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Chifflet S, Chu van T, Bui Van V, Pham The T, Mari X, Pradel N. Analysis of the metals and metalloids concentrations and of the bacterial population in sediments of the Red River Delta, Vietnam. Front Microbiol 2024; 15:1394998. [PMID: 38933021 PMCID: PMC11201535 DOI: 10.3389/fmicb.2024.1394998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
In this study, we discuss for the first time the relationships between the diversity of the bacterial population and of the metals and metalloids concentrations in the sediments of the Red River Delta, Vietnam. The analysis of the 16S rRNA by the Illumina technology revealed a diversified population and a potential of bioremediation by the microorganisms, notably by the Bacilli relatively abundant in the Bach Dang estuary, where high metals and metalloids concentrations were highlighted. This work offers new information on the environmental context of the delta and highlights the potential impact that metals and metalloids may have on the bacterial population. Further investigations on the role of the bacteria in the biogeochemistry of this ecosystem will be of interest for the development of bioremediation processes.
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Affiliation(s)
- Sandrine Chifflet
- Aix Marseille Université, IRD, Université de Toulon, CNRS, MIO, UM 110, Marseille, France
| | - Thuoc Chu van
- Institute of Marine Environment and Resources (IMER), Vietnam Academy of Science and Technology (VAST), Haiphong, Vietnam
| | - Vuong Bui Van
- Institute of Marine Environment and Resources (IMER), Vietnam Academy of Science and Technology (VAST), Haiphong, Vietnam
| | - Thu Pham The
- Institute of Marine Environment and Resources (IMER), Vietnam Academy of Science and Technology (VAST), Haiphong, Vietnam
| | - Xavier Mari
- Aix Marseille Université, IRD, Université de Toulon, CNRS, MIO, UM 110, Marseille, France
- Institute of Marine Environment and Resources (IMER), Vietnam Academy of Science and Technology (VAST), Haiphong, Vietnam
| | - Nathalie Pradel
- Aix Marseille Université, IRD, Université de Toulon, CNRS, MIO, UM 110, Marseille, France
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Mondal S, Biswas B, Chowdhury R, Sengupta R, Mandal A, Kotal HN, Giri CK, Ghosh A, Saha S, Begam MM, Mukherjee C, Das I, Basak SK, Mitra Ghosh M, Ray K. Estuarine mangrove niches select cultivable heterotrophic diazotrophs with diverse metabolic potentials-a prospective cross-dialog for functional diazotrophy. Front Microbiol 2024; 15:1324188. [PMID: 38873137 PMCID: PMC11174608 DOI: 10.3389/fmicb.2024.1324188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 05/10/2024] [Indexed: 06/15/2024] Open
Abstract
Introduction Biological nitrogen fixation (BNF), an unparalleled metabolic novelty among living microorganisms on earth, globally contributes ~88-101 Tg N year-1 to natural ecosystems, ~56% sourced from symbiotic BNF while ~22-45% derived from free-living nitrogen fixers (FLNF). The success of symbiotic BNF is largely dependent on its interaction with host-plant, however ubiquitous environmental heterotrophic FLNFs face many limitations in their immediate ecological niches to sustain unhindered BNF. The autotrophic FLNFs like cyanobacteria and oceanic heterotrophic diazotrophs have been well studied about their contrivances acclimated/adapted by these organisms to outwit the environmental constraints for functional diazotrophy. However, FLNF heterotrophs face more adversity in executing BNF under stressful estuarine/marine/aquatic habitats. Methods In this study a large-scale cultivation-dependent investigation was accomplished with 190 NCBI accessioned and 45 non-accessioned heterotrophic FLNF cultivable bacterial isolates (total 235) from halophilic estuarine intertidal mangrove niches of Indian Sundarbans, a Ramsar site and UNESCO proclaimed World Heritage Site. Assuming ~1% culturability of the microbial community, the respective niches were also studied for representing actual bacterial diversity via cultivation-independent next-generation sequencing of V3-V4 rRNA regions. Results Both the studies revealed a higher abundance of culturable Gammaproteobacteria followed by Firmicutes, the majority of 235 FLNFs studied belonging to these two classes. The FLNFs displayed comparable selection potential in media for free nitrogen fixers and iron-oxidizing bacteria, linking diazotrophy with iron oxidation, siderophore production, phosphorus solubilization, phosphorus uptake and accumulation as well as denitrification. Discussion This observation validated the hypothesis that under extreme estuarine mangrove niches, diazotrophs are naturally selected as a specialized multidimensional entity, to expedite BNF and survive. Earlier metagenome data from mangrove niches demonstrated a microbial metabolic coupling among C, N, P, S, and Fe cycling in mangrove sediments, as an adaptive trait, evident with the co-abundant respective functional genes, which corroborates our findings in cultivation mode for multiple interrelated metabolic potential facilitating BNF in a challenging intertidal mangrove environment.
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Affiliation(s)
- Sumana Mondal
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
| | - Biswajit Biswas
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
- Department of Microbiology, St. Xavier’s College (Autonomous), Kolkata, India
| | - Rajojit Chowdhury
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
- Department of Botany, Sree Chaitanya College, Habra, India
| | - Rudranil Sengupta
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
| | - Anup Mandal
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
| | - Hemendra Nath Kotal
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
| | - Chayan Kumar Giri
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
| | - Anjali Ghosh
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
| | - Subhajit Saha
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
| | - Mst Momtaj Begam
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
- Department of Botany, Kalimpong College, Darjeeling, India
| | - Chandan Mukherjee
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
- School of Biological and Life Sciences, Galgotias University, Greater Noida, India
| | - Ipsita Das
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
| | | | | | - Krishna Ray
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
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Gao M, Dong Y, Deng H, Qiu W, Song Z. Impact of microplastics on microbial-mediated soil sulfur transformations in flooded conditions. JOURNAL OF HAZARDOUS MATERIALS 2024; 468:133857. [PMID: 38402685 DOI: 10.1016/j.jhazmat.2024.133857] [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: 11/21/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 02/27/2024]
Abstract
As emerging environmental pollutants, microplastics have become a crucial focus in environmental science research. Despite this, the impact of microplastics on soil in flooding conditions remains largely unexplored. Addressing this gap, our study examined the influence of polystyrene (PS) and polyphenylene sulfide (PPS) on the microbial populations in black soil, meadow soil, and paddy soil under flooded conditions. Given the significant regulatory influence exerted by microorganisms on sulfur transformations, our study was primarily focused on evaluating the microbial contributions to alterations in soil sulfur species. Our findings revealed several notable trends: In black soil, both PS and PPS led to a marked increase in the abundance of γ-proteobacteria and Subgroup_6, while reducing Clostridia. Ignavibacteria were found to be lower under PPS compared to PS. In meadow soil, the introduction of PPS resulted in increased levels of KD4-96 and γ-proteobacteria, while α-proteobacteria decreased. Chloroflexia under PPS was observed to be lower than under PS conditions. In paddy soil, our study identified a significant rise in Bacteroidia and Ignavibacteria, accompanied by a decrease in α-proteobacteria and γ-proteobacteria. γ-proteobacteria levels under PPS were notably higher than those under PS conditions. These shifts in microbial communities induced by both PS and PPS had a direct impact on adenosine 5'-phosphosulfate reductase, sulfite reductase, and polysulfide dioxygenase. Consequently, these changes led to soil organic sulfur decrease and sulfide increase. This study not only offers a theoretical framework but also provides empirical evidence for understanding the effects of microplastics on soil microorganisms and their role in regulating nutrient cycling, particularly in flood-prone conditions. Furthermore, this study underscores the importance of ensuring an adequate supply of sulfur in agricultural practices, such as rice and lotus root cultivation, to support optimal crop growth in the presence of microplastic pollution.
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Affiliation(s)
- Minling Gao
- Department of Materials and Environmental Engineering, Shantou University, Shantou 515063, China
| | - Youming Dong
- Department of Materials and Environmental Engineering, Shantou University, Shantou 515063, China
| | - Hui Deng
- Department of Materials and Environmental Engineering, Shantou University, Shantou 515063, China
| | - Weiwen Qiu
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 3230, Hamilton 3214, New Zealand
| | - Zhengguo Song
- Department of Materials and Environmental Engineering, Shantou University, Shantou 515063, China.
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Dong Y, Gao M, Cai Q, Qiu W, Xiao L, Chen Z, Peng H, Liu Q, Song Z. The impact of microplastics on sulfur REDOX processes in different soil types: A mechanism study. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133432. [PMID: 38219596 DOI: 10.1016/j.jhazmat.2024.133432] [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: 09/28/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/16/2024]
Abstract
Microplastics can potentially affect the physical and chemical properties of soil, as well as soil microbial communities. This could, in turn, influence soil sulfur REDOX processes and the ability of soil to supply sulfur effectively. However, the specific mechanisms driving these effects remain unclear. To explore this, soil microcosm experiments were conducted to assess the impacts of polystyrene (PS) and polyphenylene sulfide (PPS) microplastics on sulfur reduction-oxidation (REDOX) processes in black, meadow, and paddy soils. The findings revealed that PS and PPS most significantly decreased SO42- in black soil by 9.4%, elevated SO42- in meadow soil by 20.8%, and increased S2- in paddy soil by 20.5%. PS and PPS microplastics impacted the oxidation process of sulfur in soil by influencing the activity of sulfur dioxygenase, which was mediated by α-proteobacteria and γ-proteobacteria, and the oxidation process was negatively influenced by soil organic matter. PS and PPS microplastics impacted the reduction process of sulfur in soil by influencing the activity of adenosine-5'-phosphosulfate reductase, sulfite reductase, which was mediated by Desulfuromonadales and Desulfarculales, and the reduction process was positively influenced by soil organic matter. In addition to their impacts on microorganisms, it was found that PP and PPS microplastics directly influenced the structure of soil enzymes, leading to alterations in soil enzyme activity. This study sheds light on the mechanisms by which microplastics impact soil sulfur REDOX processes, providing valuable insights into how microplastics influence soil health and functioning, which is essential for optimizing crop growth and maximizing yield in future agricultural practices.
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Affiliation(s)
- Youming Dong
- Department of Materials and Environmental Engineering, Shantou University, Shantou 515063, China
| | - Minling Gao
- Department of Materials and Environmental Engineering, Shantou University, Shantou 515063, China
| | - Qiqi Cai
- Department of Materials and Environmental Engineering, Shantou University, Shantou 515063, China
| | - Weiwen Qiu
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 3230, Hamilton 3240, New Zealand
| | - Ling Xiao
- Department of Materials and Environmental Engineering, Shantou University, Shantou 515063, China
| | - Zimin Chen
- Department of Materials and Environmental Engineering, Shantou University, Shantou 515063, China
| | - Hongchang Peng
- Department of Materials and Environmental Engineering, Shantou University, Shantou 515063, China
| | - Qinghai Liu
- Institute of Agricultural Product Quality Standard and Testing Research, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850032, China
| | - Zhengguo Song
- Department of Materials and Environmental Engineering, Shantou University, Shantou 515063, China.
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Dong Y, Gao M, Qiu W, Xiao L, Cheng Z, Peng H, Song Z. Investigating the impact of microplastics on sulfur mineralization in different soil types: A mechanism study. JOURNAL OF HAZARDOUS MATERIALS 2024; 464:132942. [PMID: 37992502 DOI: 10.1016/j.jhazmat.2023.132942] [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: 07/29/2023] [Revised: 10/19/2023] [Accepted: 11/04/2023] [Indexed: 11/24/2023]
Abstract
Microplastics can affect the physicochemical properties of soil and soil microorganisms, potentially resulting in changes in the soil sulfur mineralization and its capacity to supply available sulfur. However, the specific mechanisms underlying these effects remain unclear. We performed soil microcosm experiments, in which the effects of polystyrene (PS) and polyphenylene sulfide (PPS) microplastics on sulfur mineralization were examined in black, meadow, and paddy soils under flooded and dry conditions. Under dry condition, the presence of PS and PPS microplastics impeded sulfur (S) mineralization in black and paddy soils, but promoted sulfur mineralization in meadow soil. The size of microplastics was identified as the primary factor influencing sulfur mineralization in black soil, while in meadow soil, it was influenced by the microplastics type. In the case of paddy soil, the concentration of microplastics was the key factor affecting sulfur mineralization. During the flooding period, PS and PPS microplastics in black and paddy soils curtailed sulfur mineralization, however expedited sulfur mineralization in meadow soil, with PS enhancing soil sulfur mineralization more pronouncedly than PPS in black soil. The type and concentration of microplastics were identified as the main factors affecting sulfur mineralization in black soil, while in paddy soil, it was influenced by the size of microplastics. The principal regulating factors of soil sulfur mineralization were the sulphatase and arylsulfatase enzymes produced by Actinobacteria, Xanthomonadales, and Rhizobiales microorganisms, while organic matter and Olsen-P also had an influential role. Additionally, microplastics directly affected the structure of soil enzymes, thereby altering soil enzyme activities. This study provided insights into the mechanism by which microplastics affect soil sulfur mineralization, offering significant implications for assessing the influence of microplastics on soil sulfur availability and making informed decisions about sulfur application in future agricultural practices.
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Affiliation(s)
- Youming Dong
- Department of Materials and Environmental Engineering, Shantou University, Shantou 515063, China
| | - Minling Gao
- Department of Materials and Environmental Engineering, Shantou University, Shantou 515063, China
| | - Weiwen Qiu
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 4704, Christchurch 8140, New Zealand
| | - Ling Xiao
- Department of Materials and Environmental Engineering, Shantou University, Shantou 515063, China
| | - Zimin Cheng
- Department of Materials and Environmental Engineering, Shantou University, Shantou 515063, China
| | - Hongchang Peng
- Department of Materials and Environmental Engineering, Shantou University, Shantou 515063, China
| | - Zhengguo Song
- Department of Materials and Environmental Engineering, Shantou University, Shantou 515063, China.
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Skoog EJ, Bosak T. Predicted metabolic roles and stress responses provide insights into candidate phyla Hydrogenedentota and Sumerlaeota as members of the rare biosphere in biofilms from various environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13228. [PMID: 38192240 PMCID: PMC10866078 DOI: 10.1111/1758-2229.13228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/11/2023] [Indexed: 01/10/2024]
Abstract
Pustular mats from Shark Bay, Western Australia, host complex microbial communities bound within an organic matrix. These mats harbour many poorly characterized organisms with low relative abundances (<1%), such as candidate phyla Hydrogenedentota and Sumerlaeota. Here, we aim to constrain the metabolism and physiology of these candidate phyla by analyzing two representative metagenome-assembled genomes (MAGs) from a pustular mat. Metabolic reconstructions of these MAGs suggest facultatively anaerobic, chemoorganotrophic lifestyles of both organisms and predict that both MAGs can metabolize a diversity of carbohydrate substrates. Ca. Sumerlaeota possesses genes involved in degrading chitin, cellulose and other polysaccharides, while Ca. Hydrogenedentota can metabolize cellulose derivatives in addition to glycerol, fatty acids and phosphonates. Both Ca. phyla can respond to nitrosative stress and participate in nitrogen metabolism. Metabolic comparisons of MAGs from Shark Bay and those from various polyextreme environments (i.e., hot springs, hydrothermal vents, subsurface waters, anaerobic digesters, etc.) reveal similar metabolic capabilities and adaptations to hypersalinity, oxidative stress, antibiotics, UV radiation, nitrosative stress, heavy metal toxicity and life in surface-attached communities. These adaptations and capabilities may account for the widespread nature of these organisms and their contributions to biofilm communities in a range of extreme surface and subsurface environments.
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Affiliation(s)
- Emilie J. Skoog
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Integrative Oceanography DivisionScripps Institution of Oceanography, UC San DiegoLa JollaCaliforniaUSA
| | - Tanja Bosak
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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Dong Y, Li Y, Ge M, Takatsu T, Wang Z, Zhang X, Ding D, Xu Q. Distinct gut microbial communities and functional predictions in divergent ophiuroid species: host differentiation, ecological niches, and adaptation to cold-water habitats. Microbiol Spectr 2023; 11:e0207323. [PMID: 37889056 PMCID: PMC10715168 DOI: 10.1128/spectrum.02073-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/20/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE Gastrointestinal microorganisms are critical to the survival and adaptation of hosts, and there are few studies on the differences and functions of gastrointestinal microbes in widely distributed species. This study investigated the gut microbes of two ophiuroid species (Ophiura sarsii and its subspecies O. sarsii vadicola) in cold-water habitats of the Northern Pacific Ocean. The results showed that a combination of host and environmental factors shapes the intestinal microbiota of ophiuroids. There was a high similarity in microbial communities between the two groups living in different regions, which may be related to their similar ecological niches. These microorganisms played a vital role in the ecological success of ophiuroids as the foundation for their adaptation to cold-water environments. This study revealed the complex relationship between hosts and their gut microbes, providing insights into the role they play in the adaptation and survival of marine species.
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Affiliation(s)
- Yue Dong
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Yixuan Li
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China
| | - Meiling Ge
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Tetsuya Takatsu
- Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Zongling Wang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Xuelei Zhang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Dewen Ding
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Qinzeng Xu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
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Jiang S, Xue Y, Wang M, Wang H, Liu L, Dai Y, Liu X, Yue T, Zhao J. Sediment-seawater exchange altered adverse effects of ocean acidification towards marine microalgae. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 874:162533. [PMID: 36870492 DOI: 10.1016/j.scitotenv.2023.162533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/17/2023] [Accepted: 02/25/2023] [Indexed: 06/18/2023]
Abstract
Ocean acidification (OA) exhibits high threat to marine microalgae. However, the role of marine sediment in the OA-induced adverse effect towards microalgae is largely unknown. In this work, the effects of OA (pH 7.50) on the growth of individual and co-cultured microalgae (Emiliania huxleyi, Isochrysis galbana, Chlorella vulgaris, Phaeodactylum tricornutum, and Platymonas helgolandica tsingtaoensis) were systematically investigated in the sediment-seawater systems. OA inhibited E. huxleyi growth by 25.21 %, promoted P. helgolandica (tsingtaoensis) growth by 15.49 %, while did not cause any effect on the other three microalgal species in the absence of sediment. In the presence of the sediment, OA-induced growth inhibition of E. huxleyi was significantly mitigated, because the released chemicals (N, P and Fe) from seawater-sediment interface increased the photosynthesis and reduced oxidative stress. For P. tricornutum, C. vulgaris and P. helgolandica (tsingtaoensis), the growth was significantly increased in the presence of sediment in comparison with those under OA alone or normal seawater (pH 8.10). For I. galbana, the growth was inhibited when the sediment was introduced. Additionally, in the co-culturing system, C. vulgaris and P. tricornutum were the dominant species, while OA increased the proportions of dominant species and decreased the community stability as indicated by Shannon and Pielou's indexes. After the introduction of sediment, the community stability was recovered, but remained lower than that under normal condition. This work demonstrated the role of sediment in the biological responses to OA, and could be helpful for better understanding the impact of OA on marine ecosystems.
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Affiliation(s)
- Shiyang Jiang
- Institute of Coastal Environmental Pollution Control, Key Laboratory of Marine Environment and Ecology (Ministry of Education), and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266100, China
| | - Yinhao Xue
- Institute of Coastal Environmental Pollution Control, Key Laboratory of Marine Environment and Ecology (Ministry of Education), and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266100, China
| | - Meng Wang
- Institute of Coastal Environmental Pollution Control, Key Laboratory of Marine Environment and Ecology (Ministry of Education), and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266100, China
| | - Hao Wang
- Institute of Coastal Environmental Pollution Control, Key Laboratory of Marine Environment and Ecology (Ministry of Education), and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266100, China
| | - Lu Liu
- Institute of Coastal Environmental Pollution Control, Key Laboratory of Marine Environment and Ecology (Ministry of Education), and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266100, China
| | - Yanhui Dai
- Institute of Coastal Environmental Pollution Control, Key Laboratory of Marine Environment and Ecology (Ministry of Education), and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266100, China.
| | - Xia Liu
- Institute of Coastal Environmental Pollution Control, Key Laboratory of Marine Environment and Ecology (Ministry of Education), and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266100, China
| | - Tongtao Yue
- Institute of Coastal Environmental Pollution Control, Key Laboratory of Marine Environment and Ecology (Ministry of Education), and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266100, China
| | - Jian Zhao
- Institute of Coastal Environmental Pollution Control, Key Laboratory of Marine Environment and Ecology (Ministry of Education), and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266100, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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Liu Z, Liu G, Guo X, Li Y, Ji N, Xu X, Sun Q, Yang J. Diversity of the protease-producing bacteria and their extracellular protease in the coastal mudflat of Jiaozhou Bay, China: in response to clam naturally growing and aquaculture. Front Microbiol 2023; 14:1164937. [PMID: 37275176 PMCID: PMC10236810 DOI: 10.3389/fmicb.2023.1164937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/24/2023] [Indexed: 06/07/2023] Open
Abstract
The booming mudflat aquaculture poses an accumulation of organic matter and a certain environmental threat. Protease-producing bacteria are key players in regulating the nitrogen content in ecosystems. However, knowledge of the diversity of protease-producing bacteria in coastal mudflats is limited. This study investigated the bacterial diversity in the coastal mudflat, especially protease-producing bacteria and their extracellular proteases, by using culture-independent methods and culture-dependent methods. The clam aquaculture area exhibited a higher concentration of carbon, nitrogen, and phosphorus when compared with the non-clam area, and a lower richness and diversity of bacterial community when compared with the clam naturally growing area. The major classes in the coastal mud samples were Bacteroidia, Gammaproteobacteria, and Alphaproteobacteria. The Bacillus-like bacterial community was the dominant cultivated protease-producing group, accounting for 52.94% in the non-clam area, 30.77% in the clam naturally growing area, and 50% in the clam aquaculture area, respectively. Additionally, serine protease and metalloprotease were the principal extracellular protease of the isolated coastal bacteria. These findings shed light on the understanding of the microbes involved in organic nitrogen degradation in coastal mudflats and lays a foundation for the development of novel protease-producing bacterial agents for coastal mudflat purification.
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Affiliation(s)
- Zhiyun Liu
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Guangchao Liu
- College of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Xuzhen Guo
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Yang Li
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
- Qingdao Special Food Research Institute, Qingdao, China
| | - Na Ji
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
- Qingdao Special Food Research Institute, Qingdao, China
| | - Xingfeng Xu
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
- Qingdao Special Food Research Institute, Qingdao, China
| | - Qingjie Sun
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
- Qingdao Special Food Research Institute, Qingdao, China
| | - Jie Yang
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
- Qingdao Special Food Research Institute, Qingdao, China
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Patil MP, Jeong I, Woo HE, Kim JO, Lee DI, Kim K. Natural Variations in the Benthic Environment and Bacterial Communities of Coastal Sediments around Aquaculture Farms in South Korea. Indian J Microbiol 2023; 63:100-105. [PMID: 37188235 PMCID: PMC10172443 DOI: 10.1007/s12088-023-01067-8] [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: 11/22/2022] [Accepted: 02/18/2023] [Indexed: 03/02/2023] Open
Abstract
The aim of this study was to examine the possible seasonal variations in the nutrients (dissolved inorganic nitrogen-DIN and phosphorus) and benthic bacterial communities in marine aquaculture surrounding sediments. The study areas were Geoje, Tongyeong, and Changwon bays in Korea, which are famous for oysters (Magallana gigas), Halocynthia roretzi, and warty sea squirt (Styela clava) farming, respectively. The study sites included semi-enclosed coastal areas with a low seawater exchange rate. Subtidal sediment samples were collected seasonally from the area surrounding the aquacultures between April and December 2020. Seasonal variations in nutrients were observed, with the highest concentration of DIN in August. For phosphorus, site-specific variations were also observed. To investigate the variations in benthic bacterial communities, the advanced technique of 16S rRNA gene amplicon sequencing was applied, and the results indicated a seasonal variation pattern and predominance of Proteobacteria (59.39-69.73%), followed by Bacteroidetes (6.55-12.85%) and Chloroflexi (2.04-4.50%). This study provides a reference for future studies on natural variations in the benthic environment and bacterial communities in the areas surrounding aquacultures. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-023-01067-8.
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Affiliation(s)
- Maheshkumar Prakash Patil
- Industry-University Cooperation Foundation, Pukyong National University, 45 Yongso-Ro, Nam-Gu, Busan, 48513 South Korea
| | - Ilwon Jeong
- Department of Ocean Engineering, Pukyong National University, 45 Yongso-Ro, Nam-Gu, Busan, 48513 South Korea
| | - Hee-Eun Woo
- Department of Ocean Engineering, Pukyong National University, 45 Yongso-Ro, Nam-Gu, Busan, 48513 South Korea
| | - Jong-Oh Kim
- Department of Microbiology, Pukyong National University, 45 Yongso-Ro, Nam-Gu, Busan, 48513 South Korea
- School of Marine and Fisheries Life Science, Pukyong National University, 45 Yongso-Ro, Nam-Gu, Busan, 48513 South Korea
| | - Dae In Lee
- Marine Environmental Management Division, National Institute of Fisheries Science, Busan, 46083 South Korea
| | - Kyunghoi Kim
- Department of Ocean Engineering, Pukyong National University, 45 Yongso-Ro, Nam-Gu, Busan, 48513 South Korea
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11
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Kalkan S. Multimodal analysis of south-eastern Black Sea sediment bacterial population diversity. MARINE POLLUTION BULLETIN 2022; 183:114063. [PMID: 36057154 DOI: 10.1016/j.marpolbul.2022.114063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/15/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
This study focused on marine sediments from the Black Sea, mainly due to bacterial diversity-induced public health / biotechnology application value. Sediment samples were gathered from 14 locations at differing depths across Turkish shores on a seasonal basis over 10 months, with bacterial identifications performed through using multimodal analytical platforms. Overall, 26 differing, predominantly Gram-positive (57.5 %) bacterial species were identified for this region, including Bacillaceae (50.0 %) and Pseudomonadaceae (15.0 %). The most dominant classes were identified as Bacilli (52.5 %) and Gammaproteobacteria (40.0 %). Ten isolates (25 %) to the species level and thirty-six isolates (90 %) to the genus level were identified using VITEK® MS and Bruker Microflex® LT/SH, in comparison to 16S rRNA sequencing results. Identified species - particularly, novel reported species - can contribute to the knowledge of microbial life dwelling upon sediments of the south-eastern regions of the Black Sea.
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Affiliation(s)
- Samet Kalkan
- Recep Tayyip Erdogan University, Faculty of Fisheries, Ataturk Street Fener District, 53100 Merkez, Rize, Turkey.
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12
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Liu J, Wang X, Liu J, Liu X, Zhang XH, Liu J. Comparison of assembly process and co-occurrence pattern between planktonic and benthic microbial communities in the Bohai Sea. Front Microbiol 2022; 13:1003623. [PMID: 36386657 PMCID: PMC9641972 DOI: 10.3389/fmicb.2022.1003623] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/05/2022] [Indexed: 10/10/2023] Open
Abstract
Unraveling the mechanisms structuring microbial community is a central goal in microbial ecology, but a detailed understanding of how community assembly processes relate to living habitats is still lacking. Here, via 16S rRNA gene amplicon sequencing, we investigated the assembly process of microbial communities in different habitats [water verse sediment, free-living (FL) verse particle-associated (PA)] and their impacts on the inter-taxa association patterns in the coastal Bohai Sea, China. The results showed clear differences in the composition and diversity of microbial communities among habitats, with greater dissimilarities between water column and sediment than between FL and PA communities. The microbial community assembly was dominated by dispersal limitation, ecological drift, and homogeneous selection, but their relative importance varied in different habitats. The planktonic communities were mainly shaped by dispersal limitation and ecological drift, whereas homogeneous selection played a more important role in structuring the benthic communities. Furthermore, the assembly mechanisms differed between FL and PA communities, especially in the bottom water with a greater effect of ecological drift and dispersal limitation on the FL and PA fractions, respectively. Linking assembly process to co-occurrence pattern showed that the relative contribution of deterministic processes (mainly homogeneous selection) increased under closer co-occurrence relationships. By contrast, stochastic processes exerted a higher effect when there were less inter-taxa connections. Overall, our findings demonstrate contrasting ecological processes underpinning microbial community distribution in different habitats including different lifestyles, which indicate complex microbial dynamic patterns in coastal systems with high anthropogenic perturbations.
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Affiliation(s)
- Jinmei Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System and College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaolei Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System and College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jiao Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System and College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoyue Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System and College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System and College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Jiwen Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System and College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
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13
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Hu L, Li Q, Yan J, Liu C, Zhong J. Vegetation restoration facilitates belowground microbial network complexity and recalcitrant soil organic carbon storage in southwest China karst region. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153137. [PMID: 35041964 DOI: 10.1016/j.scitotenv.2022.153137] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 05/16/2023]
Abstract
Soil organic carbon (SOC) is an important component of soil ecosystems, and soils are a hotbed of microorganisms playing critical roles in soil functions and ecosystem services. Understanding the interaction between SOC and soil microbial community is of paramount significance in predicting the C fate in soils following vegetation restoration. In this study, high-throughput sequencing of 16S rRNA and ITS genes combined with 13C NMR spectroscopy analysis were applied to characterize SOC chemical compounds and elucidate associated soil microbial community. Our results indicated that the contents of SOC, total nitrogen, total phosphorus, microbial biomass carbon and biomass nitrogen, dissolved organic carbon, available potassium, exchangeable calcium and soil moisture increased significantly (P < 0.05) along with the vegetation restoration processes from corn land, grassland, shrub land, to secondary and primary forests. Moreover, the Alkyl C and O-alkyl C abundance increased with vegetation recovery, but no significant differences of Alkyl C were observed in different successional stages. In contrast, the relative abundance of Methoxyl C showed an opposite trend. The dominate phyla Proteobacteria, Acidobacteria, Actinobacteria, Ascomycota and Basidiomycota were strongly related to SOC. And, SOC was found to be the determining factor shaping soil bacterial and fungal communities in vegetation restoration processes. The complexity of soil bacteria and fungi interactions along the vegetation restoration chronosequence increased. Determinism was the major assembly mechanism of bacterial community while stochasticity dominated the assembly of fungal community. Bryobacter, Haliangium, and MND1 were identified as keystone genera in co-occurrence network. Besides, the dominant functional groups across all vegetation restoration processes were mainly involved in soil C and N cycles and linked to the enhanced recalcitrant SOC storage. Our results provide invaluable reference to advance the understanding of microbe response to vegetation restoration processes and highlight the impact of microbes on recalcitrant SOC storage.
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Affiliation(s)
- Linan Hu
- Institute of Groundwater and Earth Sciences, Jinan University, Guangzhou 510632, China; Key Laboratory of Karst Dynamics, MNR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin 541004, China; International Research Center on Karst under the Auspices of UNESCO, Guilin 541004, China
| | - Qiang Li
- Key Laboratory of Karst Dynamics, MNR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin 541004, China; International Research Center on Karst under the Auspices of UNESCO, Guilin 541004, China.
| | - Jiahui Yan
- Key Laboratory of Karst Dynamics, MNR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin 541004, China; International Research Center on Karst under the Auspices of UNESCO, Guilin 541004, China
| | - Chun Liu
- Institute of Groundwater and Earth Sciences, Jinan University, Guangzhou 510632, China; Department of Ecology, Jinan University, Guangzhou 510632, China.
| | - Juxin Zhong
- Key Laboratory of Karst Dynamics, MNR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin 541004, China; International Research Center on Karst under the Auspices of UNESCO, Guilin 541004, China
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14
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Quach NT, Dam HT, Tran DM, Vu THN, Nguyen QV, Nguyen KT, Nguyen QH, Phi CB, Le TH, Chu HH, Thuoc Doan V, Shyu DJH, Kang H, Li WJ, Phi QT. Diversity of microbial community and its metabolic potential for nitrogen and sulfur cycling in sediments of Phu Quoc island, Gulf of Thailand. Braz J Microbiol 2021; 52:1385-1395. [PMID: 33856662 DOI: 10.1007/s42770-021-00481-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 03/29/2021] [Indexed: 11/29/2022] Open
Abstract
Although Phu Quoc island, Gulf of Thailand possesses diverse marine and coastal ecosystems, biodiversity and metabolic capability of microbial communities remain poorly investigated. The aim of our study was to evaluate the biodiversity and metabolic potential of sediment microbial communities in Phu Quoc island. The marine sediments were collected from three different areas and analyzed by using 16S rRNA gene-based amplicon approach. A total of 1,143,939 reads were clustered at a 97% sequence similarity into 8,331 unique operational taxonomic units, representing 52 phyla. Bacteria and archaea occupied averagely around 86% and 14%, respectively, of the total prokaryotic community. Proteobacteria, Planctomycetes, Chloroflexi, and Thaumarchaeota were the dominant phyla in all sediments, which were involved in nitrogen and sulfur metabolism. Sediments harboring of higher nitrogen sources were found to coincide with increased abundance of archaeal phylum Thaumarchaeota. Predictive functional analysis showed high abundance prokaryotic genes associated with nitrogen cycling including nifA-Z, amoABC, nirA, narBIJ, napA, nxrAB, nrfA-K, nirBD, nirS, nirK, norB-Z, nlnA, ald, and ureA-J, based on taxonomic groups detected by 16S rRNA sequencing. Although the key genes involved in sulfur cycling were found to be at low to undetectable levels, the other genes encoding for sulfur-related biological processes were present, suggesting that alternative pathways may be involved in sulfur cycling at our study site. In conclusion, our study for the first time shed light on diversity of microbial communities in Phu Quoc island.
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Affiliation(s)
- Ngoc Tung Quach
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam
| | - Hang Thuy Dam
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Hanoi, 10000, Vietnam
| | - Dinh Man Tran
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam.
| | - Thi Hanh Nguyen Vu
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam
| | - Quoc Viet Nguyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam
| | - Kim Thoa Nguyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam
| | - Quang Huy Nguyen
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam
| | | | - Thanh Ha Le
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Hanoi, 10000, Vietnam
| | - Hoang Ha Chu
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam
| | - Van Thuoc Doan
- Hanoi National University of Education, Hanoi, 10000, Vietnam
| | - Douglas J H Shyu
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan
| | - Heonjoong Kang
- School of Earth and Environmental Sciences, College of Natural Sciences, Seoul National University NS80, Seoul, 08826, Korea
| | - Wen-Jun Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Quyet Tien Phi
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam. .,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam.
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15
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Dong Y, Li Y, He P, Wang Z, Fan S, Zhang Z, Zhang X, Xu Q. Gut Microbial Composition and Diversity in Four Ophiuroid Species: Divergence Between Suspension Feeder and Scavenger and Their Symbiotic Microbes. Front Microbiol 2021; 12:645070. [PMID: 33815331 PMCID: PMC8017295 DOI: 10.3389/fmicb.2021.645070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/19/2021] [Indexed: 12/31/2022] Open
Abstract
Gut microbiota have important roles in the survival and adaptation of the host. Ophiuroids, as the worldwide dominant benthos, have ecological roles in benthic-pelagic coupling in the sea floor. However, little is known about the composition and diversity of their gut microbiota and its potential functions in benthic ecosystems. In present study, we preformed 16S rRNA sequencing and function analysis in four dominant species (Stegophiura sladeni, Ophiopholis mirabilis, Ophiura sarsii vadicola, and Ophiura kinbergi) with two feeding types (suspension feeding/herbivores and scavenger/carnivores) from the Yellow Sea, China. Results showed that 56 phyla and 569 genera of microbiota were identified among ophiuroid guts. Multivariate and diversity analyses showed that the ophiuroid gut microbiota were independent and have higher biodiversity to the sediment microbial in the Yellow Sea. Phyla Proteobacteria, Firmicutes, Tenericutes, and Bacteroidetes were the dominant bacteria, with more than 80% abundance among the four ophiuroid species. A comparison among the gut microbial compositions among four ophiuroids showed the similarity of two offshore carnivore ophiuroids (S. sladeni and O. sarsii vadicola) and variation in the dominant microbiota types of three nearshore ophiuroids (S. sladeni, O. mirabilis, and O. kinbergi). The functional analysis revealed the significant differences of the environment-related expression in S. sladeni gut microbiota between nearshore and offshore environments. The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) functional annotation showed the significant divergence of metabolism pathways between two nearshore species, the herbivores O. mirabilis and carnivores S. sladeni, such as the Lipid metabolism, Carbohydrate metabolism, and Metabolism of cofactors and vitamins. The homolog search and phylogenetic analysis identified the first gut symbiotic Candidatus Hepatoplasma in S. sladeni with important roles for the nutrient metabolisms. Overall, our study reported the comprehensive data of ophiuroid gut microbiota, while the functional microbiome provides insight into the physiology and environmental adaptation in ophiuroids.
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Affiliation(s)
- Yue Dong
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yixuan Li
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China.,Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Peiqing He
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Zongling Wang
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shiliang Fan
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | | | - Xuelei Zhang
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Qinzeng Xu
- MNR Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
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16
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Jokanović S, Kajan K, Perović S, Ivanić M, Mačić V, Orlić S. Anthropogenic influence on the environmental health along Montenegro coast based on the bacterial and chemical characterization. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 271:116383. [PMID: 33387780 DOI: 10.1016/j.envpol.2020.116383] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 12/15/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
Coastal marine sediments are particularly exposed to human activities. The function of a coastal ecosystem is largely affected by eutrophication, wastewater discharges, chemical pollution, port activities, industry and tourism. Bacterial classification can be used as a measure in assessing the harmful effects on the ecosystem. This study provided insight into the environmental health of the coastal region of Montenegro analyzing the possible impact of PAHs and PCBs upon the bacterial community diversity and function as well as nutrients. Two stations at the shipyards were defined as very high PAH polluted together with PCB concentration exceeding threshold values. The bacterial community at the OTU level clustered together all stations except the most polluted site (SBL), the main tourist destination in Montenegro (BDV) and the estuary site (ADB) forming the independent clusters. Bacterial community based on the OTU level was driven by PAHs, TOC and silt content. The lowest richness and diversity were indicated at the site with the highest concentration of PAHs and PCBs with the highest abundance of Alphaproteobacteria followed by Gammaproteobacteria. OTUs affiliated to phyla BRC1, Dadabacteria and Spirochaetes were present with a total abundance higher than 1% only at the most polluted site indicating their persistence and possible potential for degradation of aromatic compounds. To compare functional capabilities potentially related to biodegradation of aromatic compounds and active transport systems, PICRUSt was used to predict metagenomes of the sediments. From our data, we identified specific bacterial community and predicted metabolic pathways that give us a picture of the environmental health along the coast of Montenegro, which provides us a new insight into human-induced pollution impacts on the coastal ecosystem.
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Affiliation(s)
- Sandra Jokanović
- Institute of Marine Biology, University of Montenegro, 85 330, Kotor, Montenegro
| | - Katarina Kajan
- Ruđer Bošković Institute, Division of Materials Chemistry, 10 000, Zagreb, Croatia; Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), University of Split, 21 000, Split, Croatia
| | - Svetlana Perović
- Faculty of Science and Mathematics, University of Montenegro, 81 000, Podgorica, Montenegro
| | - Maja Ivanić
- Ruđer Bošković Institute, Division for Marine and Environmental Research, 10 000, Zagreb, Croatia
| | - Vesna Mačić
- Institute of Marine Biology, University of Montenegro, 85 330, Kotor, Montenegro
| | - Sandi Orlić
- Ruđer Bošković Institute, Division of Materials Chemistry, 10 000, Zagreb, Croatia; Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), University of Split, 21 000, Split, Croatia.
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17
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Zhou J, Wang Y, Lei Q. Using Bioinformatics to Quantify the Variability and Diversity of the Microbial Community Structure in Pond Ecosystems of a Subtropical Catchment. Curr Bioinform 2021. [DOI: 10.2174/1574893615999200422120819] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
In rural China, many natural water bodies and farmlands have been
converted into fish farming ponds as an economic developmental strategy. There is still a limited
understanding of how the diversity and structure of microbial communities change in nature and
become managed fish pond ecosystems.
Objective:
We aimed to identify the changes of the diversity and structure of microbial community
and driving mechanism in pond ecosystems.
Methods:
The datasets of 16S rRNA amplicon sequencing and the concentrations of N and P
fractions were achieved in water samples of pond ecosystems. Bioinformatics analysis was used to
analyze the diversity and structure of the microbial communities.
Results:
Our results indicated that the diversity and structure of the microbial communities in the
natural ponds were significantly different from ones in managed fish ponds. The nutrients of N and
P and water environmental factors were responsible for 46.3% and 19.5% of the changes in the
structure and diversity of the microbial community, respectively.
Conclusion:
The N and P fractions and water environmental factors influenced the microbial
community structure and diversity in pond ecosystems. Fish farming indirectly affected the
microbial community by altering the contents of N and P fractions in water bodies of ponds, when
a natural pond was converted into a managed fish pond.
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Affiliation(s)
- Jiaogen Zhou
- School of Urban and Environmental Science, Huaiyin Normal University, Jiangsu 223300, China
| | - Yang Wang
- School of Urban and Environmental Science, Huaiyin Normal University, Jiangsu 223300, China
| | - Qiuliang Lei
- Key Laboratory of Non-point Source Pollution Control, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
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18
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Lee AH, Lee J, Noh J, Lee C, Hong S, Kwon BO, Kim JJ, Khim JS. Characteristics of long-term changes in microbial communities from contaminated sediments along the west coast of South Korea: Ecological assessment with eDNA and physicochemical analyses. MARINE POLLUTION BULLETIN 2020; 160:111592. [PMID: 32927183 DOI: 10.1016/j.marpolbul.2020.111592] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/14/2020] [Accepted: 08/22/2020] [Indexed: 06/11/2023]
Abstract
The environmental DNA (eDNA) metabarcoding was applied to assess benthic ecological health in the west coast of South Korea by investigating a long-term microbial community change (2015-17). The ecological interaction among microorganisms, from phylum to family level, and their associations to environmental variables across the five regions were highlighted. As part of the study, the available chemistry and toxicological data in the regions during the monitoring periods were incorporated into an integrated sediment triad assessment. The bacterial communities were dominated by Proteobacteria (34.2%), Bacteroidetes (13.8%), and Firmicutes (10.8%). Proteobacteria and Bacteroidetes dominated consistently across regions and years, while Firmicutes and Cyanobacteria significantly varied by region and years (p < 0.05). The abundance of this phylum declined over time with the increasing abundance of Cyanobacteria, indicating their independent interactions to certain environmental changes. Planctomycetes and Gemmatimonadetes linked to some contaminants (ΣPAHs and Cu), implying indicator taxa. Overall, eDNA-based microbial community analysis combined with exposures of contaminants and responses of microorganisms is a promising strategy for the assessment of benthic ecological health in contaminated sediments from coastal waters.
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Affiliation(s)
- Aslan Hwanhwi Lee
- School of Earth and Environmental Sciences & Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Junghyun Lee
- School of Earth and Environmental Sciences & Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Junsung Noh
- School of Earth and Environmental Sciences & Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Changkeun Lee
- School of Earth and Environmental Sciences & Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Seongjin Hong
- Department of Ocean Environmental Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Bong-Oh Kwon
- Department of Marine Biotechnology, Kunsan National University, Kunsan 54150, Republic of Korea
| | - Jae-Jin Kim
- Division of Environmental Science & Ecological Engineering, College of Life Science & Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Jong Seong Khim
- School of Earth and Environmental Sciences & Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea.
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19
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Feng J, Zhang L, Xia X, Hu W, Zhou P. Effect of geographic variation on the proteome of sea cucumber (Stichopus japonicus). Food Res Int 2020; 136:109498. [PMID: 32846579 DOI: 10.1016/j.foodres.2020.109498] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 06/09/2020] [Accepted: 06/24/2020] [Indexed: 12/26/2022]
Abstract
Sea cucumber is a sensitive organism that is easily challenged by environmental change. The aim of this study was to characterize the proteome of sea cucumbers from 5 main Chinese origins, including Xiamen (XM), Dalian (DL), Weihai (WH), Yantai (YT) and Qingdao (QD). In this work, a tandem mass tag (TMT) labeling proteomic approach was applied to identify and quantify the proteome of sea cucumber. A total of 5051 proteins were identified in the body wall; among those proteins, 1594 proteins (31.6%) were identified as enzyme proteins, and 33 proteins belonged to collagen. In addition, the 10 most highly abundant proteins were further discussed. Among all quantified proteins, 2266 were significantly differentially expressed proteins (SDEPs) across the 5 origins. These SDEPs were related to pigmentation (5 proteins), antioxidant activity (13 proteins), and immune system processes (29 proteins). Based on SDEPs, DL differed the most from QD and XM, as well as WH and YT, as shown in principal component analysis (PCA) and hierarchical clustering. In conclusion, one-fourth of the significantly different proteins found in the sea cucumber body wall among the 5 main Chinese locations indicated the sensitivity of sea cucumber to variations in temperature, environment, and feeding.
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Affiliation(s)
- Jianhui Feng
- State Key Laboratory of Food Science & Technology, Jiangnan University, Wuxi, Jiangsu Province 214122, China
| | - Lina Zhang
- State Key Laboratory of Food Science & Technology, Jiangnan University, Wuxi, Jiangsu Province 214122, China.
| | - Xubin Xia
- Shandong Homey Aquatic Development CO., Rongcheng, Shandong Province 264000, China
| | - Wei Hu
- Shandong Homey Aquatic Development CO., Rongcheng, Shandong Province 264000, China
| | - Peng Zhou
- State Key Laboratory of Food Science & Technology, Jiangnan University, Wuxi, Jiangsu Province 214122, China.
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Comparative metagenomics reveals the microbial diversity and metabolic potentials in the sediments and surrounding seawaters of Qinhuangdao mariculture area. PLoS One 2020; 15:e0234128. [PMID: 32497143 PMCID: PMC7272022 DOI: 10.1371/journal.pone.0234128] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/19/2020] [Indexed: 11/19/2022] Open
Abstract
Qinhuangdao coastal area is an important mariculture area in North China. Microbial communities play an important role in driving biogeochemical cycle and energy flow. It is necessary to identify the microbial communities and their functions in the coastal mariculture area of Qinhuangdao. In this study, the microbial community compositions and their metabolic potentials in the sediments and their surrounding seawaters of Qinhuangdao mariculture area were uncovered by the 16S rRNA gene amplicon sequencing and metagenomic shotgun sequencing approaches. The results of amplicon sequencing showed that Gammaproteobacteria and Alphaproteobacteria were predominant classes. Our datasets showed a clear shift in microbial taxonomic groups and the metabolic pathways in the sediments and surrounding seawaters. Metagenomic analysis showed that purine metabolism, ABC transporters, and pyrimidine metabolism were the most abundant pathways. Genes related to two-component system, TCA cycle and nitrogen metabolism exhibited higher abundance in sediments compared with those in seawaters. The presence of cadmium-resistant genes and ABC transporters suggested the ability of microorganisms to resist the toxicity of cadmium. In summary, this study provides comprehensive and significant differential signatures in the microbial community and metabolic pathways in Qinhuangdao mariculture area, and can develop effective microbial indicators to monitor mariculture area in the future.
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21
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Long-Term Phytoremediation of Coastal Saline Soil Reveals Plant Species-Specific Patterns of Microbial Community Recruitment. mSystems 2020; 5:5/2/e00741-19. [PMID: 32127422 PMCID: PMC7055657 DOI: 10.1128/msystems.00741-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Soil salinization is one of the major land degradation processes that decreases soil fertility and crop production worldwide. In this study, a long-term coastal saline soil remediation experiment was conducted with three salt-tolerant plant species: Lycium chinense Mill. (LCM), Tamarix chinensis Lour. (TCL), and Gossypium hirsutum Linn. (GHL). The three plant species successfully remediated the saline soil but showed different efficacies. The archaeal, bacterial, and fungal communities in barren soil and in four rhizocompartments (distal-rhizosphere soil, proximal-rhizosphere soil, rhizoplane, and endosphere) of the three plant species were assessed. All three plant species significantly decreased the richness of the archaeal communities but increased that of the bacterial and fungal communities in both the rhizosphere and rhizoplane compared with those in the barren soil. The archaeal and bacterial community structures were strongly influenced by the rhizocompartment, while specific fungal communities were recruited by different plant species. The microbial taxa whose abundance either increased or decreased significantly during remediation were identified. Soil electrical conductivity (EC) was identified as the main factor driving the variation in microbial community composition between the remediated and barren soil, and total nitrogen (TN), total carbon (TC), and available potassium (AK) were the main factors driving the differences among plant species. This report provides new insights into the responses of the root zone microbial communities of different salt-tolerant plant species during phytoremediation.IMPORTANCE Despite knowing that phytoremediation by salt-tolerant plants is an effective technology for ameliorating saline soils and that microorganisms contribute significantly to plant stress tolerance and soil fertility, we still lack a comprehensive understanding of how microbes respond to the growth of salt-tolerant plants and the subsequent decline in soil salinity. The results of this study revealed different response patterns among bacterial, archaeal, and fungal communities and indicated that the decline in archaeal abundance might be a sign of successful remediation of coastal saline soils. The recruitment of specific fungal communities by different plant species indicated the importance of fungi in plant species-specific remediation functions. We also identified the taxa that may play key roles during remediation, and these taxa could potentially be used as indicators of phytoremediation. Overall, these findings highlight the importance of microbes in the phytoremediation of saline soil and suggest that the mechanisms involved are plant species specific.
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22
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Tang BL, Yang J, Chen XL, Wang P, Zhao HL, Su HN, Li CY, Yu Y, Zhong S, Wang L, Lidbury I, Ding H, Wang M, McMinn A, Zhang XY, Chen Y, Zhang YZ. A predator-prey interaction between a marine Pseudoalteromonas sp. and Gram-positive bacteria. Nat Commun 2020; 11:285. [PMID: 31941905 PMCID: PMC6962226 DOI: 10.1038/s41467-019-14133-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/13/2019] [Indexed: 12/23/2022] Open
Abstract
Predator-prey interactions play important roles in the cycling of marine organic matter. Here we show that a Gram-negative bacterium isolated from marine sediments (Pseudoalteromonas sp. strain CF6-2) can kill Gram-positive bacteria of diverse peptidoglycan (PG) chemotypes by secreting the metalloprotease pseudoalterin. Secretion of the enzyme requires a Type II secretion system. Pseudoalterin binds to the glycan strands of Gram positive bacterial PG and degrades the PG peptide chains, leading to cell death. The released nutrients, including PG-derived D-amino acids, can then be utilized by strain CF6-2 for growth. Pseudoalterin synthesis is induced by PG degradation products such as glycine and glycine-rich oligopeptides. Genes encoding putative pseudoalterin-like proteins are found in many other marine bacteria. This study reveals a new microbial interaction in the ocean. Predator-prey interactions play important roles in the cycling of marine organic matter. Here the authors show that a Gram-negative bacterium isolated from marine sediments can kill and feed on Gram-positive bacteria by secreting a peptidoglycan-degrading enzyme.
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Affiliation(s)
- Bai-Lu Tang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Jie Yang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Peng Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China.,College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China
| | - Hui-Lin Zhao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Hai-Nan Su
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Chun-Yang Li
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266373, China
| | - Yang Yu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Shuai Zhong
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Lei Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Ian Lidbury
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Haitao Ding
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, 200136, China
| | - Min Wang
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China
| | - Andrew McMinn
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Yin Chen
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China.,School of Life Sciences, University of Warwick, Coventry, UK
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China. .,College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China. .,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266373, China.
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