Wenhai Road, Aoshanwei Town, Jimo, Qingdao, 266237, China
| | - Tie Zhang
- CAS and Shandong Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, 168 Wenhai Road, Aoshanwei Town, Jimo, Qingdao, 266237, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
2
|
Zhang X, Wu Y, Liu S, Li J, Jiang Z, Luo H, Huang X. Plant growth and development of tropical seagrass determined rhizodeposition and its related microbial community. MARINE POLLUTION BULLETIN 2024; 199:115940. [PMID: 38150979 DOI: 10.1016/j.marpolbul.2023.115940] [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: 10/07/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/29/2023]
Abstract
In the recent study, we investigated the seasonal variations in root exudation and microbial community structure in the rhizosphere of seagrass Enhalus acoroides in the South China Sea. We found that the quantity and quality of root exudates varied seasonally, with higher exudation rates and more bioavailable dissolved organic matter (DOM) during the seedling and vegetative stages in spring and summer. Using Illumina NovaSeq sequencing, we analyzed bacterial and fungal communities and discovered that microbial diversity and composition were influenced by root exudate characteristics s and seagrass biomass, which were strongly dependent on seagrass growth stages. Certain bacterial groups, such as Ruegeria, Sulfurovum, Photobacterium, and Ralstonia were closely associated with root exudation and may contribute to sulfur cycling, nitrogen fixation, and carbon remineralization, which were important for plant early development. Similarly, specific fungal taxa, including Astraeus, Alternaria, Rocella, and Tomentella, were enriched in spring and summer and showed growth-promoting abilities. Overall, our study suggests that seagrass secretes different compounds in its exudates at various developmental stages, shaping the rhizosphere microbial assemblages.
Collapse
Affiliation(s)
- Xia Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou 510301, China
| | - Yunchao Wu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou 510301, China
| | - Songlin Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinlong Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhijian Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongxue Luo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoping Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; Guangdong Provincial Key Laboratory of Applied Marine Biology, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
3
|
Hui M, Wang A, Cheng J, Sha Z. Full-length 16S rRNA amplicon sequencing reveals the variation of epibiotic microbiota associated with two shrimp species of Alvinocarididae: possibly co-determined by environmental heterogeneity and specific recognition of hosts. PeerJ 2022; 10:e13758. [PMID: 35966925 PMCID: PMC9368993 DOI: 10.7717/peerj.13758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 06/29/2022] [Indexed: 01/17/2023] Open
Abstract
Shrimps of the family Alvinocarididae, endemic species to deep sea chemosynthetic ecosystems, harbor epibiotic microbes on gills which probably play important roles in the survival of the shrimps. Among them, Alvinocaris longirostris and Shinkaicaris leurokolos occupy different ecological niches within the same hydrothermal vent in Okinawa Trough, and A. longirostris also exists in a methane seep of the South China Sea. In this study, full-length 16S rRNA sequences of the gill associated bacteria of two alvinocaridid species from different chemosynthetically ecological niches were first captured by single-molecule real-time sequencing. Totally, 120,792 optimized circular consensus sequences with ∼1,450 bp in length were obtained and clustered into 578 operational taxonomic units. Alpha diversity analysis showed seep A. longirostris had the highest species richness and evenness (average Chao1 = 213.68, Shannon = 3.39). Beta diversity analysis revealed that all samples were clearly divided into three groups, and microbial community of A. longirostris from seep and vent were more related than the other comparisons. By permutational multivariate analysis of variance, the most significant community compositional variance was detected between seep A. longirostris and vent S. leurokolos (R 2 = 0.731, P = 0.001). The taxon tags were further classified into 21 phyla, 40 classes, 89 orders, 124 families and 135 genera. Overall, the microbial communities were dominated by Campylobacteria and Gammaproteobacteria. Alphaproteobacteria, Bacteroidia, Verrucomicrobiae, Bacilli and other minor groups were also detected at lower abundance. Taxonomic groups recovered from the vent S. leurokolos samples were only dominated by Sulfurovaceae (94.06%). In comparison, gill-associated microbiota of vent A. longirostris consisted of more diverse sulfur-oxidizing bacteria, including Sulfurovaceae (69.21%), Thiotrichaceae (6.77%) and a putative novel Gammaproteobacteria group (14.37%), while in seep A. longirostris, Gammaproteobacteria un-group (44.01%) constituted the major component, following the methane-oxidizing bacteria Methylomonadaceae (19.38%), and Sulfurovaceae (18.66%). Therefore, the gill associated bacteria composition and abundance of alvinocaridid shrimps are closely related to the habitat heterogeneity and the selection of microbiota by the host. However, the interaction between these alvinocaridid shrimps and the epibiotic communities requires further study based on metagenome sequencing and fluorescence in situ hybridization.
Collapse
Affiliation(s)
- Min Hui
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Aiyang Wang
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China,,Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,,University of Chinese Academy of Sciences, Beijing, China
| | - Jiao Cheng
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhongli Sha
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China,,Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,,University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
4
|
Steiner TM, Lettl C, Schindele F, Goebel W, Haas R, Fischer W, Eisenreich W. Substrate usage determines carbon flux via the citrate cycle in Helicobacter pylori. Mol Microbiol 2021; 116:841-860. [PMID: 34164854 DOI: 10.1111/mmi.14775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 06/07/2021] [Accepted: 06/19/2021] [Indexed: 12/31/2022]
Abstract
Helicobacter pylori displays a worldwide infection rate of about 50%. The Gram-negative bacterium is the main reason for gastric cancer and other severe diseases. Despite considerable knowledge about the metabolic inventory of H. pylori, carbon fluxes through the citrate cycle (TCA cycle) remained enigmatic. In this study, different 13 C-labeled substrates were supplied as carbon sources to H. pylori during microaerophilic growth in a complex medium. After growth, 13 C-excess and 13 C-distribution were determined in multiple metabolites using GC-MS analysis. [U-13 C6 ]Glucose was efficiently converted into glyceraldehyde but only less into TCA cycle-related metabolites. In contrast, [U-13 C5 ]glutamate, [U-13 C4 ]succinate, and [U-13 C4 ]aspartate were incorporated at high levels into intermediates of the TCA cycle. The comparative analysis of the 13 C-distributions indicated an adaptive TCA cycle fully operating in the closed oxidative direction with rapid equilibrium fluxes between oxaloacetate-succinate and α-ketoglutarate-citrate. 13 C-Profiles of the four-carbon intermediates in the TCA cycle, especially of malate, together with the observation of an isocitrate lyase activity by in vitro assays, suggested carbon fluxes via a glyoxylate bypass. In conjunction with the lack of enzymes for anaplerotic CO2 fixation, the glyoxylate bypass could be relevant to fill up the TCA cycle with carbon atoms derived from acetyl-CoA.
Collapse
Affiliation(s)
- Thomas M Steiner
- Bavarian NMR Center-Structural Membrane Biochemistry, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Clara Lettl
- Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, München, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, München, Germany
| | - Franziska Schindele
- Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, München, Germany
| | - Werner Goebel
- Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, München, Germany
| | - Rainer Haas
- Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, München, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, München, Germany
| | - Wolfgang Fischer
- Chair of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, München, Germany.,German Center for Infection Research (DZIF), Partner Site Munich, München, Germany
| | - Wolfgang Eisenreich
- Bavarian NMR Center-Structural Membrane Biochemistry, Department of Chemistry, Technische Universität München, Garching, Germany
| |
Collapse
|
5
|
van Vliet DM, von Meijenfeldt FB, Dutilh BE, Villanueva L, Sinninghe Damsté JS, Stams AJ, Sánchez‐Andrea I. The bacterial sulfur cycle in expanding dysoxic and euxinic marine waters. Environ Microbiol 2021; 23:2834-2857. [PMID: 33000514 PMCID: PMC8359478 DOI: 10.1111/1462-2920.15265] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 09/03/2020] [Accepted: 09/28/2020] [Indexed: 01/29/2023]
Abstract
Dysoxic marine waters (DMW, < 1 μM oxygen) are currently expanding in volume in the oceans, which has biogeochemical, ecological and societal consequences on a global scale. In these environments, distinct bacteria drive an active sulfur cycle, which has only recently been recognized for open-ocean DMW. This review summarizes the current knowledge on these sulfur-cycling bacteria. Critical bottlenecks and questions for future research are specifically addressed. Sulfate-reducing bacteria (SRB) are core members of DMW. However, their roles are not entirely clear, and they remain largely uncultured. We found support for their remarkable diversity and taxonomic novelty by mining metagenome-assembled genomes from the Black Sea as model ecosystem. We highlight recent insights into the metabolism of key sulfur-oxidizing SUP05 and Sulfurimonas bacteria, and discuss the probable involvement of uncultivated SAR324 and BS-GSO2 bacteria in sulfur oxidation. Uncultivated Marinimicrobia bacteria with a presumed organoheterotrophic metabolism are abundant in DMW. Like SRB, they may use specific molybdoenzymes to conserve energy from the oxidation, reduction or disproportionation of sulfur cycle intermediates such as S0 and thiosulfate, produced from the oxidation of sulfide. We expect that tailored sampling methods and a renewed focus on cultivation will yield deeper insight into sulfur-cycling bacteria in DMW.
Collapse
Affiliation(s)
- Daan M. van Vliet
- Laboratory of MicrobiologyWageningen University and Research, Stippeneng 4, 6708WEWageningenNetherlands
| | | | - Bas E. Dutilh
- Theoretical Biology and Bioinformatics, Science for LifeUtrecht University, Padualaan 8, 3584 CHUtrechtNetherlands
| | - Laura Villanueva
- Department of Marine Microbiology and BiogeochemistryRoyal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Landsdiep 4, 1797 SZ, 'tHorntje (Texel)Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and BiogeochemistryRoyal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Landsdiep 4, 1797 SZ, 'tHorntje (Texel)Netherlands
- Department of Earth Sciences, Faculty of GeosciencesUtrecht University, Princetonlaan 8A, 3584 CBUtrechtNetherlands
| | - Alfons J.M. Stams
- Laboratory of MicrobiologyWageningen University and Research, Stippeneng 4, 6708WEWageningenNetherlands
- Centre of Biological EngineeringUniversity of Minho, Campus de Gualtar, 4710‐057BragaPortugal
| | - Irene Sánchez‐Andrea
- Laboratory of MicrobiologyWageningen University and Research, Stippeneng 4, 6708WEWageningenNetherlands
| |
Collapse
|
6
|
Meziti A, Nikouli E, Hatt JK, Konstantinidis KT, Kormas KA. Time series metagenomic sampling of the Thermopyles, Greece, geothermal springs reveals stable microbial communities dominated by novel sulfur-oxidizing chemoautotrophs. Environ Microbiol 2021; 23:3710-3726. [PMID: 33350070 DOI: 10.1111/1462-2920.15373] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/19/2020] [Indexed: 11/29/2022]
Abstract
Geothermal springs are essentially unaffected by environmental conditions aboveground as they are continuously supplied with subsurface water with little variability in chemistry. Therefore, changes in their microbial community composition and function, especially over a long period, are expected to be limited but this assumption has not yet been rigorously tested. Toward closing this knowledge gap, we applied whole metagenome sequencing to 17 water samples collected between 2010 and 2016 from the Thermopyles sulfur-rich geothermal springs in central Greece. As revealed by 16S rRNA gene fragments recovered in the metagenomes, Epsilonproteobacteria-related operational taxonomic units (OTUs) dominated most samples and grouping of samples based on OTU abundances exhibited no apparent seasonal pattern. Similarities between samples regarding functional gene content were high, with all samples sharing >70% similarity in functional pathways. These community-wide patterns were further confirmed by analysis of metagenome-assembled genomes (MAGs), which showed that novel species and genera of the chemoautotrophic Campylobacterales order dominated the springs. These MAGs carried different pathways for thiosulfate or sulfide oxidation coupled to carbon fixation pathways. Overall, our study showed that even in the long term, functions of microbial communities in a moderately hot terrestrial spring remain stable, presumably driving the corresponding stability in community structure.
Collapse
Affiliation(s)
- A Meziti
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, 38446, Greece.,School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science and Technology Building, 311 Ferst Drive, Atlanta, GA, 30332, USA
| | - E Nikouli
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, 38446, Greece.,School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science and Technology Building, 311 Ferst Drive, Atlanta, GA, 30332, USA
| | - J K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science and Technology Building, 311 Ferst Drive, Atlanta, GA, 30332, USA
| | - K T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science and Technology Building, 311 Ferst Drive, Atlanta, GA, 30332, USA.,School of Biological Sciences, Georgia Institute of Technology, Ford Environmental Sciences and Technology Building, 311 Ferst Drive, Atlanta, GA, 30332, USA
| | - K A Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, 38446, Greece
| |
Collapse
|
7
|
Sun Y, Song Z, Zhang H, Liu P, Hu X. Seagrass vegetation affect the vertical organization of microbial communities in sediment. MARINE ENVIRONMENTAL RESEARCH 2020; 162:105174. [PMID: 33099080 DOI: 10.1016/j.marenvres.2020.105174] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/11/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
Seagrasses represent high primary productivity and provide important ecosystem services to the marine environment. Seagrass-associated microbial communities are playing essential ecological functional roles in biogeochemical cycles. However, little is known about the effect of seagrass vegetation on microbial communities in sediment. In the present study, the sediment cores of seagrass bed (dominated by Zostera japonica and Zostera marine) and degradation area in Swan Lake (China) were sampled; then, biogeochemical parameters were analyzed, and microbial community composition was investigated by using high-throughput sequencing of the 16S rRNA gene. The results showed that the presence of seagrass could lead to a decrease in the richness and diversity of the microbial community. In the vertical direction, a pronounced shift from Proteobacteria-dominated upper layers to Chloroflexi and Crenarchaeota-dominated deep layers in all sediment cores were observed. Besides, Bathyarchaeia is more abundant at degradation area, while Vibrionaceae, Sulfurovum and Lokiarchaeial overrepresent at the seagrass bed area. Vibrionaceae was abundant in the rhizosphere of Z. marina and Z. japonica, and the proportions reached 84.45% and 63.89%, respectively. This enrichment of Vibrio spp. may be caused by the macrobenthic species near the seagrass rhizosphere, and these Vibrio spp. reduced the diversity and stability of microbial community, which may lead to the degradation of seagrass. This study would provide clues for the distribution patterns and niche preferences of seagrass microbiome. The conservation strategy of seagrass would be further elucidated from the perspective of the microbiome.
Collapse
Affiliation(s)
- Yanyu Sun
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Costal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zenglei Song
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Costal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haikun Zhang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Costal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, China
| | - Pengyuan Liu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Costal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoke Hu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Costal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, China.
| |
Collapse
|
8
|
Park S, Kwon HS, Lee CH, Ahn IS. Correlation between fixation of high-concentration CO2 and glutamate accumulation in Sulfurovum lithotrophicum 42BKTT. J IND ENG CHEM 2020. [DOI: 10.1016/j.jiec.2020.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
9
|
Sun QL, Zhang J, Wang MX, Cao L, Du ZF, Sun YY, Liu SQ, Li CL, Sun L. High-Throughput Sequencing Reveals a Potentially Novel Sulfurovum Species Dominating the Microbial Communities of the Seawater-Sediment Interface of a Deep-Sea Cold Seep in South China Sea. Microorganisms 2020; 8:microorganisms8050687. [PMID: 32397229 PMCID: PMC7284658 DOI: 10.3390/microorganisms8050687] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/01/2020] [Accepted: 05/04/2020] [Indexed: 12/14/2022] Open
Abstract
In the Formosa cold seep of the South China Sea (SCS), large amounts of methane and sulfide hydrogen are released from the subseafloor. In this study, we systematically investigated the microbial communities in the seawater–sediment interface of Formosa cold seep using high-throughput sequencing techniques including amplicon sequencing based on next-generation sequencing and Pacbio amplicon sequencing platforms, and metagenomics. We found that Sulfurovum dominated the microbial communities in the sediment–seawater interface, including the seawater close to the seepage, the surface sediments, and the gills of the dominant animal inhabitant (Shinkaia crosnieri). A nearly complete 16S rRNA gene sequence of the dominant operational taxonomic units (OTUs) was obtained from the Pacbio sequencing platforms and classified as OTU-L1, which belonged to Sulfurovum. This OTU was potentially novel as it shared relatively low similarity percentages (<97%) of the gene sequence with its close phylogenetic species. Further, a draft genome of Sulfurovum was assembled using the binning technique based on metagenomic data. Genome analysis suggested that Sulfurovum sp. in this region may fix carbon by the reductive tricarboxylic acid (rTCA) pathway, obtain energy by oxidizing reduced sulfur through sulfur oxidizing (Sox) pathway, and utilize nitrate as electron acceptors. These results demonstrated that Sulfurovum probably plays an important role in the carbon, sulfur, and nitrogen cycles of the Formosa cold seep of the SCS. This study improves our understanding of the diversity, distribution, and function of sulfur-oxidizing bacteria in deep-sea cold seep.
Collapse
Affiliation(s)
- Qing-Lei Sun
- CAS Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Q.-L.S.); (J.Z.); (Y.-Y.S.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Jian Zhang
- CAS Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Q.-L.S.); (J.Z.); (Y.-Y.S.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.-X.W.); (L.C.); (Z.-F.D.)
| | - Min-Xiao Wang
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.-X.W.); (L.C.); (Z.-F.D.)
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Lei Cao
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.-X.W.); (L.C.); (Z.-F.D.)
| | - Zeng-Feng Du
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.-X.W.); (L.C.); (Z.-F.D.)
- Key Lab of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yuan-Yuan Sun
- CAS Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Q.-L.S.); (J.Z.); (Y.-Y.S.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Shi-Qi Liu
- Faculty of Science, University of Amsterdam, 1098XH Amsterdam, The Netherlands;
| | - Chao-Lun Li
- Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (M.-X.W.); (L.C.); (Z.-F.D.)
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (C.-L.L.); (L.S.); Tel.: +86-532-8289-8599 (C.-L.L.); +86-532-8289-8829 (L.S.)
| | - Li Sun
- CAS Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Q.-L.S.); (J.Z.); (Y.-Y.S.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Correspondence: (C.-L.L.); (L.S.); Tel.: +86-532-8289-8599 (C.-L.L.); +86-532-8289-8829 (L.S.)
| |
Collapse
|
10
|
Genomic Evidence for Formate Metabolism by Chloroflexi as the Key to Unlocking Deep Carbon in Lost City Microbial Ecosystems. Appl Environ Microbiol 2020; 86:AEM.02583-19. [PMID: 32033949 PMCID: PMC7117926 DOI: 10.1128/aem.02583-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 01/31/2020] [Indexed: 02/06/2023] Open
Abstract
Primitive forms of life may have originated around hydrothermal vents at the bottom of the ancient ocean. The Lost City hydrothermal vent field, fueled by just rock and water, provides an analog for not only primitive ecosystems but also potential extraterrestrial rock-powered ecosystems. The microscopic life covering the towering chimney structures at the Lost City has been previously documented, yet little is known about the carbon cycling in this ecosystem. These results provide a better understanding of how carbon from the deep subsurface can fuel rich microbial ecosystems on the seafloor. The Lost City hydrothermal field on the Mid-Atlantic Ridge supports dense microbial life on the lofty calcium carbonate chimney structures. The vent field is fueled by chemical reactions between the ultramafic rock under the chimneys and ambient seawater. These serpentinization reactions provide reducing power (as hydrogen gas) and organic compounds that can serve as microbial food; the most abundant of these are methane and formate. Previous studies have characterized the interior of the chimneys as a single-species biofilm inhabited by the Lost City Methanosarcinales, but they also indicated that this methanogen is unable to metabolize formate. The new metagenomic results presented here indicate that carbon cycling in these Lost City chimney biofilms could depend on the metabolism of formate by Chloroflexi populations. Additionally, we present evidence for metabolically diverse, formate-utilizing Sulfurovum populations and new genomic and phylogenetic insights into the unique Lost City Methanosarcinales. IMPORTANCE Primitive forms of life may have originated around hydrothermal vents at the bottom of the ancient ocean. The Lost City hydrothermal vent field, fueled by just rock and water, provides an analog for not only primitive ecosystems but also potential extraterrestrial rock-powered ecosystems. The microscopic life covering the towering chimney structures at the Lost City has been previously documented, yet little is known about the carbon cycling in this ecosystem. These results provide a better understanding of how carbon from the deep subsurface can fuel rich microbial ecosystems on the seafloor.
Collapse
|
11
|
Fernández-Cadena JC, Ruíz-Fernández PS, Fernández-Ronquillo TE, Díez B, Trefault N, Andrade S, De la Iglesia R. Detection of sentinel bacteria in mangrove sediments contaminated with heavy metals. MARINE POLLUTION BULLETIN 2020; 150:110701. [PMID: 31796235 DOI: 10.1016/j.marpolbul.2019.110701] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 10/29/2019] [Accepted: 10/29/2019] [Indexed: 06/10/2023]
Abstract
Mangroves in the Northwest Coast of South America are contaminated with heavy metals due to wastewater discharges from industries, affecting the biota from this environment. However, bacteria proliferate in these harsh environmental conditions becoming possible sentinel of these contaminations. In this study, bacterial community composition was analyzed by throughput sequencing of the 16S rRNA gene from polluted and pristine mangrove sediments affected by marked differences in heavy metal concentrations. Core bacteria were dominated by Proteobacteria, Firmicutes, and Bacteroidetes phyla, with strong differences between sites at class and genus levels, correlated with metal levels. Increment of abundance on specific OTUs were associated with either elevated or decreased concentrations of metals and with the sulfur cycle. The abundance of Sulfurovum lithotrophicum, Leptolinea tardivitalis, Desulfococcus multivorans and Aminobacterium colombiense increases when metals rise. On contrary, Bacillus stamsii, Nioella nitrareducens and Clostridiisalibacter paucivorans abundance increases when metal levels are reduced. We propose these OTUs as bacterial sentinels, whose abundance can help monitor the restoration programs of contaminated mangrove sediments in the future.
Collapse
Affiliation(s)
| | - P S Ruíz-Fernández
- Instituto Milenio de Oceanografía, Universidad de Concepción, Concepción, Chile
| | | | - B Díez
- Departamento de Genética Molecular y Microbiología. Facultad de Ciencias Biológicas. Pontificia Universidad Católica de Chile. Santiago, Chile
| | - N Trefault
- Centro GEMA- Genómica, Ecología y Medio Ambiente. Facultad de Ciencias. Universidad Mayor, Chile
| | - S Andrade
- Centro GEMA- Genómica, Ecología y Medio Ambiente. Facultad de Ciencias. Universidad Mayor, Chile
| | - R De la Iglesia
- Departamento de Genética Molecular y Microbiología. Facultad de Ciencias Biológicas. Pontificia Universidad Católica de Chile. Santiago, Chile.
| |
Collapse
|
12
|
Böhnke S, Sass K, Gonnella G, Diehl A, Kleint C, Bach W, Zitoun R, Koschinsky A, Indenbirken D, Sander SG, Kurtz S, Perner M. Parameters Governing the Community Structure and Element Turnover in Kermadec Volcanic Ash and Hydrothermal Fluids as Monitored by Inorganic Electron Donor Consumption, Autotrophic CO 2 Fixation and 16S Tags of the Transcriptome in Incubation Experiments. Front Microbiol 2019; 10:2296. [PMID: 31649639 PMCID: PMC6794353 DOI: 10.3389/fmicb.2019.02296] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/20/2019] [Indexed: 12/01/2022] Open
Abstract
The microbial community composition and its functionality was assessed for hydrothermal fluids and volcanic ash sediments from Haungaroa and hydrothermal fluids from the Brothers volcano in the Kermadec island arc (New Zealand). The Haungaroa volcanic ash sediments were dominated by epsilonproteobacterial Sulfurovum sp. Ratios of electron donor consumption to CO2 fixation from respective sediment incubations indicated that sulfide oxidation appeared to fuel autotrophic CO2 fixation, coinciding with thermodynamic estimates predicting sulfide oxidation as the major energy source in the environment. Transcript analyses with the sulfide-supplemented sediment slurries demonstrated that Sulfurovum prevailed in the experiments as well. Hence, our sediment incubations appeared to simulate environmental conditions well suggesting that sulfide oxidation catalyzed by Sulfurovum members drive biomass synthesis in the volcanic ash sediments. For the Haungaroa fluids no inorganic electron donor and responsible microorganisms could be identified that clearly stimulated autotrophic CO2 fixation. In the Brothers hydrothermal fluids Sulfurimonas (49%) and Hydrogenovibrio/Thiomicrospira (15%) species prevailed. Respective fluid incubations exhibited highest autotrophic CO2 fixation if supplemented with iron(II) or hydrogen. Likewise catabolic energy calculations predicted primarily iron(II) but also hydrogen oxidation as major energy sources in the natural fluids. According to transcript analyses with material from the incubation experiments Thiomicrospira/Hydrogenovibrio species dominated, outcompeting Sulfurimonas. Given that experimental conditions likely only simulated environmental conditions that cause Thiomicrospira/Hydrogenovibrio but not Sulfurimonas to thrive, it remains unclear which environmental parameters determine Sulfurimonas’ dominance in the Brothers natural hydrothermal fluids.
Collapse
Affiliation(s)
- Stefanie Böhnke
- Molecular Biology of Microbial Consortia, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Katharina Sass
- Molecular Biology of Microbial Consortia, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Giorgio Gonnella
- Center for Bioinformatics (ZBH), Universität Hamburg, Hamburg, Germany
| | - Alexander Diehl
- Department of Geosciences, MARUM - Centre for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Charlotte Kleint
- Department of Physics and Earth Sciences, Jacobs University Bremen, Bremen, Germany
| | - Wolfgang Bach
- Department of Geosciences, MARUM - Centre for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Rebecca Zitoun
- Department of Chemistry, University of Otago, Dunedin, New Zealand
| | - Andrea Koschinsky
- Department of Physics and Earth Sciences, Jacobs University Bremen, Bremen, Germany
| | - Daniela Indenbirken
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Sylvia G Sander
- Department of Chemistry, University of Otago, Dunedin, New Zealand
| | - Stefan Kurtz
- Center for Bioinformatics (ZBH), Universität Hamburg, Hamburg, Germany
| | - Mirjam Perner
- Molecular Biology of Microbial Consortia, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| |
Collapse
|