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Yang M, Zhao L, Yu X, Shu W, Cao F, Liu Q, Liu M, Wang J, Jiang Y. Microbial community structure and co-occurrence network stability in seawater and microplastic biofilms under prometryn pollution in marine ecosystems. MARINE POLLUTION BULLETIN 2024; 199:115960. [PMID: 38159383 DOI: 10.1016/j.marpolbul.2023.115960] [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: 10/06/2023] [Revised: 11/20/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Abstract
Prometryn has been extensively detected in marine environment because of its widespread usage in agriculture and aquaculture and has been concerns since its serious effects on aquatic organisms. However, its impact on the microbial community in the marine ecosystem including seawater and biofilm is still unclear. Therefore, a short-term indoor microcosm experiment of prometryn exposure was conducted. This study found that prometryn had a more significant impact on the structure and stability of the microbial community in seawater compared to microplastic biofilms. Additionally, we observed that the assembly of the microbial community in biofilms was more affected by stochastic processes than in seawater under the exposure of prometryn. Our study provided evidence for the increasing impact of the microbial communities under the stress of prometryn and microplastics.
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Affiliation(s)
- Mengyao Yang
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Lingchao Zhao
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Xiaowen Yu
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Wangxinze Shu
- Fisheries College, Ocean University of China, Qingdao 266003, China
| | - Furong Cao
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Qian Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Mingjian Liu
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; MoE Key Laboratory of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Jun Wang
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yong Jiang
- College of Marine Life Sciences & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; MoE Key Laboratory of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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2
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Chen C, Li P, Yin M, Wang J, Sun Y, Ju W, Liu L, Li ZH. Deciphering characterization of seasonal variations in microbial communities of marine ranching: Diversity, co-occurrence network patterns, and assembly processes. MARINE POLLUTION BULLETIN 2023; 197:115739. [PMID: 37925991 DOI: 10.1016/j.marpolbul.2023.115739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/25/2023] [Accepted: 10/30/2023] [Indexed: 11/07/2023]
Abstract
Offshore coastal marine ranching ecosystems are one of the most productive ecosystems. The results showed that the composition and structure of the microbial communities varied considerably with the season. Co-occurrence network analysis demonstrated that the microbial network was more complex in summer and positively correlated links (cooperative or symbiotic) were dominated in autumn and winter. Null model indicated that the ecological processes of the bacterial communities were mainly governed by deterministic processes (mainly homogeneous selection) in summer. For microeukaryotic communities, assembly processes were more regulated by stochastic processes in all seasons. For rare taxa, assembly processes were regulated by stochastic processes and were not affected by seasonality. Changes in water temperature due to seasonal variations were the main, but not the only, environmental factor driving changes in microbial communities. This study will improve the understanding of offshore coastal ecosystems through the perspective of microbial ecology.
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Affiliation(s)
- Chengzhuang Chen
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Ping Li
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Minghao Yin
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Jinxin Wang
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Yongjun Sun
- Homey Group Co. Ltd, Rongcheng, Shandong 264306, China
| | - Wenming Ju
- Homey Group Co. Ltd, Rongcheng, Shandong 264306, China
| | - Ling Liu
- Marine College, Shandong University, Weihai, Shandong 264209, China
| | - Zhi-Hua Li
- Marine College, Shandong University, Weihai, Shandong 264209, China.
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3
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Zhang T, Zhou K, Wang Y, Xu J, Zheng Q, Luo T, Jiao N. Genomic insights into the adaptation of Synechococcus to the coastal environment on Xiamen. Front Microbiol 2023; 14:1292150. [PMID: 38059125 PMCID: PMC10696648 DOI: 10.3389/fmicb.2023.1292150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/01/2023] [Indexed: 12/08/2023] Open
Abstract
Synechococcus are widely distributed in the global ocean, from the pelagic zone to coastal waters. However, little is known about Synechococcus in coastal seawater due to limitations in isolation and culture conditions. In this study, a combination of metagenomic sequencing technology, flow cytometry sorting, and multiple displacement amplification was used to investigate Synechococcus in the coastal seawater of Xiamen Island. The results revealed 18 clades of Synechococcus and diverse metabolic genes that appear to contribute to their adaptation to the coastal environment. Intriguingly, some metabolic genes related to the metabolism of carbohydrates, energy, nucleotides, and amino acids were found in 89 prophage regions that were detected in 16,258 Synechococcus sequences. The detected metabolic genes can enable prophages to contribute to the adaptation of Synechococcus hosts to the coastal marine environment. The detection of prophages also suggests that the cyanophages have infected Synechococcus. On the other hand, the identification of 773 genes associated with antiviral defense systems indicates that Synechococcus in Xiamen have evolved genetic traits in response to cyanophage infection. Studying the community diversity and functional genes of Synechococcus provides insights into their role in environmental adaptation and marine ecosystems.
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Affiliation(s)
- Ting Zhang
- Fujian Key Laboratory of Marine Carbon Sequestration, Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, Fujian, China
| | - Kun Zhou
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
| | - Yanhui Wang
- Fujian Key Laboratory of Marine Carbon Sequestration, Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, Fujian, China
| | - Jinxin Xu
- Fujian Key Laboratory of Marine Carbon Sequestration, Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, Fujian, China
| | - Qiang Zheng
- Fujian Key Laboratory of Marine Carbon Sequestration, Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, Fujian, China
| | - Tingwei Luo
- Fujian Key Laboratory of Marine Carbon Sequestration, Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, Fujian, China
| | - Nianzhi Jiao
- Fujian Key Laboratory of Marine Carbon Sequestration, Carbon Neutral Innovation Research Center, Xiamen University, Xiamen, Fujian, China
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4
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Zhao H, Yang S, Qin X, Huang J, Huang H, Li W, Jiang G, Tang J, Dong K, Li N. Disentangling the Ecological Processes and Driving Forces Shaping the Seasonal Pattern of Halobacteriovorax Communities in a Subtropical Estuary. MICROBIAL ECOLOGY 2023; 86:1881-1892. [PMID: 36799977 DOI: 10.1007/s00248-023-02195-w] [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: 10/25/2022] [Accepted: 02/11/2023] [Indexed: 06/18/2023]
Abstract
Halobacteriovorax are predatory bacteria that have a significant ecological role in marine environments. However, understanding of dynamics of populations, driving forces, and community composition of Halobacteriovorax groups in natural marine environments is still limited. Here, we used high-throughput sequencing to study the underlying mechanisms governing the diversity and assembly of the Halobacteriovorax community at spatiotemporal scales in a subtropical estuary. Phylogenetic analysis showed that 10 of 15 known Halobacteriovorax clusters were found in the studied estuary. Halobacteriovorax α-diversity and β-diversity exhibited significant seasonal variation. Variation partitioning analysis showed that the effect of nutrients was greater than that of other measured water properties on Halobacteriovorax community distribution. The results of Spearman's and Mantel's tests indicated that the trophic pollutants dissolved inorganic phosphorus (DIP) and NH4+-N in the estuary were the key factors that significantly affected Halobacteriovorax species and community diversity. In addition, this work indicated that the biological stoichiometry (especially N/P) of nutrients exerted a significant influence on the Halobacteriovorax community. Furthermore, we found that both deterministic and stochastic processes contributed to the turnover of Halobacteriovorax communities, and environmental filtering dominated the assembly of estuarine Halobacteriovorax communities. Overall, we provide new insights into the mechanisms in the generation and maintenance of the Halobacteriovorax community in marine environments.
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Affiliation(s)
- Huaxian Zhao
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, 530001, China
| | - Shu Yang
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, 530001, China
| | - Xinyi Qin
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, 530001, China
| | - Jiongqing Huang
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, 530001, China
| | - Haifeng Huang
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, 530001, China
| | - Wenjing Li
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, 530001, China
| | - Gonglingxia Jiang
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, 530001, China
| | - Jinli Tang
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, 530001, China
| | - Ke Dong
- Department of Biological Sciences, Kyonggi University, 154-42, Gwanggyosan-ro, Yeongtong-gu Gyeonggi-do, Suwon-si, 16227, South Korea
| | - Nan Li
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, 530001, China.
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Airborne Prokaryotic, Fungal and Eukaryotic Communities of an Urban Environment in the UK. ATMOSPHERE 2022. [DOI: 10.3390/atmos13081212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Bioaerosols often contain human pathogens and allergens affecting public health. However, relatively little attention has been given to bioaerosols compared with non-biological aerosols. In this study, we aimed to identify bioaerosol compositions in Manchester, UK by applying high throughput sequencing methods and to find potential sources. Samples were collected at Manchester Air Quality Super Site at the Firs Environmental Research Station in November 2019 and in February 2020. Total DNA has been extracted and sequenced targeting the 16S rRNA gene of prokaryotes, ITS region of fungal DNA and 18S rRNA gene of eukaryotes. We found marine environment-associated bacteria and archaea were relatively more abundant in the February 2020 samples compared with the November 2019 samples, consistent with the North West marine origin based on wind back-trajectory analysis. In contrast, an OTU belonging to Methylobacterium, which includes many species resistant to heavy metals, was relatively more abundant in November 2019 when there were higher metal concentrations. Fungal taxa that fruit all year were relatively more abundant in the February 2020 samples while autumn fruiting species generally had higher relative abundance in the November 2019 samples. There were higher relative abundances of land plants and algae in the February 2020 samples based on 18S rRNA gene sequencing. One of the OTUs belonging to the coniferous yew genus Taxus was more abundant in the February 2020 samples agreeing with the usual pollen season of yews in the UK which is from mid-January until late April. The result from this study suggests a potential application of bioaerosol profiling for tracing the source of atmospheric particles.
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Giraud C, Callac N, Boulo V, Lam JS, Pham D, Selmaoui-Folcher N, Wabete N. The Active Microbiota of the Eggs and the Nauplii of the Pacific Blue Shrimp Litopenaeus stylirostris Partially Shaped by a Potential Vertical Transmission. Front Microbiol 2022; 13:886752. [PMID: 35633721 PMCID: PMC9133551 DOI: 10.3389/fmicb.2022.886752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
The many ecological niches present in an organism harbor distinct microorganisms called microbiota. Different factors can influence the establishment of these commensal microbial communities. In a previous article, we have concluded that some bacterial lineages associated with the early larval stages of the Pacific blue shrimp Litopenaeus stylirostris could be acquired from the breeders via a potential vertical transmission. The present study was conducted in order to investigate this hypothesis. Using HiSeq sequencing of the V4 region of 16S rRNA gene, we analyzed the active microbiota associated with the eggs and the nauplii of L. stylirsotris as well as with the reproductive organs of their breeders. Microbial communities associated with the rearing water were also considered to discriminate environmental microbial lineages. Using these analyses, we highlight a set of core bacterial families present in all samples and composed of members of Colwelliaceae, Alteromonadaceae, Pseudoalteromonadaceae, Saccharospirillaceae, Oceanospirillaceae, Vibrionaceae, Burkholderiaceae, Rhodobacteraceae, Flavobacteraceae, and Corynebacteriaceae; showing the importance of the environment in the establishment of the larval microbiota. We also present specific bacteria affiliated to the Arcobacteraceae, Rhodobacteraceae, Comamonadaceae, and Colwelliaceae families, which were only found in the breeders and their offspring strengthening the hypothesis of a potential vertical transmission shaping the active microbiota of the eggs and the nauplii of L. stylirostris.
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Affiliation(s)
- Carolane Giraud
- UMR 9220 ENTROPIE, Ifremer (LEAD-NC), Noumea, New Caledonia
- Institut des Sciences Exactes et Appliquées (ISEA), University of New Caledonia, Noumea, New Caledonia
- *Correspondence: Carolane Giraud,
| | - Nolwenn Callac
- UMR 9220 ENTROPIE, Ifremer (LEAD-NC), Noumea, New Caledonia
- Nolwenn Callac,
| | - Viviane Boulo
- UMR 9220 ENTROPIE, Ifremer (LEAD-NC), Noumea, New Caledonia
| | | | - Dominique Pham
- UMR 9220 ENTROPIE, Ifremer (LEAD-NC), Noumea, New Caledonia
| | - Nazha Selmaoui-Folcher
- Institut des Sciences Exactes et Appliquées (ISEA), University of New Caledonia, Noumea, New Caledonia
| | - Nelly Wabete
- UMR 9220 ENTROPIE, Ifremer (LEAD-NC), Noumea, New Caledonia
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Wang Y, Xie R, Shen Y, Cai R, He C, Chen Q, Guo W, Shi Q, Jiao N, Zheng Q. Linking Microbial Population Succession and DOM Molecular Changes in Synechococcus-Derived Organic Matter Addition Incubation. Microbiol Spectr 2022; 10:e0230821. [PMID: 35380472 PMCID: PMC9045170 DOI: 10.1128/spectrum.02308-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/10/2022] [Indexed: 12/04/2022] Open
Abstract
The molecular-level interactions between phytoplankton-derived dissolved organic matter (DOM) and heterotrophic prokaryotes represent a fundamental and yet poorly understood component of the marine elemental cycle. Here, we investigated the degradation of Synechococcus-derived organic matter (SynOM) by coastal microorganisms using spectroscopic and ultrahigh-resolution mass spectrometry analyses coupled with high-throughput sequencing. The added SynOM showed a spectrum of reactivity during a 180-day dark incubation experiment. Along with the decrease in DOM bioavailability, the chemical properties of DOM molecules overall showed increases in oxidation state and aromaticity. Both the microbial community and DOM molecular compositions became more homogeneous toward the end of the incubation. The experiment was partitioned into three phases (I, II, and III) based on the total organic carbon consumption rates from 7.0 ± 1.0 to 1.0 ± 0.1 and to 0.1 ± 0.0 μmol C L-1 day-1, respectively. Diverse generalists with low abundance were present in all three phases of the experiment, while a few abundant specialists dominated specific phases, suggesting their diverse roles in the transformation of DOM molecules from labile and semilabile to recalcitrant. The changes of organic molecules belonging to CHO, CHNO, and CHOS containing formulas were closely associated with specific microbial populations, suggesting close interactions between the different bacterial metabolic potential for substrates and DOM molecular compositional characteristics. This study sheds light on the interactions between microbial population succession and DOM molecular changes processes and collectively advances our understanding of microbial processing of the marine elemental cycle. IMPORTANCE Phytoplankton are a major contributor of labile dissolved organic matter (DOM) in the upper ocean, fueling tremendous marine prokaryotic activity. Interactions between microorganisms and algae-derived DOM regulate biogeochemical cycles in the ocean, but key aspects of their interactions remain poorly understood. Under global warming and eutrophication scenarios, Synechococcus blooms are commonly observed in coastal seawaters, and they significantly influence the elemental biogeochemistry cycling in eutrophic ecosystems. To understand the interactions between Synechococcus-derived DOM and heterotrophic prokaryotes as well as their influence on the coastal environment, we investigated the degradation of DOM by coastal microbes during a 180-day dark incubation. We showed substantial DOM compositional changes that were closely linked to the developments of microbial specialists and generalists. Our study provides information on the interactions between microbial population succession and DOM molecular changes, thereby advancing our understanding of microbial processing of the marine DOM pool under the influence of climate change.
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Affiliation(s)
- Yu Wang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Rui Xie
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Yuan Shen
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Ruanhong Cai
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, China
| | - Qi Chen
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Weidong Guo
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Key Laboratory of Coastal and Wetland Ecosystems, Ministry of Education, Xiamen University, Xiamen, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, China
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Qiang Zheng
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
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Lian J, Steinert G, de Vree J, Meijer S, Heryanto C, Bosma R, Wijffels RH, Barbosa MJ, Smidt H, Sipkema D. Bacterial diversity in different outdoor pilot plant photobioreactor types during production of the microalga Nannochloropsis sp. CCAP211/78. Appl Microbiol Biotechnol 2022; 106:2235-2248. [PMID: 35166894 PMCID: PMC8930801 DOI: 10.1007/s00253-022-11815-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 12/22/2021] [Accepted: 01/29/2022] [Indexed: 11/25/2022]
Abstract
As large-scale outdoor production cannot be done in complete containment, cultures are (more) open for bacteria, which may affect the productivity and stability of the algae production process. We investigated the bacterial diversity in two indoor reactors and four pilot-scale outdoor reactors for the production of Nannochloropsis sp. CCAP211/78 spanning four months of operation from July to October. Illumina sequencing of 16S rRNA gene amplicons demonstrated that a wide variety of bacteria were present in all reactor types, with predominance of Bacteroidetes and Alphaproteobacteria. Bacterial communities were significantly different between all reactor types (except between the horizontal tubular reactor and the vertical tubular reactor) and also between runs in each reactor. Bacteria common to the majority of samples included one member of the Saprospiraceae family and one of the NS11-12_marine group (both Bacteroidetes). Hierarchical clustering analysis revealed two phases during the cultivation period separated by a major shift in bacterial community composition in the horizontal tubular reactor, the vertical tubular reactor and the raceway pond with a strong decrease of the Saprospiraceae and NS11-12_marine group that initially dominated the bacterial communities. Furthermore, we observed a less consistent pattern of bacterial taxa appearing in different reactors and runs, most of which belonging to the classes Deltaproteobacteria and Flavobacteriia. In addition, canonical correspondence analysis showed that the bacterial community composition was significantly correlated with the nitrate concentration. This study contributes to our understanding of bacterial diversity and composition in different types of outdoor reactors exposed to a range of dynamic biotic and abiotic factors. Key points • Reactor types had significantly different bacterial communities except HT and VT • The inoculum source and physiochemical factors together affect bacterial community • The bacterial family Saprospiraceae is positively correlated to microalgal growth.
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Affiliation(s)
- Jie Lian
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Georg Steinert
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Jeroen de Vree
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Sven Meijer
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Christa Heryanto
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Rouke Bosma
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - René H Wijffels
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
- Faculty of Biosciences and Aquaculture, Nord University, N8049, Bodø, Norway
| | - Maria J Barbosa
- Bioprocess Engineering, AlgaePARC, Wageningen University & Research, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
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9
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Gu B, Huang H, Zhang Y, Li R, Wang L, Wang Y, Sun J, Wang J, Zhang R, Jiao N, Xu D. High Dynamics of Ciliate Community Revealed via Short-Term, High-Frequency Sampling in a Subtropical Estuarine Ecosystem. Front Microbiol 2022; 13:797638. [PMID: 35197950 PMCID: PMC8858835 DOI: 10.3389/fmicb.2022.797638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/13/2022] [Indexed: 11/13/2022] Open
Abstract
Ciliates are pivotal components of the marine microbial food web, exerting profound impacts on oceanic biogeochemical cycling. However, the temporal dynamics of ciliate assemblages on a short time scale in the highly fluctuating estuarine ecosystem remain largely unexplored. We studied changes in the ciliate community during a short time frame in the high salinity waters (>26) of a subtropical estuary. Ciliate abundance, biomass, size and oral diameter structure, and community composition fluctuated considerably and irregularly over a few days or even a few hours. Spearman correlations and the generalized linear model revealed that heterotrophic prokaryotes (HPs) and viral abundances drove the dynamics of ciliate abundance and biomass. The structural equation model further identified a major path from the high-fluorescence content virus (HFV) to HPs and then ciliates. Given the substantial correlation between salinity and HPs/HFV, we proposed that the response of HPs and HFV to salinity drives the dynamics of ciliate biomass. Additionally, the Mantel test showed that phytoplankton pigments such as Lutein and Neoxanthin, phosphate, and pigmented picoeukaryotes were key covariates of the ciliate community composition. This study demonstrated the highly changing patterns of ciliate assemblages and identified potential processes regulating ciliate biomass and community composition on short timescales in a subtropical, hydrographically complex estuary.
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Affiliation(s)
- Bowei Gu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Hungchia Huang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Yizhe Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Ran Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Lei Wang
- College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Ying Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Jia Sun
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Jianning Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
- *Correspondence: Dapeng Xu,
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10
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Yang Y, Zhang F, Chen X, Li H, Jiao N, Zhang R. Insignificant Response of Bacterioplankton Community to Elevated pCO 2 During a Short-Term Microcosm Experiment in a Subtropical Eutrophic Coastal Ecosystem. Front Microbiol 2021; 12:730377. [PMID: 34867847 PMCID: PMC8633418 DOI: 10.3389/fmicb.2021.730377] [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: 06/24/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
Ocean acidification, as one of the major consequences of global climate change, markedly affects multiple ecosystem functions in disparate marine environments from coastal habitats to the deep ocean. Evaluation of the responses of marine microbial community to the increasing partial pressure of CO2 (pCO2) is crucial to explore the microbe-driven biogeochemical processes in the future ocean. In this study, a microcosm incubation of eutrophic coastal water from Xiamen Bay under elevated pCO2 (about 1,000 μatm) and control (ambient air, about 380-410 μatm) conditions was conducted to investigate the effect of ocean acidification on the natural bacterioplankton community. During the 5-day incubation period, the chlorophyll a concentration and bacterioplankton abundance were not significantly affected by increased pCO2. Hierarchical clustering and non-metric multidimensional scaling analysis based on Bray-Curtis similarity among the bacterioplankton community derived from the 16S rRNA genes revealed an inconspicuous impact of elevated pCO2 on the bacterial community. During the incubation period, Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, and Epsilonbacteraeota were predominant in all microcosms. Despite the distinct temporal variation in the composition of the bacterioplankton community during the experimental period, statistical analyses showed that no significant difference was found on bacterioplankton taxa between elevated pCO2 and control, indicating that the bacterioplankton at the population-level were also insensitive to elevated pCO2. Our results therefore suggest that the bacterioplankton communities in the fluctuating and eutrophic coastal ecosystems appear to be adaptable to the short-term elevated pCO2.
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Affiliation(s)
- Yunlan Yang
- College of the Environment and Ecology, Xiamen University, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Fei Zhang
- College of the Environment and Ecology, Xiamen University, Xiamen, China.,Laboratory of Marine Biology and Ecology, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, China
| | - Xiaowei Chen
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Huifang Li
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
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11
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Chen Q, Chen F, Gonsior M, Li Y, Wang Y, He C, Cai R, Xu J, Wang Y, Xu D, Sun J, Zhang T, Shi Q, Jiao N, Zheng Q. Correspondence between DOM molecules and microbial community in a subtropical coastal estuary on a spatiotemporal scale. ENVIRONMENT INTERNATIONAL 2021; 154:106558. [PMID: 33878614 DOI: 10.1016/j.envint.2021.106558] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 03/09/2021] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
Dissolved organic matter (DOM) changes in quantity and quality over time and space, especially in highly dynamic coastal estuaries. Bacterioplankton usually display seasonal and spatial variations in abundance and composition in the coastal regions, and influence the DOM pool via assimilation, transformation and release of organic molecules. The change in DOM can also affect the composition of bacterial community. However, little is known on the correspondence between DOM molecules and bacterial composition, particularly through a systematic field survey. In this study, the spatiotemporal signatures of microbial communities and DOM composition in the subtropical coastal estuary of Xiamen are investigated over one and half years. The co-occurrence analysis between bacteria and DOM suggested microorganisms likely transformed the DOM from a relatively high (>400 Da) to a low (<400 Da) molecular weight, corresponding to an apparent increase in overall aromaticity. This might be the reason why microbial transformation renders "dark" organic matter visible in mass spectrometry due to more efficient ionization of microbial metabolites, as well as photodegradation processes. K- and r-strategists exhibited different correlations with two-size categories of DOM molecules owing to their different lifestyles and responses to environmental nutrient conditions. A comparison of the environmental variables and DOM composition with the microbial communities showed that the environmental/DOM variations played a more important role in shaping the microbial communities than vice versa. This study sheds light on the interactions between microbial populations and DOM molecules at the spatiotemporal scale, improving our understanding of microbial roles in marine biogeochemical cycles.
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Affiliation(s)
- Qi Chen
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, 701 East Pratt Street, Baltimore, MD 21202, United States
| | - Michael Gonsior
- Chesapeake Biological Laboratory, University of Maryland Center for Environmental Science, 146 Williams Street, Solomons, MD 20688, United States
| | - Yunyun Li
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, 18 Fuxue Road, Changping District, Beijing 102249, China
| | - Yu Wang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, 18 Fuxue Road, Changping District, Beijing 102249, China
| | - Ruanhong Cai
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China
| | - Jinxin Xu
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China
| | - Yimeng Wang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China
| | - Dapeng Xu
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China
| | - Jia Sun
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China
| | - Ting Zhang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, 18 Fuxue Road, Changping District, Beijing 102249, China
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China
| | - Qiang Zheng
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China.
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12
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Zampieri A, Babbucci M, Carraro L, Milan M, Fasolato L, Cardazzo B. Combining Culture-Dependent and Culture-Independent Methods: New Methodology Insight on the Vibrio Community of Ruditapes philippinarum. Foods 2021; 10:1271. [PMID: 34204939 PMCID: PMC8228196 DOI: 10.3390/foods10061271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 05/30/2021] [Accepted: 05/31/2021] [Indexed: 01/01/2023] Open
Abstract
Vibrios represent a natural contaminant of seafood products. V. alginolyticus, V. cholerae, V. parahaemolyticus and V. vulnificus are the most hazardous species to human health. Given the worldwide consumption of mollusc products, reliable detection of Vibrio species is recommended to prevent human vibriosis. In this study, culture-dependent and -independent methods were compared and integrated to implement knowledge of the Manila clam Vibrio community composition. Here, 16S and recA-pyrH metabarcoding were applied to compare the microbial communities of homogenate clam samples (culture-independent method) and their culture-derived samples plated on three different media (culture-dependent method). In addition, a subset of plated clam samples was investigated using shotgun metagenomics. Homogenate metabarcoding characterized the most abundant taxa (16S) and Vibrio species (recA-pyrH). Culture-dependent metabarcoding detected the cultivable taxa, including rare species. Moreover, marine agar medium was found to be a useful substrate for the recovery of several Vibrio species, including the main human pathogenic ones. The culture-dependent shotgun metagenomics detected all the main human pathogenic Vibrio species and a higher number of vibrios with respect to the recA-pyrH metabarcoding. The study revealed that integration of culture-dependent and culture-independent methods might be a valid approach for the characterization of Vibrio biodiversity.
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Affiliation(s)
| | | | | | | | - Luca Fasolato
- Department of Comparative Biomedicine and Food Science, University of Padova, Agripolis, Viale dell’Università 16, 35020 Legnaro, Italy; (A.Z.); (M.B.); (L.C.); (M.M.); (B.C.)
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13
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Li N, Chen X, Zhao H, Tang J, Jiang G, Li Z, Li X, Chen S, Zou S, Dong K, Xu Q. Spatial distribution and functional profile of the bacterial community in response to eutrophication in the subtropical Beibu Gulf, China. MARINE POLLUTION BULLETIN 2020; 161:111742. [PMID: 33075697 DOI: 10.1016/j.marpolbul.2020.111742] [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: 07/17/2020] [Revised: 09/25/2020] [Accepted: 10/04/2020] [Indexed: 05/25/2023]
Abstract
In this study, we investigated the specific bacterial distribution and the response of bacterial communities to shifts in environmental factors in the subtropical Beibu Gulf, southern China. The abundances of Actinobacteria, Bacilli, Planctomycetia, Thermoleophilia, Anaerolineae, and Synechococcophycideae were significantly higher in high eutrophic samples than in medium eutrophic and oligotrophic samples. Bacterial alpha-diversity was found greater in high eutrophication samples than in the other samples. Besides, Ponticaulis koreensis, Nautella italic, Anaerospora hongkongensis, Candidatus Aquiluna rubra, and Roseovarius pacificus were sensitive to trophic variation and thus could be used as eco-markers. In addition, the relative abundances of functional genes involving carbohydrate and amino acid metabolism were very high among the samples. We also found temperature, Chl-a, TDN and NO3- were the main environmental drivers of bacterial community structure. Overall, this study provides new insight into the composition of bacterial community and function response to gradients of eutrophication in Beibu Gulf.
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Affiliation(s)
- Nan Li
- Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, 175 East Mingxiu Road, Nanning 530001, Guangxi, People's Republic of China
| | - Xing Chen
- Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, 175 East Mingxiu Road, Nanning 530001, Guangxi, People's Republic of China; College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, People's Republic of China
| | - Huaxian Zhao
- Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, 175 East Mingxiu Road, Nanning 530001, Guangxi, People's Republic of China
| | - Jinli Tang
- Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, 175 East Mingxiu Road, Nanning 530001, Guangxi, People's Republic of China
| | - Gonglingxia Jiang
- Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, 175 East Mingxiu Road, Nanning 530001, Guangxi, People's Republic of China
| | - Zhuoting Li
- Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, 175 East Mingxiu Road, Nanning 530001, Guangxi, People's Republic of China
| | - Xiaoli Li
- Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, 175 East Mingxiu Road, Nanning 530001, Guangxi, People's Republic of China
| | - Si Chen
- College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, People's Republic of China
| | - Shuqi Zou
- Department of biological sciences, Kyonggi University, 154-42, Gwanggyosan-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, South Korea
| | - Ke Dong
- Department of biological sciences, Kyonggi University, 154-42, Gwanggyosan-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do 16227, South Korea
| | - Qiangsheng Xu
- Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, 175 East Mingxiu Road, Nanning 530001, Guangxi, People's Republic of China.
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14
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Xu W, Gong L, Yang S, Gao Y, Ma X, Xu L, Chen H, Luo Z. Spatiotemporal Dynamics of Vibrio Communities and Abundance in Dongshan Bay, South of China. Front Microbiol 2020; 11:575287. [PMID: 33324364 PMCID: PMC7726330 DOI: 10.3389/fmicb.2020.575287] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/27/2020] [Indexed: 01/22/2023] Open
Abstract
The Vibrio genus inhabit estuarine and marine ecosystem throughout the world and can cause severe infections in humans and animals. Previous studies have demonstrated the dynamics of Vibrio at both community and population levels and assessed the close relationship between environmental factors and Vibrio diversity and abundance, such as temperature, salinity, and dissolved oxygen. It is also generally believed that aquaculture is the fastest-growing food sector, which is also applying great environmental impacts on microbial communities in aquatic ecosystems. However, our understanding of the spatiotemporal quantification of Vibrio throughout the four seasons in the aquaculture zone and response to environmental factors remains poor. To explore the spatiotemporal distribution and abundance of the Vibrio community with their related environmental factors and detect the relationships among them, we collected 10 seawater sites spanning four seasons across the whole year in Dongshan Bay for investigating the Vibrio community dynamics. Marked differences in diversity and abundance of the Vibrio community were observed between seasons, which were mainly driven by temperature, dissolved oxygen, nitrate, and nitrite. qPCR analysis showed that Vibrio abundance was most abundant in the summer (5.37 × 106 copies/L), compared with the autumn (4.58 × 106 copies/L), spring (1.18 × 106 copies/L), and winter (1.55 × 104 copies/L). A total of 22 Vibrio operational taxonomic units (OTUs) and 28 species were identified by universal bacteria 16S rRNA gene and cultivation methods, with Vibrio fortis the dominant in these aquaculture areas. To summarize, our present study is one of the few studies to research the occurrence of Vibrio in marine aquaculture of South China, and the results indicate that Vibrio are widely distributed in aquaculture environment and that a further risk assessment is needed to be conducted.
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Affiliation(s)
- Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - LinFeng Gong
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Shuai Yang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Yuanhao Gao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Xiaowan Ma
- Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai, China
| | - Limei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Haisheng Chen
- Fishery Technology Promotion Station of Dongshan, Zhangzhou, China
| | - Zhuhua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.,Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, China.,School of Marine Sciences, Nanjing University of Information Science & Technology, Nanjing, China
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15
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Wang R, Zhang Z, Sun J, Jiao N. Differences in bioavailability of canonical and non-canonical D-amino acids for marine microbes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 733:139216. [PMID: 32454292 DOI: 10.1016/j.scitotenv.2020.139216] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/22/2020] [Accepted: 05/03/2020] [Indexed: 06/11/2023]
Abstract
Dissolved organic matter (DOM) accounts for >95% of total marine organic matter, and >95% of marine DOM is refractory to biodegradation. The recalcitrancy of DOM determines its residence time and thus is of great concern regarding to carbon sequestration in the ocean. However, the recalcitrancy of DOM not only varies among different compounds but also within different conformations of a same molecule such as L-amino acids (L-AAs) and D-amino acids (D-AAs). While the former is labile, the latter is refractory and used as a proxy for estimation of bacterial refractory DOM in the ocean. However, some D-AAs are also reported to be bioavailable. To clarify the controversy, we examined the bioavailability of two types of D-AAs: canonical D-AAs, which mainly present as bacterial cell wall components, and non-canonical D-AAs (NCDAAs), which are secreted by various bacteria as signaling molecules in bacterial physiology. Bioassay experiments were conducted with nine marine bacterial strains and a natural microbial community. D-AAs were poorly utilized by the strains as sole carbon or nitrogen sources compared with L-AAs, in addition, NCDAAs were barely used compared with canonical D-AAs. In comparison, the microbial community consumed all three canonical D-AAs (D-alanine, D-aspartic acid and D-glutamic acid) as efficiently as their corresponding L-AAs when supplied separately; however, L-AAs were preferentially used over D-AAs when both forms were provided simultaneously. Remarkably, two NCDAAs, D-methionine and D-leucine, were poorly utilized regardless of the presence of the L-enantiomers. It was found for the first time that NCDAAs are relatively more refractory than canonical D-AAs to microbial utilization. This novel recognition of difference in recalcitrancy between NCDAAs and canonical D-AAs lays the foundation for a better understanding of carbon cycling and more accurate estimation of carbon storage in the ocean.
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Affiliation(s)
- Rui Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China; Institute of Marine Microbes and Ecospheres, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, People's Republic of China
| | - Zilian Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China; Institute of Marine Microbes and Ecospheres, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, People's Republic of China.
| | - Jia Sun
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China; Institute of Marine Microbes and Ecospheres, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, People's Republic of China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, People's Republic of China; Institute of Marine Microbes and Ecospheres, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen 361102, People's Republic of China.
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16
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Liu Q, Jiang Y. Application of microbial network analysis to discriminate environmental heterogeneity in Fildes Peninsula, Antarctica. MARINE POLLUTION BULLETIN 2020; 156:111244. [PMID: 32510386 DOI: 10.1016/j.marpolbul.2020.111244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/26/2020] [Accepted: 05/04/2020] [Indexed: 06/11/2023]
Abstract
In order to determine the practicability of developing a protocol for bioassessing polar marine environment based on network analysis, microplankton communities and co-occurrence patterns at Ardley Cove and Great Wall Cove (King George Island, Antarctica) were studied in January 2016 through high-through sequencing. The spatial patterns and significant differences between community structures in two coves clearly reflect those in environmental heterogeneity. Moreover, both coves had their discriminated network structure and keystones. Then multivariate analyses to quantify the relationship between environmental variation and planktonic microbes response, give further evidence that nitrate and temperature, alone or in combination with other several parameters, structuring the communities respectively indeed. This study presents the first detailed description on co-occurrence networks between microbes and local environmental parameters in Antarctic coastal water. These findings suggest that co-occurrence networks based on planktonic microbes have the robust potential to assess environmental heterogeneity in polar marine ecosystem.
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Affiliation(s)
- Qian Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yong Jiang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Key Lab of Polar Oceanography and Global Ocean Change, Ocean University of China, Qingdao 266003, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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17
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Xie R, Wang Y, Chen Q, Guo W, Jiao N, Zheng Q. Coupling Between Carbon and Nitrogen Metabolic Processes Mediated by Coastal Microbes in Synechococcus-Derived Organic Matter Addition Incubations. Front Microbiol 2020; 11:1041. [PMID: 32523578 PMCID: PMC7261836 DOI: 10.3389/fmicb.2020.01041] [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: 02/07/2020] [Accepted: 04/27/2020] [Indexed: 11/20/2022] Open
Abstract
Phytoplankton are major contributors to labile organic matter in the upper ocean. Diverse heterotrophic bacteria successively metabolize these labile compounds and drive elemental biogeochemical cycling. We investigated the bioavailability of Synechococcus-derived organic matter (SOM) by estuarine and coastal microbes during 180-day dark incubations. Variations in organic carbon, inorganic nutrients, fluorescent dissolved organic matter (FDOM), and total/active microbial communities were monitored. The entire incubations could be partitioned into three phases (labeled I, II, and III) based on the total organic carbon (TOC) consumption rates of 6.38–7.01, 0.53–0.64, and 0.10–0.13 μmol C L–1 day–1, respectively. This corresponded with accumulation processes of NH4+, NO2–, and NO3–, respectively. One tryptophan-like (C1) and three humic-like (C2, C3, and C4) FDOM components were identified. The intensity variation of C1 followed bacterial growth activities, and C2, C3, and C4 displayed labile, semi-labile, and refractory DOM characteristics, respectively. Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and Actinobacteria dominated the quickly consumed process of SOM (phase I) coupled with a substantial amount of NH4+ generation. Thaumarchaeota became an abundant population with the highest activities in phase II, especially in the free-living size-fraction, and these organisms could perform chemoautotroph processes through the ammonia oxidation. Microbial populations frequently found in the dark ocean, even the deep sea, became abundant during phase III, in which Nitrospinae/Nitrospirae obtained energy through nitrite oxidation. Our results shed light on the transformation of different biological availability of organic carbon by coastal microorganisms which coupled with the regeneration of different form of inorganic nitrogen.
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Affiliation(s)
- Rui Xie
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Yu Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China.,College of Environment and Ecology, Xiamen University, Xiamen, China
| | - Qi Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Weidong Guo
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China.,Key Laboratory of Coastal and Wetland Ecosystems, Ministry of Education, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Qiang Zheng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China.,Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
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18
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Liu D, Zhang J, Lü C, Xia Y, Liu H, Jiao N, Xun L, Liu J. Synechococcus sp. Strain PCC7002 Uses Sulfide:Quinone Oxidoreductase To Detoxify Exogenous Sulfide and To Convert Endogenous Sulfide to Cellular Sulfane Sulfur. mBio 2020; 11:e03420-19. [PMID: 32098824 PMCID: PMC7042703 DOI: 10.1128/mbio.03420-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 01/17/2020] [Indexed: 12/19/2022] Open
Abstract
Eutrophication and deoxygenation possibly occur in coastal waters due to excessive nutrients from agricultural and aquacultural activities, leading to sulfide accumulation. Cyanobacteria, as photosynthetic prokaryotes, play significant roles in carbon fixation in the ocean. Although some cyanobacteria can use sulfide as the electron donor for photosynthesis under anaerobic conditions, little is known on how they interact with sulfide under aerobic conditions. In this study, we report that Synechococcus sp. strain PCC7002 (PCC7002), harboring an sqr gene encoding sulfide:quinone oxidoreductase (SQR), oxidized self-produced sulfide to S0, present as persulfide and polysulfide in the cell. The Δsqr mutant contained less cellular S0 and had increased expression of key genes involved in photosynthesis, but it was less competitive than the wild type in cocultures. Further, PCC7002 with SQR and persulfide dioxygenase (PDO) oxidized exogenous sulfide to tolerate high sulfide levels. Thus, SQR offers some benefits to cyanobacteria even under aerobic conditions, explaining the common presence of SQR in cyanobacteria.IMPORTANCE Cyanobacteria are a major force for primary production via oxygenic photosynthesis in the ocean. A marine cyanobacterium, PCC7002, is actively involved in sulfide metabolism. It uses SQR to detoxify exogenous sulfide, enabling it to survive better than its Δsqr mutant in sulfide-rich environments. PCC7002 also uses SQR to oxidize endogenously generated sulfide to S0, which is required for the proper expression of key genes involved in photosynthesis. Thus, SQR has at least two physiological functions in PCC7002. The observation provides a new perspective for the interplays of C and S cycles.
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Affiliation(s)
- Daixi Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China
| | - Jiajie Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China
| | - Chuanjuan Lü
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yongzhen Xia
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Huaiwei Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Nianzhi Jiao
- Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China
- Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Luying Xun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- School of Molecular Biosciences, Washington State University, Pullman, Washington, USA
| | - Jihua Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China
- Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
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19
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Chen X, Ma R, Yang Y, Jiao N, Zhang R. Viral Regulation on Bacterial Community Impacted by Lysis-Lysogeny Switch: A Microcosm Experiment in Eutrophic Coastal Waters. Front Microbiol 2019; 10:1763. [PMID: 31417537 PMCID: PMC6685395 DOI: 10.3389/fmicb.2019.01763] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/16/2019] [Indexed: 11/13/2022] Open
Abstract
Marine viruses are major drivers of global biogeochemical cycles and energy fluxes, yet the importance of viral impacts on the succession and diversity of the bacterial community remains largely unexplored. Here, we explored viral life strategy and its potential effect on the bacterial community by experimental incubations of eutrophic coastal waters under lysogen-induced and non-induced treatments. The lysogen-induced treatment showed relatively constant viral and bacterial abundances, lytic and lysogenic viral production throughout the experimental period, together with the progressive declines in not only the relative abundances for SAR11, Rhodobacteraceae, Alteromonadaceae, and SAR86 but the bacterial community diversity. Conversely, the non-induced treatment observed the marked variation in the abundances of viruses, bacteria and cells with high nucleic acid content over the time course of incubation, which was congruent with the drastic shift in lytic and lysogenic viral production as well as the succession of bacterial community. Our results supported the hypotheses that a high level of lysogeny would occur with the increasing density of bacteria with rapid growth rate, which may contribute to a relatively lower host community diversity, whereas the lysogeny to lysis switching would fuel growth opportunities for less-active or initially rare bacterial taxa and generate a more diverse bacterial community. Altogether, the present study underscored the crucial regulatory role of the viral lysis-lysogeny pattern in bacterial community dynamics, composition and diversity, highlighting the viral impact on the microbial food web and biogeochemical processes.
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Affiliation(s)
- Xiaowei Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Ruijie Ma
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Yunlan Yang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China.,College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
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