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Yu T, Wu W, Liang W, Wang Y, Hou J, Chen Y, Elvert M, Hinrichs KU, Wang F. Anaerobic degradation of organic carbon supports uncultured microbial populations in estuarine sediments. MICROBIOME 2023; 11:81. [PMID: 37081504 PMCID: PMC10116835 DOI: 10.1186/s40168-023-01531-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND A large proportion of prokaryotic microbes in marine sediments remains uncultured, hindering our understanding of their ecological functions and metabolic features. Recent environmental metagenomic studies suggested that many of these uncultured microbes contribute to the degradation of organic matter, accompanied by acetogenesis, but the supporting experimental evidence is limited. RESULTS Estuarine sediments were incubated with different types of organic matters under anaerobic conditions, and the increase of uncultured bacterial populations was monitored. We found that (1) lignin stimulated the increase of uncultured bacteria within the class Dehalococcoidia. Their ability to metabolize lignin was further supported by the presence of genes associated with a nearly complete degradation pathway of phenolic monomers in the Dehalococcoidia metagenome-assembled genomes (MAGs). (2) The addition of cellulose stimulated the increase of bacteria in the phylum Ca. Fermentibacterota and family Fibrobacterales, a high copy number of genes encoding extracellular endoglucanase or/and 1,4-beta-cellobiosidase for cellulose decomposition and multiple sugar transporters were present in their MAGs. (3) Uncultured lineages in the order Bacteroidales and the family Leptospiraceae were enriched by the addition of casein and oleic acid, respectively, a high copy number of genes encoding extracellular peptidases, and the complete β-oxidation pathway were found in those MAGs of Bacteroidales and Leptospiraceae, respectively. (4) The growth of unclassified bacteria of the order Clostridiales was found after the addition of both casein and cellulose. Their MAGs contained multiple copies of genes for extracellular peptidases and endoglucanase. Additionally, 13C-labeled acetate was produced in the incubations when 13C-labeled dissolved inorganic carbon was provided. CONCLUSIONS Our results provide new insights into the roles of microorganisms during organic carbon degradation in anaerobic estuarine sediments and suggest that these macro and single molecular organic carbons support the persistence and increase of uncultivated bacteria. Acetogenesis is an additional important microbial process alongside organic carbon degradation. Video Abstract.
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Affiliation(s)
- Tiantian Yu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240, China
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Weichao Wu
- Organic Geochemistry Group, MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
- Faculty of Geosciences, University of Bremen, 28359, Bremen, Germany
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Wenyue Liang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jialin Hou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yunru Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Marcus Elvert
- Organic Geochemistry Group, MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
- Faculty of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
- Faculty of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Fengping Wang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240, China.
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Zhao J, Chakrabarti S, Chambers R, Weisenhorn P, Travieso R, Stumpf S, Standen E, Briceno H, Troxler T, Gaiser E, Kominoski J, Dhillon B, Martens-Habbena W. Year-around survey and manipulation experiments reveal differential sensitivities of soil prokaryotic and fungal communities to saltwater intrusion in Florida Everglades wetlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159865. [PMID: 36461566 DOI: 10.1016/j.scitotenv.2022.159865] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
Global sea-level rise is transforming coastal ecosystems, especially freshwater wetlands, in part due to increased episodic or chronic saltwater exposure, leading to shifts in biogeochemistry, plant- and microbial communities, as well as ecological services. Yet, it is still difficult to predict how soil microbial communities respond to the saltwater exposure because of poorly understood microbial sensitivity within complex wetland soil microbial communities, as well as the high spatial and temporal heterogeneity of wetland soils and saltwater exposure. To address this, we first conducted a two-year survey of microbial community structure and bottom water chemistry in submerged surface soils from 14 wetland sites across the Florida Everglades. We identified ecosystem-specific microbial biomarker taxa primarily associated with variation in salinity. Bacterial, archaeal and fungal community composition differed between freshwater, mangrove, and marine seagrass meadow sites, irrespective of soil type or season. Especially, methanogens, putative denitrifying methanotrophs and sulfate reducers shifted in relative abundance and/or composition between wetland types. Methanogens and putative denitrifying methanotrophs declined in relative abundance from freshwater to marine wetlands, whereas sulfate reducers showed the opposite trend. A four-year experimental simulation of saltwater intrusion in a pristine freshwater site and a previously saltwater-impacted site corroborated the highest sensitivity and relative increase of sulfate reducers, as well as taxon-specific sensitivity of methanogens, in response to continuously pulsing of saltwater treatment. Collectively, these results suggest that besides increased salinity, saltwater-mediated increased sulfate availability leads to displacement of methanogens by sulfate reducers even at low or temporal salt exposure. These changes of microbial composition could affect organic matter degradation pathways in coastal freshwater wetlands exposed to sea-level rise, with potential consequences, such as loss of stored soil organic carbon.
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Affiliation(s)
- Jun Zhao
- Fort Lauderdale Research and Education Center and Department of Microbiology & Cell Science, University of Florida, Davie, FL, USA
| | - Seemanti Chakrabarti
- Fort Lauderdale Research and Education Center and Department of Microbiology & Cell Science, University of Florida, Davie, FL, USA
| | - Randolph Chambers
- College of William and Mary, W.M. Keck Environmental Field Laboratory, P.O. Box 8795, Williamsburg, VA, USA
| | | | - Rafael Travieso
- Institute of Environment, Florida International University, Miami, FL, USA
| | - Sandro Stumpf
- Institute of Environment, Florida International University, Miami, FL, USA
| | - Emily Standen
- Institute of Environment, Florida International University, Miami, FL, USA
| | - Henry Briceno
- Department of Biological Sciences and Institute of Environment, Florida International University, Miami, FL, USA
| | - Tiffany Troxler
- Department of Earth and Environment and Sea Level Solutions Center in the Institute of Environment, Florida International University, Miami, FL, USA
| | - Evelyn Gaiser
- Department of Biological Sciences and Institute of Environment, Florida International University, Miami, FL, USA
| | - John Kominoski
- Department of Biological Sciences and Institute of Environment, Florida International University, Miami, FL, USA
| | - Braham Dhillon
- Fort Lauderdale Research and Education Center and Department of Plant Pathology, University of Florida, Davie, FL, USA
| | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center and Department of Microbiology & Cell Science, University of Florida, Davie, FL, USA.
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Torregrosa-Crespo J, Miralles-Robledillo JM, Bernabeu E, Pire C, Martínez-Espinosa RM. Denitrification in hypersaline and coastal environments. FEMS Microbiol Lett 2023; 370:fnad066. [PMID: 37422443 PMCID: PMC10423024 DOI: 10.1093/femsle/fnad066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/09/2023] [Accepted: 07/05/2023] [Indexed: 07/10/2023] Open
Abstract
As the association of denitrification with global warming and nitrogen removal from ecosystems has gained attention in recent decades, numerous studies have examined denitrification rates and the distribution of denitrifiers across different environments. In this minireview, reported studies focused on coastal saline environments, including estuaries, mangroves, and hypersaline ecosystems, have been analysed to identify the relationship between denitrification and saline gradients. The analyses of the literature and databases stated the direct effect of salinity on the distribution patterns of denitrifiers. However, few works do not support this hypothesis thus making this topic controversial. The specific mechanisms by which salinity influences denitrifier distribution are not fully understood. Nevertheless, several physical and chemical environmental parameters, in addition to salinity, have been shown to play a role in structuring the denitrifying microbial communities. The prevalence of nirS or nirK denitrifiers in ecosystems is a subject of debate in this work. In general terms, in mesohaline environments, the predominant nitrite reductase is NirS type and, NirK is found predominantly in hypersaline environments. Moreover, the approaches used by different researchers are quite different, resulting in a huge amount of unrelated information, making it difficult to establish comparative analysis. The main techniques used to analyse the distribution of denitrifying populations along salt gradients have been also discussed.
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Affiliation(s)
- Javier Torregrosa-Crespo
- Biochemistry and Molecular Biology, and Edaphology and Agricultural Chemistry Department, Faculty of Sciences, University of Alicante, Carretera San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Alicante, Spain
| | - Jose María Miralles-Robledillo
- Biochemistry and Molecular Biology, and Edaphology and Agricultural Chemistry Department, Faculty of Sciences, University of Alicante, Carretera San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Alicante, Spain
| | - Eric Bernabeu
- Biochemistry and Molecular Biology, and Edaphology and Agricultural Chemistry Department, Faculty of Sciences, University of Alicante, Carretera San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Alicante, Spain
| | - Carmen Pire
- Biochemistry and Molecular Biology, and Edaphology and Agricultural Chemistry Department, Faculty of Sciences, University of Alicante, Carretera San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef” (IMEM), University of Alicante, Carretera San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Alicante, Spain
| | - Rosa María Martínez-Espinosa
- Biochemistry and Molecular Biology, and Edaphology and Agricultural Chemistry Department, Faculty of Sciences, University of Alicante, Carretera San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef” (IMEM), University of Alicante, Carretera San Vicente del Raspeig s/n, 03690 San Vicente del Raspeig, Alicante, Spain
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Huang JN, Wen B, Miao L, Liu X, Li ZJ, Ma TF, Xu L, Gao JZ, Chen ZZ. Microplastics drive nitrification by enriching functional microorganisms in aquaculture pond waters. CHEMOSPHERE 2022; 309:136646. [PMID: 36183890 DOI: 10.1016/j.chemosphere.2022.136646] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 09/24/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
The plastisphere refers to biofilm formation on the microplastic (MP) surface, but its subsequent functions, especially driving the nitrogen biogeochemical cycle, are rarely studied. Here, MPs were incubated in the pelagic water and benthic water-sediment interface of an aquaculture pond, and the two corresponding microcosms amended with incubated plastisphere were simulated. The results showed decreased ammonia concentrations and increased nitrification rates in microcosms with either pelagic or benthic plastispheres. To uncover the possible mechanisms, the community structure and function of the plastisphere were investigated. As clarified by 16S rRNA, the community diversity of the pelagic plastisphere was significantly higher than that of the corresponding hydrosphere. Plastisphere communities, especially those incubated in pelagic water, were separated from the hydrosphere. Moreover, the abundance of Proteobacteria increased while the abundance of Cyanobacteria decreased in both plastispheres. Metagenome further revealed that the abundance of amoA and annotated Nitrososphaeraceae_archaeon and hao and affiliated Nitrosomonas_europaea, which contributed to ammonia oxidation to nitrite, was higher in the benthic plastisphere. Comparing the pelagic plastisphere with the corresponding hydrosphere, however, the abundance of nxrA and annotated Nitrobacter hamburgensis and nxrB and the affiliated Nitrospira moscoviensis, which are involved in nitrite oxidation, was more abundant in the plastisphere. These findings suggest that the plastisphere might selectively enrich functional microorganisms and genes in a habitat-dependent manner to promote nitrification in aquaculture ponds.
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Affiliation(s)
- Jun-Nan Huang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 201306, China
| | - Bin Wen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.
| | - Lin Miao
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 201306, China
| | - Xin Liu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 201306, China
| | - Zhong-Jun Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 201306, China
| | - Teng-Fei Ma
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 201306, China
| | - Lei Xu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 201306, China
| | - Jian-Zhong Gao
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Zai-Zhong Chen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.
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Du M, Zheng M, Liu A, Wang L, Pan X, Liu J, Ran X. Effects of emerging contaminants and heavy metals on variation in bacterial communities in estuarine sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 832:155118. [PMID: 35398136 DOI: 10.1016/j.scitotenv.2022.155118] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/19/2022] [Accepted: 04/04/2022] [Indexed: 06/14/2023]
Abstract
Emerging contaminants (ECs) and heavy metals (HMs) are universally present together in estuarine sediments; despite this, their effects on microbial communities have been widely studied separately, rather than in consort. In this study, the combined effects of ECs and HMs on microbial communities were investigated in sediments from 11 major river estuaries around the Bohai Sea, China. Proteobacteria, Bacteroidetes, and Firmicutes were the dominant phyla in the sediments. Using Shannon indices, total phosphorus and total organic carbon were shown to affect microbial community structure. Redundancy analysis of microbial variation implicated Cd and As as the greatest pollutants, followed by Mn, Fe, Zn and Cu; no impacts from galaxolide (HHCB) and tonalide (AHTN) were found. Correlation analysis demonstrated that the concentration of ECs increased the abundance of certain bacteria (e.g., Haliangium, Altererythrobacter, Gaiella and Erythrobacter), and therefore these can be used as potential contamination indicators. Shannon indices and Chao1 indices showed that there were differences in the richness and diversity of bacterial communities in the sediments of 11 rivers. The principal coordinate analysis displayed higher similarity of bacterial community composition in estuarine sediments in Liaoning province than other regions. The results can be used to predict changes in estuary ecosystems to maintain their ecological balance and health.
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Affiliation(s)
- Ming Du
- College of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China
| | - Minggang Zheng
- Marine Ecology Research Center, First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Aifeng Liu
- College of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China
| | - Ling Wang
- College of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China.
| | - Xin Pan
- College of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China
| | - Jun Liu
- Marine Ecology Research Center, First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Xiangbin Ran
- Marine Ecology Research Center, First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
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Fusi M, Booth JM, Marasco R, Merlino G, Garcias-Bonet N, Barozzi A, Garuglieri E, Mbobo T, Diele K, Duarte CM, Daffonchio D. Bioturbation Intensity Modifies the Sediment Microbiome and Biochemistry and Supports Plant Growth in an Arid Mangrove System. Microbiol Spectr 2022; 10:e0111722. [PMID: 35647697 PMCID: PMC9241789 DOI: 10.1128/spectrum.01117-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/06/2022] [Indexed: 01/04/2023] Open
Abstract
In intertidal systems, the type and role of interactions among sediment microorganisms, animals, plants and abiotic factors are complex and not well understood. Such interactions are known to promote nutrient provision and cycling, and their dynamics and relationships may be of particular importance in arid microtidal systems characterized by minimal nutrient input. Focusing on an arid mangrove ecosystem on the central Red Sea coast, we investigated the effect of crab bioturbation intensity (comparing natural and manipulated high levels of bioturbation intensity) on biogeochemistry and bacterial communities of mangrove sediments, and on growth performance of Avicennia marina, over a period of 16 months. Along with pronounced seasonal patterns with harsh summer conditions, in which high sediment salinity, sulfate and temperature, and absence of tidal flooding occur, sediment bacterial diversity and composition, sediment physicochemical conditions, and plant performance were significantly affected by crab bioturbation intensity. For instance, bioturbation intensity influenced components of nitrogen, carbon, and phosphate cycling, bacterial relative abundance (i.e., Bacteroidia, Proteobacteria and Rhodothermi) and their predicted functionality (i.e., chemoheterotrophy), likely resulting from enhanced metabolic activity of aerobic bacteria. The complex interactions among bacteria, animals, and sediment chemistry in this arid mangrove positively impact plant growth. We show that a comprehensive approach targeting multiple biological levels provides useful information on the ecological status of mangrove forests. IMPORTANCE Bioturbation is one of the most important processes that governs sediment biocenosis in intertidal systems. By facilitating oxygen penetration into anoxic layers, bioturbation alters the overall sediment biogeochemistry. Here, we investigate how high crab bioturbation intensity modifies the mangrove sediment bacterial community, which is the second largest component of mangrove sediment biomass and plays a significant role in major biogeochemical processes. We show that the increase in crab bioturbation intensity, by ameliorating the anoxic condition of mangrove sediment and promoting sediment bacterial diversity in favor of a beneficial bacterial microbiome, improves mangrove tree growth in arid environments. These findings have significant implications because they show how crabs, by farming the mangrove sediment, can enhance the overall capacity of the system to sustain mangrove growth, fighting climate change.
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Affiliation(s)
- Marco Fusi
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Centre for Conservation and Restoration Science, School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
| | - Jenny Marie Booth
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Coastal Research Group, Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
| | - Ramona Marasco
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Giuseppe Merlino
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Neus Garcias-Bonet
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Alan Barozzi
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Elisa Garuglieri
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Tumeka Mbobo
- National Research Foundation-South African Institute for Aquatic Biodiversity Institute, Makhanda, South Africa
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Cape Town, South Africa
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
| | - Karen Diele
- Centre for Conservation and Restoration Science, School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
| | - Carlos M. Duarte
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Daniele Daffonchio
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Pan Y, Li G, Su L, Zheng P, Wang Y, Shen Z, Chen Z, Han Q, Gong J. Seagrass Colonization Alters Diversity, Abundance, Taxonomic, and Functional Community Structure of Benthic Microbial Eukaryotes. Front Microbiol 2022; 13:901741. [PMID: 35770161 PMCID: PMC9234489 DOI: 10.3389/fmicb.2022.901741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/03/2022] [Indexed: 11/26/2022] Open
Abstract
Seagrass form high productive ecosystems in coastal environments. However, the effects of these coastal plants on the structure and function of the belowground eukaryotic microbiome remain elusive. In this study, we characterized the community of microbial eukaryotes (microeukaryotes) in both vegetated and unvegetated sediments using 18S rRNA gene amplicon sequencing and quantitative PCR. Analysis of sequencing data showed that the eelgrass (Zostera marina) colonization decreased the alpha diversity indices of benthic microeukaryotes. Apicomplexa represented an average of 83% of reads across all samples, with a higher proportion at the vegetated sites. The taxonomic community structure was significantly different between these two types of sediments, for which the concentration ofNH 4 + in sediment porewater and salinity could account. Phylogenetic analyses of long 18S rRNA genes (around 1,030 bp) indicated these apicomplexan parasites are closely related to gregarine Lecudina polymorpha. Determination of 18S rRNA gene abundances provided evidence that the eelgrass markedly promoted the biomass of the gregarine and all microeukaryotes in the seagrass-colonized sediments and confirmed that the gregarine was hosted by a polychaete species. Significantly higher gene abundances of heterotrophs and mixotrophs were found at the vegetated sites, which could be explained by the finer sediments and short supply of dissolved inorganic nitrogen, respectively. The pigmented protists were more abundant in 18S rRNA gene copies at the lower and higher pH levels than at the intermediate. Nevertheless, the fractions of heterotrophs and phototrophs in the community were significantly related to porewater N:P ratio. These results indicate that seagrass colonization significantly induces an increase in overall biomass and a decrease in diversity of benthic microeukaryotes, making them more heterotrophic. This study also highlights that the hotspot of eukaryotic parasites could be linked with the high productivity of a natural ecosystem.
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Affiliation(s)
- Ying Pan
- School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Guihao Li
- Laboratory of Microbial Ecology and Matter Cycle, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Lei Su
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Pengfei Zheng
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Yaping Wang
- Laboratory of Microbial Ecology and Matter Cycle, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Zhuo Shen
- Laboratory of Microbial Ecology and Matter Cycle, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Zigui Chen
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Qiuying Han
- College of Ecology and Environment, Hainan Tropical Ocean University, Sanya, China
| | - Jun Gong
- Laboratory of Microbial Ecology and Matter Cycle, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, China
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Fang J, Jiang W, Meng S, He W, Wang G, Guo E, Yan Y. Polychaete Bioturbation Alters the Taxonomic Structure, Co-occurrence Network, and Functional Groups of Bacterial Communities in the Intertidal Flat. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02036-2. [PMID: 35604433 DOI: 10.1007/s00248-022-02036-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Polychaetes are important benthic macrofauna that lives in sediments, usually in intertidal flats with high organic content and high sulfide. It has been suggested that polychaete bioturbation could perform environmental remediation. During the process, the microbial community plays important roles. Here, we used high-throughput sequencing technology to study the bioturbation effects on the bacterial community in the polychaete (Perinereis aibuhitensis) burrows at different tidal positions in intertidal flat. The results showed that the bacterial communities were dramatically influenced by the polychaete bioturbation. The ACE, Chao, and Shannon indices of the polychaete burrows increased in summer. Dominant phyla in the polychaete burrows were Proteobacteria, Campilobacterota, Desulfobacterota, Chloroflexi, and Bacteroidota, and the dominant bacterial families were Sulfurvaceae, Flavobacteriaceae, Rhodobacteraceae, Woeseiaceae, Desulfobulbaceae, and Sulfurimonadaceae. Results of linear discriminant analysis effect size (LEfSe) showed that groups that include organic matter degraders, such as Bacteroidota, Flavobacteriaceae, Rhodobacteraceae, Woeseiaceae, and groups that include sulfur oxidizers, such as Campilobacterota, Sulfurovaceae, Rhodobacteraceae, Desulfobulbaceae, and Sulfurimonadaceae, were significantly increased due to the polychaete bioturbation. The polychaete bioturbation reduced the complexity of the bacterial co-occurrence network while increased its modularity and homogeneity. The polychaete bioturbation also changed the functional groups, which significantly enhanced in functional groups of aerobic nitrite oxidation, nitration, dark thiosulfate oxidation, dark sulfur oxidation, and dark sulfite oxidation, while nitrogen respiration and nitrate respiration decreased. These results provide insight into the impact of bacterial communities under the intertidal polychaete bioturbation.
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Affiliation(s)
- Jinghui Fang
- Laboratory for Marine Fisheries Science and Food Production Processes, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, People's Republic of China
| | - Wenwen Jiang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China.
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangdong, 510275, People's Republic of China.
| | - Shan Meng
- Laboratory for Marine Fisheries Science and Food Production Processes, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, People's Republic of China
- China Ocean Press, Beijing, 100081, People's Republic of China
| | - Wei He
- Laboratory for Marine Fisheries Science and Food Production Processes, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, People's Republic of China
| | - Guodong Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China
- Homey Group Co. Ltd, Rongcheng, 264306, People's Republic of China
| | - Enmian Guo
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China
| | - Yisu Yan
- Qingdao Dagang Customs, Qingdao, 266011, People's Republic of China
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9
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Palit K, Rath S, Chatterjee S, Das S. Microbial diversity and ecological interactions of microorganisms in the mangrove ecosystem: Threats, vulnerability, and adaptations. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:32467-32512. [PMID: 35182344 DOI: 10.1007/s11356-022-19048-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Mangroves are among the world's most productive ecosystems and a part of the "blue carbon" sink. They act as a connection between the terrestrial and marine ecosystems, providing habitat to countless organisms. Among these, microorganisms (e.g., bacteria, archaea, fungi, phytoplankton, and protozoa) play a crucial role in this ecosystem. Microbial cycling of major nutrients (carbon, nitrogen, phosphorus, and sulfur) helps maintain the high productivity of this ecosystem. However, mangrove ecosystems are being disturbed by the increasing concentration of greenhouse gases within the atmosphere. Both the anthropogenic and natural factors contribute to the upsurge of greenhouse gas concentration, resulting in global warming. Changing climate due to global warming and the increasing rate of human interferences such as pollution and deforestation are significant concerns for the mangrove ecosystem. Mangroves are susceptible to such environmental perturbations. Global warming, human interventions, and its consequences are destroying the ecosystem, and the dreadful impacts are experienced worldwide. Therefore, the conservation of mangrove ecosystems is necessary for protecting them from the changing environment-a step toward preserving the globe for better living. This review highlights the importance of mangroves and their microbial components on a global scale and the degree of vulnerability of the ecosystems toward anthropic and climate change factors. The future scenario of the mangrove ecosystem and the resilience of plants and microbes have also been discussed.
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Affiliation(s)
- Krishna Palit
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Sonalin Rath
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Shreosi Chatterjee
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India.
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10
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Mai Z, Zeng X, Wei X, Sun C, Niu J, Yan W, Du J, Sun Y, Cheng H. Mangrove restoration promotes the anti-scouribility of the sediments by modifying inherent microbial community and extracellular polymeric substance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 811:152369. [PMID: 34919933 DOI: 10.1016/j.scitotenv.2021.152369] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Coastal erosion will aggravate the loss of shorelines and threaten the safety of coastal engineering facilities. Mangrove is often considered as an efficient coastal guard; however the mechanisms involved in anti-scouribility ascribed to mangrove are still poorly understood. Thus, two artificial mangrove forests (including exotic Sonneratia apetala and native Kandelia obovata) and an unvegetated mudflat control were selected to explore the potential function of microbial extracellular polymeric substance (EPS) on the anti-scouribility of the sediments. A cohesive strength meter was used for the analysis of anti-scouribility, while a sequential extraction and 16S high-throughput sequencing were employed to evaluate the changes in EPS and microbial community driven by mangrove restoration. Principal component, redundancy, and two-matrix correlation heatmap analyses were performed for the analyses of the correlations among shear stress, EPS, microbes, and soil properties. The results showed an obvious enhancement of anti-scouribility after mangrove restoration. Compared to those of unvegetated mudflat, shear stress increased from 1.94 N/m2 to 3.26 and 4.93 N/m2 in the sediments of S. apetala and K. obovata stands, respectively. Mangrove restoration also promoted EPS content in the sediments, irrespective of EPS components and sub-fractions. Both extracellular protein and polysaccharide were found to be positively correlated with anti-scouribility. Coinciding with increased anti-scouribility and EPS, increased bacterial abundances were also detected in the sediments after mangrove restoration (especially K. obovata), whereas Proteobacteria and Bacteroides may be important and influential for EPS secretion and anti-scouribility promotion. Nevertheless, increased total organic carbon, total nitrogen and total phosphorus induced by mangrove restoration may also partially contribute to improvement of anti-scouribility. In conclusion, this is the first study to provide evidence for a link between mangrove restoration and increased EPS which improve resistance to scouring. The present study provides a novel perspective on the revealing of the function of mangrove on erosion mitigation.
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Affiliation(s)
- Zhimao Mai
- State Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-resources and Ecology, Key Laboratory of Ocean and Marginal Sea Geology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Xin Zeng
- State Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-resources and Ecology, Key Laboratory of Ocean and Marginal Sea Geology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Xing Wei
- State Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-resources and Ecology, Key Laboratory of Ocean and Marginal Sea Geology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Cuici Sun
- State Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-resources and Ecology, Key Laboratory of Ocean and Marginal Sea Geology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Jianwei Niu
- State Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-resources and Ecology, Key Laboratory of Ocean and Marginal Sea Geology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Wenwen Yan
- The First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061,China; Key Laboratory of Marine Environment and Ecology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Jun Du
- The First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061,China
| | - Yingting Sun
- State Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-resources and Ecology, Key Laboratory of Ocean and Marginal Sea Geology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Hao Cheng
- State Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-resources and Ecology, Key Laboratory of Ocean and Marginal Sea Geology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.
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11
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Govindarajan A, Crum M, Adolacion J, Kiaghadi A, Acuña-Gonzalez E, Rifai HS, Willson RC. Sediment and their bacterial communities in an industrialized estuary after Hurricane Harvey. MARINE POLLUTION BULLETIN 2022; 175:113359. [PMID: 35124375 DOI: 10.1016/j.marpolbul.2022.113359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 12/26/2021] [Accepted: 01/15/2022] [Indexed: 06/14/2023]
Abstract
Estuaries experience variable physicochemical conditions, especially after hurricanes and due to anthropogenic sources of pollution. Their microbial communities are not as well understood in terms of community structure and diversity, particularly in response to stresses from pollution and severe events. This study presents a 16S rRNA-based description of sediment microbial communities in the Houston Ship Channel-Galveston Bay estuary after Hurricane Harvey in 2017. A total of 11 sites were sampled, and microbial genomic DNA was isolated from sediment. The presence and abundance of specific bacterial and archaeal taxa in the sediment indicated pollutant inputs from identified legacy sources. The abundance of certain microbial groups was explained by the mobilization of contaminated sediment and sediment transport due to Harvey. Several microorganisms involved in the biodegradation of xenobiotics were observed. The spatial occurrence of Dehalococcoidia, a degrader of persistent polychlorinated compounds, was explained in relation to sediment properties and contaminant concentrations.
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Affiliation(s)
| | - Mary Crum
- Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Jay Adolacion
- School of Engineering and Science, Tecnológico de Monterrey, Monterrey, Mexico
| | - Amin Kiaghadi
- Civil and Environmental Engineering, University of Houston, Houston, TX, USA
| | - Edgar Acuña-Gonzalez
- School of Medicine and Health Sciences, Tecnológico de Monterrey, Monterrey, Mexico
| | - Hanadi S Rifai
- Civil and Environmental Engineering, University of Houston, Houston, TX, USA.
| | - Richard C Willson
- Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
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12
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Huang J, Zhu J, Liu S, Luo Y, Zhao R, Guo F, Li B. Estuarine salinity gradient governs sedimentary bacterial community but not antibiotic resistance gene profile. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:151390. [PMID: 34740654 DOI: 10.1016/j.scitotenv.2021.151390] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
Antibiotic resistance gene (ARG) pollution in estuarine environment has drawn great attention, and it is not clear if the physical and chemical parameters such as salinity, total organic carbon, total nitrogen, total phosphorus and antibiotics affects the distribution of ARGs. Herein, we deciphered the ARG profiles and microbial community compositions in sediments from Jiulong River Estuary (JRE) and Min River Estuary (MRE) of China using high-throughput sequencing-based metagenomics analysis. Furthermore, we explored the influence of salinity on bacterial community and ARG profiles. The results showed that Proteobacteria, Chloroflexi, and Acidobacteria were the dominant phyla in these two estuaries. The abundance of ARGs ranged from 1.05 × 10-1 to 2.93 × 10-1 copy of ARG per copy of 16S rRNA gene in all the sediment samples and the profiles of ARGs presented similar patterns in two estuaries. Multidrug resistance genes were the dominant ARG types in both estuaries, with an overall abundance of 2.39 × 10-2-1.07 × 10-1 copy of ARG per copy of 16S rRNA gene, followed by genes conferring resistance to bacitracin and macrolide-lincosamide-streptogramin. Salinity was an important influencing factor on the bacterial community but not on the ARG profiles. Instead, stochastic processes exerted the main influence on the distribution of ARGs. The comparison of ARG profiles among estuary sediments, marine sediments, and samples from anthropogenic pollution environments revealed remarkable similarity of ARG profiles between samples from estuary sediments and those from municipal wastewater treatment plants. These results suggested that the complex emission of anthropogenic pollution could cause the stochastic ecological pattern of ARGs.
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Affiliation(s)
- Jin Huang
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China; Shenzhen Environmental Science and New Energy Laboratory, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen 518055, China
| | - Jun Zhu
- School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Xiamen University, Xiamen, China
| | - Siguang Liu
- Fujian Institute of Oceanography, Xiamen, China
| | - Yuanrong Luo
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, China
| | - Renxin Zhao
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Feng Guo
- School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Xiamen University, Xiamen, China; Key Laboratory of Fujian Provincial University for Microorganism Resource, Xiamen, China.
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China.
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13
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Water Column Microbial Communities Vary along Salinity Gradients in the Florida Coastal Everglades Wetlands. Microorganisms 2022; 10:microorganisms10020215. [PMID: 35208670 PMCID: PMC8874701 DOI: 10.3390/microorganisms10020215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 01/04/2023] Open
Abstract
Planktonic microbial communities mediate many vital biogeochemical processes in wetland ecosystems, yet compared to other aquatic ecosystems, like oceans, lakes, rivers or estuaries, they remain relatively underexplored. Our study site, the Florida Everglades (USA)—a vast iconic wetland consisting of a slow-moving system of shallow rivers connecting freshwater marshes with coastal mangrove forests and seagrass meadows—is a highly threatened model ecosystem for studying salinity and nutrient gradients, as well as the effects of sea level rise and saltwater intrusion. This study provides the first high-resolution phylogenetic profiles of planktonic bacterial and eukaryotic microbial communities (using 16S and 18S rRNA gene amplicons) together with nutrient concentrations and environmental parameters at 14 sites along two transects covering two distinctly different drainages: the peat-based Shark River Slough (SRS) and marl-based Taylor Slough/Panhandle (TS/Ph). Both bacterial as well as eukaryotic community structures varied significantly along the salinity gradient. Although freshwater communities were relatively similar in both transects, bacterioplankton community composition at the ecotone (where freshwater and marine water mix) differed significantly. The most abundant taxa in the freshwater marshes include heterotrophic Polynucleobacter sp. and potentially phagotrophic cryptomonads of the genus Chilomonas, both of which could be key players in the transfer of detritus-based biomass to higher trophic levels.
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14
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Mai Z, Ye M, Wang Y, Foong SY, Wang L, Sun F, Cheng H. Characteristics of Microbial Community and Function With the Succession of Mangroves. Front Microbiol 2021; 12:764974. [PMID: 34950118 PMCID: PMC8689078 DOI: 10.3389/fmicb.2021.764974] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/05/2021] [Indexed: 12/02/2022] Open
Abstract
In this study, 16S high-throughput and metagenomic sequencing analyses were employed to explore the changes in microbial community and function with the succession of mangroves (Sonneratia alba, Rhizophora apiculata, and Bruguiera parviflora) along the Merbok river estuary in Malaysia. The sediments of the three mangroves harbored their own unique dominant microbial taxa, whereas R. apiculata exhibited the highest microbial diversity. In general, Gammaproteobacteria, Actinobacteria, Alphaproteobacteria, Deltaproteobacteria, and Anaerolineae were the dominant microbial classes, but their abundances varied significantly among the three mangroves. Principal coordinates and redundancy analyses revealed that the specificity of the microbial community was highly correlated with mangrove populations and environmental factors. The results further showed that R. apiculata exhibited the highest carbon-related metabolism, coinciding with the highest organic carbon and microbial diversity. In addition, specific microbial taxa, such as Desulfobacterales and Rhizobiales, contributed the highest functional activities related to carbon metabolism, prokaryote carbon fixation, and methane metabolism. The present results provide a comprehensive understanding of the adaptations and functions of microbes in relation to environmental transition and mangrove succession in intertidal regions. High microbial diversity and carbon metabolism in R. apiculata might in turn facilitate and maintain the formation of climax mangroves in the middle region of the Merbok river estuary.
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Affiliation(s)
- Zhimao Mai
- State Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Mai Ye
- State Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Academy of Environmental Science, Guangzhou, China
| | - Youshao Wang
- State Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Swee Yeok Foong
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Lin Wang
- State Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Fulin Sun
- State Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Daya Bay Marine Biology Research Station, Chinese Academy of Sciences, Shenzhen, China
| | - Hao Cheng
- State Key Laboratory of Tropical Oceanography, Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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15
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Padhy SR, Bhattacharyya P, Nayak SK, Dash PK, Mohapatra T. A unique bacterial and archaeal diversity make mangrove a green production system compared to rice in wetland ecology: A metagenomic approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 781:146713. [PMID: 33784529 DOI: 10.1016/j.scitotenv.2021.146713] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
Mangrove provides significant ecosystem services, however, 40% of tropical mangrove was lost in last century due to climate change induced sea-level rise and anthropogenic activities. Sundarban-India, the largest contiguous mangrove of the world lost 10.5% of its green during 1930-2013 which primarily converted to rice-based systems. Presently degraded mangrove and adjacent rice ecology in Sundarban-India placed side by side and create typical ecology which is distinct in nature in respect to soil physicochemical properties, carbon dynamics, and microbial diversities. We investigated the structural and functional diversities of bacteria and archaea through Illumina MiSeq metagenomic analysis using V3-V4 region of 16S rRNA gene approach that drives greenhouse gases emission and carbon-pools. Remote sensing-data base were used to select the sites for collecting the soil and gas samples. The methane and nitrous oxide emissions were lower in mangrove (-0.04 mg m-2 h-1 and -52.8 μg m-2 h-1) than rice (0.26 mg m-2 h-1 and 44.7 μg m-2 h-1) due to less availability of carbon-substrates and higher sulphate availability (85.8% more than rice). The soil labile carbon-pools were more in mangrove, but lower microbial activities were noticed due to stress conditions. A unique microbial feature indicated by higher methanotrophs: methanogens (11.2), sulphur reducing bacteria (SRB): methanogens (93.2) ratios and lower functional diversity (7.5%) in mangrove than rice. These could be the key drivers of lower global warming potential (GWP) in mangrove that make it a green production system. Therefore, labile carbon build-up potential (38%) with less GWP (63%) even in degraded-mangrove makes it a clean production system than wetland-rice that has high potential to climate change mitigation. The whole genome metagenomic analysis would be the future research priority to identify the predominant enzymatic pathways which govern the methanogenesis and methanotrophy in this system.
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Affiliation(s)
- S R Padhy
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India; Maharaja Sriram Chandra Bhanja Deo University, Baripada, Odisha, India
| | - P Bhattacharyya
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India.
| | - S K Nayak
- Maharaja Sriram Chandra Bhanja Deo University, Baripada, Odisha, India
| | - P K Dash
- ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
| | - T Mohapatra
- Indian Council of Agricultural Research, New Delhi, India
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16
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Servais S, Kominoski JS, Fernandez M, Morales K. Saltwater and phosphorus drive unique soil biogeochemical processes in freshwater and brackish wetland mesocosms. Ecosphere 2021. [DOI: 10.1002/ecs2.3704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Shelby Servais
- Institute of Environment and Department of Biological Sciences Florida International University Miami Florida 33199 USA
| | - John S. Kominoski
- Institute of Environment and Department of Biological Sciences Florida International University Miami Florida 33199 USA
| | - Marco Fernandez
- Institute of Environment and Department of Biological Sciences Florida International University Miami Florida 33199 USA
| | - Kristina Morales
- Department of Biology University of North Carolina at Greensboro Greensboro North Carolina 27402 USA
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17
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Chuvochina M, Adame MF, Guyot A, Lovelock C, Lockington D, Gamboa-Cutz JN, Dennis PG. Drivers of bacterial diversity along a natural transect from freshwater to saline subtropical wetlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 759:143455. [PMID: 33243518 DOI: 10.1016/j.scitotenv.2020.143455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 06/11/2023]
Abstract
Tropical coastal wetlands provide a range of ecosystem services that are closely associated with microbially-driven biogeochemical processes. Knowledge of the main players and their drivers in those processes can have huge implications on the carbon and nutrient fluxes in wetland soils, and thus on the ecosystems services we derive from them. Here, we collected surface (0-5 cm) and subsurface (20-25 cm) soil samples along a transect from forested freshwater wetlands, to saltmarsh, and mangroves. For each sample, we measured a range of abiotic properties and characterised the diversity of bacterial communities using 16S rRNA gene amplicon sequencing. The alpha diversity of bacterial communities in mangroves exceeded that of freshwater wetlands, which were dominated by members of the Acidobacteria, Alphaproteobacteria and Verrucomicrobia, and associated with high soil pore-water concentrations of soluble reactive phosphorous, and nitrogen as nitrate and nitrite (N-NOX-). Bacterial communities in the saltmarsh were strongly stratified by depth and included members of the Actinobacteria, Chloroflexi, and Deltaproteobacteria. Finally, the mangroves were dominated by representatives of Deltaproteobacteria, mainly Desulfobacteraceae and Synthrophobacteraceae, and were associated with high salinity and soil pore-water concentrations of ammonium (N-NH4+). These communities suggest methane consumption in freshwater wetlands, and sulfate reduction in deep soils of marshes and in mangroves. Our work contributes to the important goal of describing reference conditions for specific wetlands in terms of both bacterial communities and their drivers. This information may be used to monitor change and assess wetland health and function.
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Affiliation(s)
- Maria Chuvochina
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia; National Centre for Groundwater Research and Training, Flinders University, Bedford Park 5042, Australia
| | | | - Adrien Guyot
- National Centre for Groundwater Research and Training, Flinders University, Bedford Park 5042, Australia; School of Civil Engineering, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Catherine Lovelock
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David Lockington
- National Centre for Groundwater Research and Training, Flinders University, Bedford Park 5042, Australia; School of Civil Engineering, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Paul G Dennis
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD 4072, Australia.
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18
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Chowdhury A, Naz A, Maiti SK. Bioaccumulation of potentially toxic elements in three mangrove species and human health risk due to their ethnobotanical uses. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:10.1007/s11356-021-12566-w. [PMID: 33638081 DOI: 10.1007/s11356-021-12566-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 01/15/2021] [Indexed: 06/12/2023]
Abstract
The aim of this study was to assess probabilistic human health risk due to ethnobotanical usage of Avicennia officinalis, Porteresia coarctata and Acanthus ilicifolius. The study was conducted at the tannery outfall near Sundarban (Ramsar wetland, India) mangrove ecosystem affected by potentially toxic elements (Cd, Cr, Cu, Hg, Mn, Ni, Pb, and Zn). Total metal concentrations (mg kg-1) were considerably higher in the polluted rhizosphere namely, Cd (1.05-1.97), Cu (36.3-38.6), Cr (144-184), Hg (0.04-0.19), Mn (163-184), Ni (37.7-46.4), Pb (20-36.6), and Zn (97-104). Ecological risk index indicated low to moderate ecological risk in this site, whereas the ecological risk factor showed high potential ecological risk due to Cd pollution. BCR Sequential extraction of metals showed more exchangeable fraction of Cd (47-55%), Cr (9-13%), Hg (11-13%), and Pb (11-15%), at the polluted site. Mercury, though present in trace amount in sediment, showed the highest bioaccumulation in all the three plants. Among the toxic trio, Hg showed the highest bioaccumulation in A. officinalis, Cd in P. coarctata but Pb has the lowest bioaccumulation potential in all the three species. Occasional fruit consumption of A. officinalis and dermal application of leaf, bark of A. officinalis (antimicrobial), A. ilicifolius (anti-inflammatory, pain reliever when applied on wounds) indicated negligible human health risk. However, long-term consumption of P. coarctata (wild rice variety) seeds posed health risk (THQ>1) both in adults and children age groups. This study concludes that nature of ethnobotanical use and metal contamination levels of the mangrove rhizosphere can impact human health. The transfer process of potentially toxic elements from rhizosphere to plants to human body should be considered while planing pollution mitigation measures. Graphical Abstract.
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Affiliation(s)
- Abhiroop Chowdhury
- School of Environment & Sustainability, O.P. Jindal Global University, Sonipat, Haryana, 131001, India.
- Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand, 826004, India.
| | - Aliya Naz
- Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand, 826004, India
| | - Subodh Kumar Maiti
- Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand, 826004, India
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Li YL, Guo HQ, Ge ZM, Wang DQ, Liu WL, Xie LN, Li SH, Tan LS, Zhao B, Li XZ, Tang JW. Sea-level rise will reduce net CO 2 uptake in subtropical coastal marshes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 747:141214. [PMID: 32795794 DOI: 10.1016/j.scitotenv.2020.141214] [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: 04/03/2020] [Revised: 07/22/2020] [Accepted: 07/22/2020] [Indexed: 06/11/2023]
Abstract
Coastal marshes have a significant capacity to sequester carbon; however, sea-level rise (SLR) is expected to result in prolonged flooding and saltwater intrusion in coastal regions. To explore the effects of SLR projections on net CO2 uptake in coastal marshes, we conducted a "double-check" investigation, including the eddy covariance (EC) measurements of the CO2 fluxes in subtropical coastal marshes along inundation and salinity gradients, in combination with a mesocosm experiment for analyzing CO2 flux components under waterlogging and increased salinity conditions. During the same measurement periods, the net ecosystem CO2 exchange (NEEEC based on the EC dataset) in an oligohaline marsh was higher than that in a low-elevation mesohaline marsh, whereas the NEEEC was lower than that in a high-elevation freshwater marsh. The declines in NEEEC between the marshes could be attributed to a greater decrease in gross primary production relative to ecosystem respiration. Waterlogging slightly increased the NEEms (NEE based on the mesocosms) because of inhibited soil respiration and slight changes in plant photosynthesis and shoot respiration. However, the NEEms measured during the drainage period decreased significantly due to the stimulated soil respiration. The NEEms decreased with increasing salinity (except under mild salinity), and waterlogging exacerbated the adverse impacts of salinity. The amplificatory effect of decreases in both leaf photosynthesis and growth under hydrological stresses contributed more to reduce the NEEms than to respiratory effluxes. Both waterlogging and increased salinity reduced the root biomass, soil microbial biomass, and activities of assayed soil enzymes (except for cellulase under waterlogging conditions), leading to limited soil respiration. The declines in plant growth, photosynthesis, and soil respiration could also be attributed to the decrease in soil nutrients under waterlogging and increased salinity conditions. We propose that the coupling of SLR-driven hydrological effects lowers the capacity of CO2 uptake in subtropical coastal marshes.
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Affiliation(s)
- Ya-Lei Li
- State Key Laboratory of Estuarine and Coastal Research, Institute of Eco-Chongming, East China Normal University, Shanghai, China
| | - Hai-Qiang Guo
- Key Laboratory for Biodiversity Science and Ecological Engineering (Ministry of Education), Fudan University, Shanghai, China
| | - Zhen-Ming Ge
- State Key Laboratory of Estuarine and Coastal Research, Institute of Eco-Chongming, East China Normal University, Shanghai, China; Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station (Ministry of Education & Shanghai Science and Technology Committee), Shanghai, China.
| | - Dong-Qi Wang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographical Sciences, East China Normal University, Shanghai, China
| | - Wen-Liang Liu
- Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station (Ministry of Education & Shanghai Science and Technology Committee), Shanghai, China; School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Li-Na Xie
- State Key Laboratory of Estuarine and Coastal Research, Institute of Eco-Chongming, East China Normal University, Shanghai, China
| | - Shi-Hua Li
- State Key Laboratory of Estuarine and Coastal Research, Institute of Eco-Chongming, East China Normal University, Shanghai, China
| | - Li-Shan Tan
- State Key Laboratory of Estuarine and Coastal Research, Institute of Eco-Chongming, East China Normal University, Shanghai, China
| | - Bin Zhao
- Key Laboratory for Biodiversity Science and Ecological Engineering (Ministry of Education), Fudan University, Shanghai, China
| | - Xiu-Zhen Li
- State Key Laboratory of Estuarine and Coastal Research, Institute of Eco-Chongming, East China Normal University, Shanghai, China; Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station (Ministry of Education & Shanghai Science and Technology Committee), Shanghai, China
| | - Jian-Wu Tang
- State Key Laboratory of Estuarine and Coastal Research, Institute of Eco-Chongming, East China Normal University, Shanghai, China; Yangtze Delta Estuarine Wetland Ecosystem Observation and Research Station (Ministry of Education & Shanghai Science and Technology Committee), Shanghai, China
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Shifts in the Bacterial Population and Ecosystem Functions in Response to Vegetation in the Yellow River Delta Wetlands. mSystems 2020; 5:5/3/e00412-20. [PMID: 32518198 PMCID: PMC7289592 DOI: 10.1128/msystems.00412-20] [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] [Indexed: 11/20/2022] Open
Abstract
Vegetation represents probably the most crucial step for the ecosystem functions of wetlands, but it is unclear how microbial populations and functions shift along with vegetation. In this study, we found that the richness and diversity of soil bacteria increased with vegetation levels and that the community composition was distinctly shifted from bare to vegetative places. The bare land displayed an extremely high abundance of Cyanobacteria as a monospecies genus, while a Gemmatimonadetes genus was predominant as multiple species in all the vegetative wetlands, suggesting their important ecosystem functions and potential mechanisms. Expression of the genes related to photosynthesis was enriched exclusively in bare land. Genes involved in biological organic carbon metabolism and the cycling of main elements (C, N, S, and P) were highly expressed in vegetative wetlands and were mostly included in the metagenome-assembled genome (MAG) of Gemmatimonadetes Some compounds identified from soil metabolomic results also corresponded to pathways involving these key active genes. Cyanobacteria is thus responsible for the carbon sink in early infertile wetlands, and Gemmatimonadetes plays a crucial role in ecosystem functions in vegetative wetlands. Our results highlight that the soil microbial populations execute ecosystem functions for wetlands and that vegetation is the determinant for the population and functional shifts in the coastal estuarine wetland of the Yellow River Delta.IMPORTANCE Vegetation probably represents the most crucial step for the ecosystem functions of wetlands, but it is unclear how microbial populations and functions shift in pace with the colonization and succession of vegetation. In this study, we found that a Cyanobacteria monospecies genus and a Gemmatimonadetes multispecies genus are fastidiously predominant in the bare and vegetative wetlands of the Yellow River Delta, respectively. Consistently, photosynthesis genes were enriched exclusively in bare land, while genes involved in biological organic carbon metabolism and the cycling of main elements were highly expressed in vegetative wetlands, were mostly included in the MAG of Gemmatimonadetes, and were consistent with soil metabolomic results. Our results provide insight into the adaptive succession of predominant bacterial species and their ecosystem functions in response to the presence of vegetation.
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Neshani A, Sedighian H, Mirhosseini SA, Ghazvini K, Zare H, Jahangiri A. Antimicrobial peptides as a promising treatment option against Acinetobacter baumannii infections. Microb Pathog 2020; 146:104238. [PMID: 32387392 DOI: 10.1016/j.micpath.2020.104238] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 04/26/2020] [Accepted: 04/27/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND With the increasing rate of antibiotic resistance in Acinetobacter, the World Health Organization introduced the carbapenem-resistant isolates in the priority pathogens list for which innovative new treatments are urgently needed. Antimicrobial peptides (AMPs) are one of the antimicrobial agents with high potential to produce new anti-Acinetobacter drugs. This review aims to summarize recent advances and compare AMPs with anti-Acinetobacter baumannii activity. METHODS Active AMPs against Acinetobacter were considered, and essential features, including structure, mechanism of action, anti-A. baumannii potent, and other prominent characteristics, were investigated and compared to each other. In this regard, the Google Scholar search engine and databases of PubMed, Scopus, and Web of Science were used. RESULTS Forty-six anti-Acinetobacter peptides were identified and classified into ten groups: Cathelicidins, Defensins, Frog AMPs, Melittin, Cecropins, Mastoparan, Histatins, Dermcidins, Tachyplesins, and computationally designed AMPs. According to the Minimum Inhibitory Concentration (MIC) reports, six peptides of Melittin, Histatin-8, Omega76, AM-CATH36, Hymenochirin, and Mastoparan have the highest anti-A. baumannii power against sensitive and antibiotic-resistant isolates. All anti-Acinetobacter peptides except Dermcidin have a net positive charge. Most of these peptides have alpha-helical structure; however, β-sheet and other structures have been observed among them. The mechanism of action of these antimicrobial agents is divided into two categories of membrane-based and intracellular target-based attack. CONCLUSION Evidence from this review indicates that AMPs would be likely among the main anti-A. baumannii drugs in the post-antibiotic era. Also, the application of computer science to increase anti-A. baumannii activity and reduce toxicity could be helpful.
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Affiliation(s)
- Alireza Neshani
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran; Department of Laboratory Sciences, School of Paramedical Sciences, Mashhad University of Medical Sciences, Mashhad, Iran; Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamid Sedighian
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Seyed Ali Mirhosseini
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Kiarash Ghazvini
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hosna Zare
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Abolfazl Jahangiri
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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Jiang X, Liu W, Yao L, Liu G, Yang Y. The roles of environmental variation and spatial distance in explaining diversity and biogeography of soil denitrifying communities in remote Tibetan wetlands. FEMS Microbiol Ecol 2020; 96:5818761. [PMID: 32275304 DOI: 10.1093/femsec/fiaa063] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 04/02/2020] [Indexed: 01/06/2023] Open
Abstract
The relative importance of local environments and dispersal limitation in shaping denitrifier community structure remains elusive. Here, we collected soils from 36 riverine, lacustrine and palustrine wetland sites on the remote Tibetan Plateau and characterized the soil denitrifier communities using high-throughput amplicon sequencing of the nirS and nirK genes. Results showed that the richness of nirS-type denitrifiers in riverine wetlands was significantly higher than that in lacustrine wetlands but not significantly different from that in palustrine wetlands. There was no clear distinction in nir community composition among the three kinds of wetlands. Irrespective of wetland type, the soil denitrification rate was positively related to the abundance, but not the α-diversity, of denitrifying communities. Soil moisture, carbon availability and soil temperature were the main determinants of diversity [operational taxonomic unit (OTU) number] and abundance of thenirS-type denitrifier community, while water total organic carbon, soil NO3- and soil moisture were important in controlling nirK-type denitrifier diversity and abundance. The nirS community composition was influenced by water electrical conductivity, soil temperature and water depth, while the nirK community composition was affected by soil electrical conductivity. Spatial distance explained more variation in the nirS community composition than in the nirK community composition. Our findings highlight the importance of both environmental filtering and spatial distance in explaining diversity and biogeography of soil nir communities in remote and relatively undisturbed wetlands.
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Affiliation(s)
- Xiaoliang Jiang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.,Collaborative Innovation Center of Water Security for Water Source Region of Mid-line of South-to-North Diversion Project of Henan Province, Nanyang Normal University, Nanyang 473061, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenzhi Liu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.,Collaborative Innovation Center of Water Security for Water Source Region of Mid-line of South-to-North Diversion Project of Henan Province, Nanyang Normal University, Nanyang 473061, China
| | - Lunguang Yao
- Collaborative Innovation Center of Water Security for Water Source Region of Mid-line of South-to-North Diversion Project of Henan Province, Nanyang Normal University, Nanyang 473061, China
| | - Guihua Liu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Yuyi Yang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.,School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
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Fu J, Luo Y, Sun P, Gao J, Zhao D, Yang P, Hu T. Effects of shade stress on turfgrasses morphophysiology and rhizosphere soil bacterial communities. BMC PLANT BIOLOGY 2020; 20:92. [PMID: 32122321 PMCID: PMC7053125 DOI: 10.1186/s12870-020-2300-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 02/21/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND The shade represents one of the major environmental limitations for turfgrass growth. Shade influences plant growth and alters plant metabolism, yet little is known about how shade affects the structure of rhizosphere soil microbial communities and the role of soil microorganisms in plant shade responses. In this study, a glasshouse experiment was conducted to examine the impact of shade on the growth and photosynthetic capacity of two contrasting shade-tolerant turfgrasses, shade-tolerant dwarf lilyturf (Ophiopogon japonicus, OJ) and shade-intolerant perennial turf-type ryegrass (Lolium perenne, LP). We also examined soil-plant feedback effects on shade tolerance in the two turfgrass genotypes. The composition of the soil bacterial community was assayed using high-throughput sequencing. RESULTS OJ maintained higher photosynthetic capacity and root growth than LP under shade stress, thus OJ was found to be more shade-tolerant than LP. Shade-intolerant LP responded better to both shade and soil microbes than shade-tolerant OJ. The shade and live soil decreased LP growth, but increased biomass allocation to shoots in the live soil. The plant shade response index of LP is higher in live soil than sterile soil, driven by weakened soil-plant feedback under shade stress. In contrast, there was no difference in these values for OJ under similar shade and soil treatments. Shade stress had little impact on the diversity of the OJ and the LP bacterial communities, but instead impacted their composition. The OJ soil bacterial communities were mostly composed of Proteobacteria and Acidobacteria. Further pairwise fitting analysis showed that a positive correlation of shade-tolerance in two turfgrasses and their bacterial community compositions. Several soil properties (NO3--N, NH4+-N, AK) showed a tight coupling with several major bacterial communities under shade stress. Moreover, OJ shared core bacterial taxa known to promote plant growth and confer tolerance to shade stress, which suggests common principles underpinning OJ-microbe interactions. CONCLUSION Soil microorganisms mediate plant responses to shade stress via plant-soil feedback and shade-induced change in the rhizosphere soil bacterial community structure for OJ and LP plants. These findings emphasize the importance of understanding plant-soil interactions and their role in the mechanisms underlying shade tolerance in shade-tolerant turfgrasses.
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Affiliation(s)
- Juanjuan Fu
- Department of Grassland Science, College of Grassland Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Yilan Luo
- Department of Grassland Science, College of Grassland Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Pengyue Sun
- Department of Grassland Science, College of Grassland Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Jinzhu Gao
- Department of Grassland Science, College of Grassland Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Donghao Zhao
- Department of Grassland Science, College of Grassland Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Peizhi Yang
- Department of Grassland Science, College of Grassland Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Tianming Hu
- Department of Grassland Science, College of Grassland Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
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Ceccon DM, Faoro H, Lana PDC, Souza EMD, Pedrosa FDO. Metataxonomic and metagenomic analysis of mangrove microbiomes reveals community patterns driven by salinity and pH gradients in Paranaguá Bay, Brazil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 694:133609. [PMID: 31400683 DOI: 10.1016/j.scitotenv.2019.133609] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/18/2019] [Accepted: 07/25/2019] [Indexed: 06/10/2023]
Abstract
While environmental drivers regulate the structure of mangrove microbial communities, their exact nature and the extent of their influence require further elucidation. By means of 16S rRNA gene-based sequencing, we determined the microbial taxonomic profiles of mangroves in the subtropical Paranaguá Bay, Brazil, considering as potential drivers: salinity, as represented by two sectors in the extremes of a salinity gradient (<5 PSU and >30 PSU); proximity to/absence of the prevailing plants, Avicennia schaueriana, Laguncularia racemosa, Rhizophora mangle, and Spartina alterniflora; and the chemical composition of the sediments. Salinity levels within the estuary had the strongest influence on microbial structure, and pH was important to separate two communities within the high salinity environment. About one fourth of the total variation in community structure resulted from covariation of salinity and the overall chemical composition, which might indicate that the chemical profile was also related to salinity. The most prevalent bacterial phyla associated with the mangrove soils analyzed included Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, and Cyanobacteria. Taxonomic and functional comparisons of our results for whole-genome sequencing with available data from other biomes showed that the studied microbiomes cluster first according to biome type, then to matrix type and salinity status. Metabolic functions were more conserved than organisms within mangroves and across all biomes, indicating that core functions are preserved in any of the given conditions regardless of the specific organisms harboring them.
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Affiliation(s)
- Denny Marcel Ceccon
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Helisson Faoro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Paulo da Cunha Lana
- Center for Marine Studies, Universidade Federal do Paraná, Pontal do Paraná, Brazil
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Nascimento FJA, Dahl M, Deyanova D, Lyimo LD, Bik HM, Schuelke T, Pereira TJ, Björk M, Creer S, Gullström M. Above-below surface interactions mediate effects of seagrass disturbance on meiobenthic diversity, nematode and polychaete trophic structure. Commun Biol 2019; 2:362. [PMID: 31602411 PMCID: PMC6778119 DOI: 10.1038/s42003-019-0610-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 09/12/2019] [Indexed: 11/08/2022] Open
Abstract
Ecological interactions between aquatic plants and sediment communities can shape the structure and function of natural systems. Currently, we do not fully understand how seagrass habitat degradation impacts the biodiversity of belowground sediment communities. Here, we evaluated indirect effects of disturbance of seagrass meadows on meiobenthic community composition, with a five-month in situ experiment in a tropical seagrass meadow. Disturbance was created by reducing light availability (two levels of shading), and by mimicking grazing events (two levels) to assess impacts on meiobenthic diversity using high-throughput sequencing of 18S rRNA amplicons. Both shading and simulated grazing had an effect on meiobenthic community structure, mediated by seagrass-associated biotic drivers and sediment abiotic variables. Additionally, shading substantially altered the trophic structure of the nematode community. Our findings show that degradation of seagrass meadows can alter benthic community structure in coastal areas with potential impacts to ecosystem functions mediated by meiobenthos in marine sediments.
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Affiliation(s)
| | - Martin Dahl
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Diana Deyanova
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Liberatus D. Lyimo
- School of Biological Sciences, University of Dodoma, Box 338, Dodoma, Tanzania
| | - Holly M. Bik
- Department of Nematology, University of California—Riverside, 900 University Avenue, Riverside, CA 92521 USA
| | - Taruna Schuelke
- Department of Nematology, University of California—Riverside, 900 University Avenue, Riverside, CA 92521 USA
| | - Tiago José Pereira
- Department of Nematology, University of California—Riverside, 900 University Avenue, Riverside, CA 92521 USA
| | - Mats Björk
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, LL57 2UW UK
| | - Martin Gullström
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
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Ben Salem F, Ben Said O, Cravo-Laureau C, Mahmoudi E, Bru N, Monperrus M, Duran R. Bacterial community assemblages in sediments under high anthropogenic pressure at Ichkeul Lake/Bizerte Lagoon hydrological system, Tunisia. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 252:644-656. [PMID: 31185353 DOI: 10.1016/j.envpol.2019.05.146] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 05/27/2019] [Accepted: 05/28/2019] [Indexed: 06/09/2023]
Abstract
Bacterial communities inhabiting sediments in coastal areas endure the effect of strong anthropogenic pressure characterized by the presence of multiple contaminants. Understanding the effect of pollutants on the organization of bacterial communities is of paramount importance in order to unravel bacterial assemblages colonizing specific ecological niches. Here, chemical and molecular approaches were combined to investigate the bacterial communities inhabiting the sediments of the Ichkeul Lake/Bizerte Lagoon, a hydrological system under anthropogenic pressure. Although the microbial community of the Ichkeul Lake sediment was different to that of the Bizerte Lagoon, common bacterial genera were identified suggesting a lake-lagoon continuum probably due to the hydrology of the system exchanging waters according to the season. These genera represent bacterial "generalists" maintaining probably general biogeochemical functions. Linear discriminant analysis effect size (LEfSe) showed significant differential abundance distribution of bacterial genera according to the habitat, the pollution type and level. Further, correlation analyses identified specific bacterial genera which abundance was linked with pesticides concentrations in the lake, while in the lagoon the abundance of specific bacterial genera was found linked with the concentrations of PAHs (Polycyclic aromatic hydrocarbons) and organic forms of Sn. As well, bacterial genera which abundance was not correlated with the concentrations of pollutants were identified in both lake and lagoon. These findings represent valuable information, pointing out specific bacterial genera associated with pollutants, which represent assets for developing bacterial tools for the implementation, the management, and monitoring of bioremediation processes to mitigate the effect of pollutants in aquatic ecosystems.
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Affiliation(s)
- Fida Ben Salem
- Laboratoire de Biosurveillance de l'Environment, Faculté des Sciences de Bizerte, Tunisia; MELODY Group, Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, Pau Cedex, 64013, France; Fédération de recherche MIRA, Université de Pau et des Pays de l'Adour, E2S-UPPA, France
| | - Olfa Ben Said
- Laboratoire de Biosurveillance de l'Environment, Faculté des Sciences de Bizerte, Tunisia; MELODY Group, Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, Pau Cedex, 64013, France; Fédération de recherche MIRA, Université de Pau et des Pays de l'Adour, E2S-UPPA, France
| | - Cristiana Cravo-Laureau
- MELODY Group, Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, Pau Cedex, 64013, France; Fédération de recherche MIRA, Université de Pau et des Pays de l'Adour, E2S-UPPA, France
| | - Ezzeddine Mahmoudi
- Laboratoire de Biosurveillance de l'Environment, Faculté des Sciences de Bizerte, Tunisia
| | - Noëlle Bru
- Laboratoire de Mathématiques et de leurs Applications, PAU UMR CNRS 5142, Université de Pau et des Pays de l'Adour, E2S-UPPA, France; Fédération de recherche MIRA, Université de Pau et des Pays de l'Adour, E2S-UPPA, France
| | - Mathilde Monperrus
- MELODY Group, Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, Pau Cedex, 64013, France; Fédération de recherche MIRA, Université de Pau et des Pays de l'Adour, E2S-UPPA, France
| | - Robert Duran
- MELODY Group, Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, Pau Cedex, 64013, France; Fédération de recherche MIRA, Université de Pau et des Pays de l'Adour, E2S-UPPA, France.
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Tran HT, Wang HC, Hsu TW, Sarkar R, Huang CL, Chiang TY. Revegetation on abandoned salt ponds relieves the seasonal fluctuation of soil microbiomes. BMC Genomics 2019; 20:478. [PMID: 31185914 PMCID: PMC6558789 DOI: 10.1186/s12864-019-5875-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 05/31/2019] [Indexed: 02/07/2023] Open
Abstract
Background Salt pond restoration aims to recover the environmental damages that accumulated over the long history of salt production. Of the restoration strategies, phytoremediation that utilizes salt-tolerant plants and soil microorganisms to reduce the salt concentrations is believed to be environmentally-friendly. However, little is known about the change of bacterial community during salt pond restoration in the context of phytoremediation. In the present study, we used 16S metagenomics to compare seasonal changes of bacterial communities between the revegetated and barren salterns at Sicao, Taiwan. Results In both saltern types, Proteobacteria, Planctomycetes, Chloroflexi, and Bacteroidetes were predominant at the phylum level. In the revegetated salterns, the soil microbiomes displayed high species diversities and underwent a stepwise transition across seasons. In the barren salterns, the soil microbiomes fluctuated greatly, indicating that mangroves tended to stabilize the soil microorganism communities over the succession. Bacteria in the order Halanaerobiaceae and archaea in the family Halobacteriaceae that were adapted to high salinity exclusively occurred in the barren salterns. Among the 441 persistent operational taxonomic units detected in the revegetated salterns, 387 (87.5%) were present as transient species in the barren salterns. Only 32 persistent bacteria were exclusively detected in the revegetated salterns. Possibly, salt-tolerant plants provided shelters for those new colonizers. Conclusions The collective data indicate that revegetation tended to stabilize the microbiome across seasons and enriched the microbial diversity in the salterns, especially species of Planctomycetes and Acidobacteria. Electronic supplementary material The online version of this article (10.1186/s12864-019-5875-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Huyen-Trang Tran
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan, 70101.,Department of Biology, Institute of Natural Science Education, Vinh University, Vinh, Nghe An, 461010, Vietnam
| | - Hao-Chu Wang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan, 70101
| | - Tsai-Wen Hsu
- Taiwan Endemic Species Research Institute, Nantou, Taiwan, 55244
| | - Rakesh Sarkar
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan, 70101
| | - Chao-Li Huang
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan, 70101.
| | - Tzen-Yuh Chiang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan, 70101.
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Li J, Hu R, Guo Y, Chen S, Xie X, Qin JG, Ma Z, Zhu C, Pei S. Bioturbation of peanut worms Sipunculus nudus on the composition of prokaryotic communities in a tidal flat as revealed by 16S rRNA gene sequences. Microbiologyopen 2019; 8:e00802. [PMID: 30734523 PMCID: PMC6692553 DOI: 10.1002/mbo3.802] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 12/31/2018] [Accepted: 12/31/2018] [Indexed: 11/21/2022] Open
Abstract
To understand the impacts of peanut worms Sipunculus nudus on the prokaryotic community composition in a tidal flat, an onsite investigation was conducted in Suixi in the Beibu Gulf (109.82E, 21.35N) in the burrow sediments, non‐burrow sediments and the sediments without peanut worm disturbance (control). The16S rRNA gene Illumina MiSeq sequencing was used to investigate the microbial communities and their response to bioturbation by S. nudus in a sandy tidal flat. A total of 18 bacteria phyla were detected, and Proteobacteria and Cyanobacteria constituted the majority of the prokaryotic community in the samples. The distribution of the relative abundances of genera showed that approximately 6.99%–17% of the reads in the samples were classified into 25 known genera. Sulfate‐reducing bacteria (Desulfococcus and Desulfosarcina) were the most abundant taxa, followed by Thermodesulfovibrionaceae LCP‐6, indicating that sulfate reduction is the main process in the sandy tidal flat. The abundances of Desulfococcus, LCP‐6 and Cyanobacterium in the non‐burrow sediment were greater than in the burrow sediment, suggesting that the anoxic condition is more suitable for Desulfococcus and LCP‐6 when the activity of S. nudus is absent. The biomass of Cyanobacterium was decreased by the feeding bioturbation of S. nudus. Meanwhile, the relative abundance of the Bacteroidetes Luteimonas in the burrow sediments was significantly greater than in the non‐burrow sediment, and there was a strong relationship between S. nudus bioturbation and increased in oxygen contents and oxidation‐reduction potentials in the burrow sediment. The abundances of Desulfococcus and LCP‐6 were greater in the middle layer (20–30 cm) than in the top layer in the non‐burrow sediment. However, the middle and bottom layers (20–30, 30–40 cm) had higher abundances of these genera than did the upper layers (0–10, 10–20 cm) in the burrow sediments. The abundances of the Fusobacteria Propionigenium and the Spirochaetes Spirochaeta were greater in the middle and bottom layers (20–30 cm, 30–40 cm) than in the top layers (0–10, 10–20 cm) in the burrow sediment, but this phenomenon was not found in the non‐burrow sediment. This study demonstrates that bioturbation by S. nudus plays an important role in reshaping the bacterial community composition in intertidal regions.
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Affiliation(s)
- Junwei Li
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization of Ministry of Agriculture of China, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, PR China
| | - Ruiping Hu
- Guangzhou Haiwei Aquatic Science and Technology Co., Ltd, Guangzhou, PR China
| | - Yongjian Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization of Ministry of Agriculture of China, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, PR China
| | - Suwen Chen
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization of Ministry of Agriculture of China, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, PR China
| | - Xiaoyong Xie
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization of Ministry of Agriculture of China, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, PR China
| | - Jian G Qin
- College of Sciences and Engineering, Flinders University, Adelaide, SA, Australia
| | - Zhenhua Ma
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization of Ministry of Agriculture of China, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, PR China
| | - Changbo Zhu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization of Ministry of Agriculture of China, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, PR China
| | - Surui Pei
- Annoroad Gene Technology Co., Ltd., Beijing, PR China
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Pan J, Chen Y, Wang Y, Zhou Z, Li M. Vertical Distribution of Bathyarchaeotal Communities in Mangrove Wetlands Suggests Distinct Niche Preference of Bathyarchaeota Subgroup 6. MICROBIAL ECOLOGY 2019; 77:417-428. [PMID: 30612184 DOI: 10.1007/s00248-018-1309-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 12/16/2018] [Indexed: 06/09/2023]
Abstract
Bathyarchaeota is a diverse, abundant, and widespread archaeal phylum that may play an important role in global carbon cycling. The vertical distribution of Bathyarchaeota and environmental impact on bathyarchaeotal community in deep-sea and lake sediments are known; however, little information is available on Bathyarchaeota in eutrophic and brackish environments, such as mangrove wetlands. In the current study, we investigated the bathyarchaeotal community in the mangrove ecosystem of Futian Nature Reserve, Shenzhen. By slicing the profile into 2-cm layers from the surface to bottom, 110 sediment samples were obtained from three mangrove and three mud flat profiles. High-throughput sequencing of archaeal 16S rRNA genes, quantification of bathyarchaeotal 16S rRNA genes with optimized quantitative primers, and the ensuing statistical analyses revealed the vertical distribution of Bathyarchaeota in the mangrove ecosystem, indicating that Bathyarchaeota was the dominant archaeal phylum therein, with Bathyarchaeota subgroups 6, 8, 15, and 17 as the most abundant subgroups. The abundance of Bathyarchaeota was higher in the mangrove than in the mud flat and other oligotrophic or freshwater habitats. Total organic carbon (TOC) and nitric oxide were significantly correlated with the abundance of Bathyarchaeota, and pH was the major factor shaping the community composition. Further, the data suggested that Bathyarchaeota subgroup 6 preferentially dwelled in slightly acidic, high TOC, and subsurface environments, indicating a potentially distinct role in the global geochemical cycle. These findings expand the knowledge of the distribution and niche preference of Bathyarchaeota, emphasizing the need for continuous characterization of bathyarchaeotal subgroups.
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Affiliation(s)
- Jie Pan
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Yulian Chen
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Yongming Wang
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Zhichao Zhou
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China.
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Behera P, Mohapatra M, Kim JY, Adhya TK, Pattnaik AK, Rastogi G. Spatial and temporal heterogeneity in the structure and function of sediment bacterial communities of a tropical mangrove forest. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:3893-3908. [PMID: 30547343 DOI: 10.1007/s11356-018-3927-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Abstract
Bacterial communities of mangrove sediments are well appreciated for their role in nutrient cycling. However, spatiotemporal variability in these communities over large geographical scale remains understudied. We investigated sediment bacterial communities and their metabolic potential in an intertidal mangrove forest of India, Bhitarkanika, using high-throughput sequencing of 16S rRNA genes and community-level physiological profiling. Bulk surface sediments from five different locations representing riverine and bay sites were collected over three seasons. Seasonality largely explained the variation in the structural and metabolic patterns of the sediment bacterial communities. Freshwater Actinobacteria were more abundant in monsoon, whereas γ-Proteobacteria demonstrated higher abundance in summer. Distinct differences in the bacterial community composition were noted between riverine and bay sites. For example, salt-loving marine bacteria affiliated to Oceanospirillales were more prominent in the bay sites than the riverine sites. L-asparagine, N-acetyl-D-glucosamine, and D-mannitol were the preferentially utilized carbon sources by bacterial communities. Bacterial community composition was largely governed by salinity and organic carbon content of the sediments. Modeling analysis revealed that the abundance of δ-Proteobacteria increased with salinity, whereas β-Proteobacteria displayed an opposite trend. Metabolic mapping of taxonomic data predicted biogeochemical functions such as xylan and chitin degradation, ammonia oxidation, nitrite reduction, and sulfate reduction in the bacterial communities suggesting their role in carbon, nitrogen, and sulfur cycling in mangrove sediments. This study has provided valuable clues about spatiotemporal heterogeneity in the structural and metabolic patterns of bacterial communities and their environmental determinants in a tropical mangrove forest.
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Affiliation(s)
- Pratiksha Behera
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, Odisha, 752030, India
| | - Madhusmita Mohapatra
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, Odisha, 752030, India
| | - Ji Yoon Kim
- Department of Integrated Biological Science, Pusan National University, Geumjeong-gu, Busan, 46241, South Korea
| | - Tapan K Adhya
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha, 751024, India
| | - Ajit K Pattnaik
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, Odisha, 752030, India
| | - Gurdeep Rastogi
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, Odisha, 752030, India.
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Dynamic Change in Enzyme Activity and Bacterial Community with long-term rice Cultivation in Mudflats. Curr Microbiol 2019; 76:361-369. [DOI: 10.1007/s00284-019-01636-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 01/17/2019] [Indexed: 11/27/2022]
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32
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Deng Y, Gui Q, Dumont M, Han C, Deng H, Yun J, Zhong W. Methylococcaceae are the dominant active aerobic methanotrophs in a Chinese tidal marsh. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:636-646. [PMID: 30411293 DOI: 10.1007/s11356-018-3560-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 10/22/2018] [Indexed: 06/08/2023]
Abstract
Although coastal marshes are net carbon sinks, they are net methane sources. Aerobic methanotrophs in coastal marsh soils are important methane consumers, but their activity and populations are poorly characterized. DNA stable-isotope probing followed by sequencing was used to determine how active methanotrophic populations differed in the main habitats of a Chinese coastal marsh. These habitats included mudflat, native plant-dominated, and alien plant-dominated habitats. Methylococcaceae was the most active methanotroph family across four habitats. Abundant methylotroph sequences, including methanotrophs and non-methane-oxidizing methylotrophs (Methylotenera and Methylophaga), constituted 50-70% of the 16S rRNA genes detected in the labeled native plant-dominated and mudflat soils. Methylotrophs were less abundant (~ 20%) in labeled alien plant-dominated soil, suggesting less methane assimilation into the target community or a different extent of carbon cross-feeding. Canonical correspondence analysis indicated a significant correlation between the active bacterial communities and soil properties (salinity, organic carbon, total nitrogen, pH, and available phosphorus). Importantly, these results highlight how changing vegetation or soil features in coastal marshes may change their resident active methanotrophic populations, which will further influence methane cycling.
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Affiliation(s)
- Yongcui Deng
- School of Geography Science, Nanjing Normal University, Nanjing, China
- Key Laboratory of Virtual Geographic Environment, Ministry of Education, Nanjing, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, Nanjing, China
| | - Qian Gui
- School of Geography Science, Nanjing Normal University, Nanjing, China
| | - Marc Dumont
- Biological Sciences, University of Southampton, Southampton, UK
| | - Cheng Han
- School of Geography Science, Nanjing Normal University, Nanjing, China
| | - Huan Deng
- School of Geography Science, Nanjing Normal University, Nanjing, China
| | - Juanli Yun
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wenhui Zhong
- School of Geography Science, Nanjing Normal University, Nanjing, China.
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China.
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, Nanjing, China.
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33
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Yin P, Yin M, Cai Z, Wu G, Lin G, Zhou J. Structural inflexibility of the rhizosphere microbiome in mangrove plant Kandelia obovata under elevated CO 2. MARINE ENVIRONMENTAL RESEARCH 2018; 140:422-432. [PMID: 30055835 DOI: 10.1016/j.marenvres.2018.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 06/08/2023]
Abstract
Rhizosphere microbial communities play an important role in mediating the decomposition of soil organic matter. Increased CO2 concentration may increase plant growth by stimulating photosynthesis or improving water use efficiency. However, possible eco-physiological influences of this greenhouse gas in mangrove plants are not well understood, especially how rhizosphere microbial communities respond to CO2 increase. We characterized the effect of elevated CO2 (eCO2) on rhizospheric microbial communities associated with the mangrove plant Kandelia candel for 20 weeks, eCO2 increased plant chlorophyll a levels and root microbial biomass. Operational taxonomic unit analysis revealed no significant effects of eCO2 on rhizospheric bacterial communities; however, some influence on archaeal community structure was observed, especially on the ammonia-oxidizing archaea. Principal component analysis showed that microbial biomass C, total nitrogen, C/N ratio, nitrate nitrogen, and salinity were the main factors structuring the microbial community. The relative contribution of environmental parameters to variability among samples was 31.0%. In addition, functional analysis by average well color development showed that carbon source utilization under eCO2 occurred in the order amino acids > carbohydrates > polymers > carboxylic acids > amines > phenolic acids; whereas, sugars, amino acids, and carboxylic acids were the preferred carbon sources in control groups. Differences in utilization ability of carbohydrates and amino acids resulted in changes in carbon metabolism between the two groups. Rhizosphere microbial communities appear to have some buffering ability in response to short-term (20 weeks) CO2 increase, during which the metabolic efficiency of carbon sources is changed. The results will help better understand the structural inflexibility and functional plasticity of the rhizosphere microbiome in mangrove plants facing a changing environment (such as global climate change).
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Affiliation(s)
- Panqing Yin
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China; The School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, Gansu Province, PR China
| | - Mengqing Yin
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China
| | - Zhonghua Cai
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China
| | - Guoqiang Wu
- The School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, Gansu Province, PR China
| | - Guanghui Lin
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China
| | - Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, Guangdong Province, PR China.
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Fraser MW, Gleeson DB, Grierson PF, Laverock B, Kendrick GA. Metagenomic Evidence of Microbial Community Responsiveness to Phosphorus and Salinity Gradients in Seagrass Sediments. Front Microbiol 2018; 9:1703. [PMID: 30105009 PMCID: PMC6077243 DOI: 10.3389/fmicb.2018.01703] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/09/2018] [Indexed: 12/17/2022] Open
Abstract
Sediment microorganisms can have profound influence on productivity and functioning of marine ecosystems through their critical roles in regulating biogeochemical processes. However, the identity of sediment microorganisms that mediate organic matter turnover and nutrient cycling in seagrass sediments is only poorly understood. Here, we used metagenomic sequencing to investigate shifts in the structure and functioning of the microbial community of seagrass sediments across a salinity and phosphorus (P) availability gradient in Shark Bay, WA, Australia. This iconic ecosystem is oligotrophic and hypersaline with abundant seagrass meadows that directly contribute Shark Bay's status as a World Heritage Site. We show that sediment phosphonate metabolism genes as well as enzyme activities increase in hypersaline conditions with lower soluble reactive phosphate in the water column. Given that sediment organic P content is also highest where P concentrations in the water column are low, we suggest that microbial processing of organic P can contribute to the P requirements of seagrasses at particularly oligotrophic sites. Seagrass meadows are often highly productive in oligotrophic waters, and our findings suggest that an increase in the functional capacity of microbial communities in seagrass sediments to break down organic P may contribute to the high productivity of seagrass meadows under oligotrophic conditions. When compared to soil and sediment metagenomes from other aquatic and terrestrial ecosystems, we also show microbial communities in seagrass sediments have a disproportionately high abundance of putative phosphorus and sulfur metabolism genes, which may have played an important evolutionary role in allowing these angiosperms to recolonize the marine environment and prosper under oligotrophic conditions.
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Affiliation(s)
- Matthew W. Fraser
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
- Oceans Institute, The University of Western Australia, Crawley, WA, Australia
| | - Deirdre B. Gleeson
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
| | - Pauline F. Grierson
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Bonnie Laverock
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
- Oceans Institute, The University of Western Australia, Crawley, WA, Australia
- School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Gary A. Kendrick
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
- Oceans Institute, The University of Western Australia, Crawley, WA, Australia
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Yu D, Wen Z, Li X, Song X, Wu H, Yang P. Effects of straw return on bacterial communities in a wheat-maize rotation system in the North China Plain. PLoS One 2018; 13:e0198087. [PMID: 29879153 PMCID: PMC5991650 DOI: 10.1371/journal.pone.0198087] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 05/14/2018] [Indexed: 11/18/2022] Open
Abstract
Straw return plays an important role in reducing the use of chemical fertilizer, promoting soil carbon sequestration, thus maintaining soil fertility and alleviating environmental pollution. To examine the effects of straw return on soil bacterial communities, quantitative PCR and high-throughput sequencing approaches were used to analyze the bacterial abundance and community structures at the depths of 5-25 cm and 25-45 cm in the soils under six-year continuous straw return and removal treatments in Langfang, Hebei, the North China Plain. As a result, straw return had no effects on soil chemical properties, bacterial abundance, richness or diversity at both soil depths. In contrast, vertical distributions of available nitrogen and available potassium were affected. Similarly, straw return also changed the vertical distributions of Proteobacteria and Chloroflexi. Principal coordinate analysis based on weighted UniFrac distance matrix indicated a moderate separation of the bacterial community in the soil treated with straw return from that with straw removal at 5-25 cm depth, but they were not distinctly distinguished at 25-45 cm depth. T-test identified increased abundance of Candidatus Latescibacteria in the soil under straw return treatment at 5-25 cm depth but no differentially abundant phyla at 25-45 cm depth was found. These results suggested a selection effect from the six-year continuous straw return treatment and the soil bacterial communities were moderately changed.
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Affiliation(s)
- Dali Yu
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
- School of Life Sciences, Qilu Normal University, Jinan, P. R. China
| | - Zhiguo Wen
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Xiumei Li
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Xiaojun Song
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Huijun Wu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
- * E-mail: (HW); (PY)
| | - Peilong Yang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
- * E-mail: (HW); (PY)
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Wang YF, Zhu HW, Wang Y, Zhang XL, Tam NFY. Diversity and Dynamics of Microbial Community Structure in Different Mangrove, Marine and Freshwater Sediments During Anaerobic Debromination of PBDEs. Front Microbiol 2018; 9:952. [PMID: 29867858 PMCID: PMC5962692 DOI: 10.3389/fmicb.2018.00952] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 04/24/2018] [Indexed: 01/11/2023] Open
Abstract
Little is known about the diversity and succession of indigenous microbial community during debromination of polybrominated diphenyl ethers (PBDEs). This study examined the diversity and dynamics of microbial community structure in eight saline (mangrove and marine) and freshwater sediment microcosms exhibiting different debrominating capabilities for hexa-BDE 153, a common congener in sediments, using terminal restriction fragment length polymorphism (T-RFLP) and clone library analyses. The results showed that microbial community structure greatly differed between the saline and freshwater microcosms, likely leading to distinct variations in their debrominating capabilities and pathways. Higher relative abundances of Chloroflexi and Deltaproteobacteria succeed by Alphaproteobacteria and Betaproteobacteria were detected in the two mangrove microcosms with the fastest debrominating capabilities mainly via para pathway, respectively; the dominance of Alphaproteobacteria resulted in less accumulation of tetra-BDEs and more complete debromination of lower brominated congeners (from di- to tetra-BDEs). Meanwhile, the shifts in both microbial community structure and PBDE profiles were relatively small in the less efficient freshwater microcosms, with relatively more ortho and meta brominated products of BDE-153 resulted. Coincidently, one of the freshwater microcosms showed sudden increases of Chloroflexi and Deltaproteobacteria by the end of incubation, which synchronized with the increase in the removal rate of BDE-153. The significant relationship between microbial community structure and PBDEs was confirmed by redundancy analysis (18.7% of total variance explained, P = 0.002). However, the relative abundance of the well-known dechlorinator Dehalococcoides showed no clear correlation with the debrominating capability across different microcosms. These findings shed light in the significance of microbial community network in different saline environments on enhancement of PBDE intrinsic debromination.
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Affiliation(s)
- Ya Fen Wang
- Laboratory of Basin Hydrology and Wetland Eco-restoration, School of Environmental Studies, China University of Geosciences, Wuhan, China.,Department of Biology and Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Hao Wen Zhu
- Department of Biology and Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Ying Wang
- Department of Biology and Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Xiang Ling Zhang
- School of Civil Engineering and Architecture, Wuhan University of Technology, Wuhan, China
| | - Nora Fung Yee Tam
- Department of Biology and Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong.,State Key Laboratory in Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong
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Liu S, Jiang Z, Deng Y, Wu Y, Zhang J, Zhao C, Huang D, Huang X, Trevathan-Tackett SM. Effects of nutrient loading on sediment bacterial and pathogen communities within seagrass meadows. Microbiologyopen 2018. [PMID: 29521006 PMCID: PMC6182560 DOI: 10.1002/mbo3.600] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Eutrophication can play a significant role in seagrass decline and habitat loss. Microorganisms in seagrass sediments are essential to many important ecosystem processes, including nutrient cycling and seagrass ecosystem health. However, current knowledge of the bacterial communities, both beneficial and detrimental, within seagrass meadows in response to nutrient loading is limited. We studied the response of sediment bacterial and pathogen communities to nutrient enrichment on a tropical seagrass meadow in Xincun Bay, South China Sea. The bacterial taxonomic groups across all sites were dominated by the Gammaproteobacteria and Firmicutes. Sites nearest to the nutrient source and with the highest NH4+ and PO43− content had approximately double the relative abundance of putative denitrifiers Vibrionales, Alteromonadales, and Pseudomonadales. Additionally, the relative abundance of potential pathogen groups, especially Vibrio spp. and Pseudoalteromonas spp., was approximately 2‐fold greater at the sites with the highest nutrient loads compared to sites further from the source. These results suggest that proximity to sources of nutrient pollution increases the occurrence of potential bacterial pathogens that could affect fishes, invertebrates and humans. This study shows that nutrient enrichment does elicit shifts in bacterial community diversity and likely their function in local biogeochemical cycling and as a potential source of infectious diseases within seagrass meadows.
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Affiliation(s)
- Songlin Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China, Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhijian Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China, Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Yiqin Deng
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Yunchao Wu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China, Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jingping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China, Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Chunyu Zhao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China, Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Delian Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China, Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoping Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China, Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Stacey M Trevathan-Tackett
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Vic., Australia
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Lee DW, Lee H, Lee AH, Kwon BO, Khim JS, Yim UH, Kim BS, Kim JJ. Microbial community composition and PAHs removal potential of indigenous bacteria in oil contaminated sediment of Taean coast, Korea. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 234:503-512. [PMID: 29216488 DOI: 10.1016/j.envpol.2017.11.097] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/20/2017] [Accepted: 11/28/2017] [Indexed: 05/15/2023]
Abstract
The tidal flats near Sinduri beach in Taean, Korea, have been severely contaminated by heavy crude oils due to the Korea's worst oil spill accident, say the Hebei Spirit Oil Spill, in 2007. Crude oil compounds, including polycyclic aromatic hydrocarbons (PAHs), pose significant environmental damages due to their wide distribution, persistence, high toxicity, mutagenicity, and carcinogenicity. Microbial community of Sinduri beach sediments samples was analyzed by metagenomic data with 16S rRNA gene amplicons. Three phyla (Proteobacteria, Firmicutes, and Bacteroidetes) accounted for approximately ≥93.0% of the total phyla based on metagenomic analysis. Proteobacteria was the dominant phylum in Sinduri beach sediments. Cultivable bacteria were isolated from PAH-enriched cultures, and bacterial diversity was investigated through performing culture characterization followed by molecular biology methods. Sixty-seven isolates were obtained, comprising representatives of Actinobacteria, Firmicutes, α- and γ-Proteobacteria, and Bacteroidetes. PAH catabolism genes, such as naphthalene dioxygenase (NDO) and aromatic ring hydroxylating dioxygenase (ARHDO), were used as genetic markers to assess biodegradation of PAHs in the cultivable bacteria. The ability to degrade PAHs was demonstrated by monitoring the removal of PAHs using a gas chromatography mass spectrometer. Overall, various PAH-degrading bacteria were widely present in Sinduri beach sediments and generally reflected the restored microbial community. Among them, Cobetia marina, Rhodococcus soli, and Pseudoalteromonas agarivorans were found to be significant in degradation of PAHs. This large collection of PAH-degrading strains represents a valuable resource for studies investigating mechanisms of PAH degradation and bioremediation in oil contaminated coastal environment, elsewhere.
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Affiliation(s)
- Dong Wan Lee
- Division of Environmental Science & Ecological Engineering, College of Life Science & Biotechnology, Korea University, Seoul, 02841, Republic of Korea; BK21 Plus Eco-Leader Education Center, Korea University, Seoul, 02841, Republic of Korea
| | - Hanbyul Lee
- Division of Environmental Science & Ecological Engineering, College of Life Science & Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Aslan Hwanhwi Lee
- Department of Civil and Geological Engineering, University of Saskatchewan, 57 Campus Drive, Saskatoon, SK, S7N 5A9, Canada
| | - Bong-Oh Kwon
- School of Earth and Environmental Science & Research Institute of Oceanography, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jong Seong Khim
- School of Earth and Environmental Science & Research Institute of Oceanography, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Un Hyuk Yim
- Oil and POPs Research Group, Korea Institute of Ocean Science and Technology, Geoje, Republic of Korea
| | - Beom Seok Kim
- Division of Biotechnology, College of Life Science & Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Jae-Jin Kim
- Division of Environmental Science & Ecological Engineering, College of Life Science & Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
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Lv B, Cui Y, Tian W, Feng D. Composition and influencing factors of bacterial communities in ballast tank sediments: Implications for ballast water and sediment management. MARINE ENVIRONMENTAL RESEARCH 2017; 132:14-22. [PMID: 29046225 DOI: 10.1016/j.marenvres.2017.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 10/08/2017] [Accepted: 10/08/2017] [Indexed: 06/07/2023]
Abstract
This study aims to reveal the composition and influencing factors of bacterial communities in ballast tank sediments. Nine samples were collected and their 16S rRNA gene sequences were analyzed by high-throughput sequencing. The analysis results showed the Shannon index in ballast tank sediments was in the range of 5.27-6.35, which was significantly higher than that in ballast water. Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi and Proteobacteria were the dominant phyla and accounted for approximately 80% of all 16S rRNA gene sequences of the samples. Besides, the high contents of sulfate reducing bacteria (SRB) and sulfur oxidizing bacteria were detected in sediments, indicating that the corrosion of metal caused by SRB might occur in ballast tank. In addition, the trace of human fecal bacteria and candidate pathogens were also detected in ballast tank sediments, and these undesirable microbes reduced the effect of ballast water exchange. Furthermore, C and N had significant effects on the bacterial community composition in ballast tank sediments. In conclusion, our findings suggest that the proper management and disposal of the ballast tank sediments should be considered in order to reduce the negative impact and ecological risks related to ballast water and sediments.
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Affiliation(s)
- Baoyi Lv
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China.
| | - Yuxue Cui
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, East China Normal University, Shanghai 200241, China
| | - Wen Tian
- Jiangyin Entry-Exit Inspection and Quarantine Bureau, Jiangyin 214442, China
| | - Daolun Feng
- College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China
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Ser HL, Tan LTH, Law JWF, Chan KG, Duangjai A, Saokaew S, Pusparajah P, Ab Mutalib NS, Khan TM, Goh BH, Lee LH. Focused Review: Cytotoxic and Antioxidant Potentials of Mangrove-Derived Streptomyces. Front Microbiol 2017; 8:2065. [PMID: 29163380 PMCID: PMC5672783 DOI: 10.3389/fmicb.2017.02065] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 10/09/2017] [Indexed: 12/31/2022] Open
Abstract
Human life expectancy is rapidly increasing with an associated increasing burden of chronic diseases, such as neurodegenerative diseases and cancer. However, there is limited progress in finding effective treatment for these conditions. For this reason, members of the genus Streptomyces have been explored extensively over the past decades as these filamentous bacteria are highly efficient in producing bioactive compounds with human health benefits. Being ubiquitous in nature, streptomycetes can be found in both terrestrial and marine environments. Previously, two Streptomyces strains (MUSC 137T and MUM 256) isolated from mangrove sediments in Peninsular Malaysia demonstrated potent antioxidant and cytotoxic activities against several human cancer cell lines on bioactivity screening. These results illustrate the importance of streptomycetes from underexplored regions aside from the terrestrial ecosystem. Here we provide the insights and significance of Streptomyces species in the search of anticancer and/or chemopreventive agents and highlight the impact of next generation sequencing on drug discovery from the Streptomyces arsenal.
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Affiliation(s)
- Hooi-Leng Ser
- Novel Bacteria and Drug Discovery Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia
- Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, Malaysia
- Biofunctional Molecule Exploratory Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Loh Teng-Hern Tan
- Novel Bacteria and Drug Discovery Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia
- Biofunctional Molecule Exploratory Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Jodi Woan-Fei Law
- Novel Bacteria and Drug Discovery Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia
- Biofunctional Molecule Exploratory Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
- Vice Chancellor Office, Jiangsu University, Zhenjiang, China
| | - Acharaporn Duangjai
- Division of Physiology, School of Medical Sciences, University of Phayao, Phayao, Thailand
- Center of Health Outcomes Research and Therapeutic Safety, School of Pharmaceutical Sciences, University of Phayao, Phayao, Thailand
| | - Surasak Saokaew
- Novel Bacteria and Drug Discovery Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia
- Biofunctional Molecule Exploratory Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia
- Center of Health Outcomes Research and Therapeutic Safety, School of Pharmaceutical Sciences, University of Phayao, Phayao, Thailand
- Pharmaceutical Outcomes Research Center, Faculty of Pharmaceutical Sciences, Naresuan University, Phitsanulok, Thailand
| | - Priyia Pusparajah
- Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Nurul-Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute, UKM Medical Centre, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Tahir Mehmood Khan
- Novel Bacteria and Drug Discovery Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia
- Biofunctional Molecule Exploratory Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia
- Department of Pharmacy, Absyn University Peshawar, Peshawar, Pakistan
- Asian Centre for Evidence Synthesis in Population, Implementation and Clinical Outcomes, Health and Well-Being Cluster, Global Asia in the 21st Century Platform, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Bey-Hing Goh
- Novel Bacteria and Drug Discovery Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia
- Biofunctional Molecule Exploratory Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia
- Center of Health Outcomes Research and Therapeutic Safety, School of Pharmaceutical Sciences, University of Phayao, Phayao, Thailand
- Asian Centre for Evidence Synthesis in Population, Implementation and Clinical Outcomes, Health and Well-Being Cluster, Global Asia in the 21st Century Platform, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Learn-Han Lee
- Novel Bacteria and Drug Discovery Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia
- Biofunctional Molecule Exploratory Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia
- Center of Health Outcomes Research and Therapeutic Safety, School of Pharmaceutical Sciences, University of Phayao, Phayao, Thailand
- Asian Centre for Evidence Synthesis in Population, Implementation and Clinical Outcomes, Health and Well-Being Cluster, Global Asia in the 21st Century Platform, Monash University Malaysia, Bandar Sunway, Malaysia
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Behera P, Mahapatra S, Mohapatra M, Kim JY, Adhya TK, Raina V, Suar M, Pattnaik AK, Rastogi G. Salinity and macrophyte drive the biogeography of the sedimentary bacterial communities in a brackish water tropical coastal lagoon. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 595:472-485. [PMID: 28395262 DOI: 10.1016/j.scitotenv.2017.03.271] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 03/28/2017] [Accepted: 03/29/2017] [Indexed: 06/07/2023]
Abstract
Brackish water coastal lagoons are least understood with respect to the seasonal and temporal variability in their sedimentary bacterial communities. These coastal lagoons are characterized by the steep environmental gradient and provide an excellent model system to decipher the biotic and abiotic factors that determine the bacterial community structure over time and space. Using Illumina sequencing of the 16S rRNA genes from a total of 100 bulk surface sediments, we investigated the sedimentary bacterial communities, their spatiotemporal distribution, and compared them with the rhizosphere sediment communities of a common reed; Phragmites karka and a native seagrass species; Halodule uninervis in Chilika Lagoon. Spatiotemporal patterns in bacterial communities were linked to specific biotic factors (e.g., presence and type of macrophyte) and abiotic factors (e.g., salinity) that drove the community composition. Comparative assessment of communities highlighted bacterial lineages that were responsible for segregating the sediment communities over distinct salinity regimes, seasons, locations, and presence and type of macrophytes. Several bacterial taxa were specific to one of these ecological factors suggesting that species-sorting processes drive specific biogeographical patterns in the bacterial populations. Modeling of proteobacterial lineages against salinity gradient revealed that α- and γ-Proteobacteria increased with salinity, whereas β-Proteobacteria displayed the opposite trend. The wide variety of biogeochemical functions performed by the rhizosphere microbiota of P. karka must be taken into consideration while formulating the management and conservation plan for this reed. Overall, this study provides a comprehensive understanding of the spatiotemporal dynamics and functionality of sedimentary bacterial communities and highlighted the role of biotic and abiotic factors in generating the biogeographical patterns in the bacterial communities of a tropical brackish water coastal lagoon.
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Affiliation(s)
- Pratiksha Behera
- Wetland Research and Training Centre, Chilika Development Authority, Barkul, Balugaon, 752030, Odisha, India
| | - Sofia Mahapatra
- Wetland Research and Training Centre, Chilika Development Authority, Barkul, Balugaon, 752030, Odisha, India
| | - Madhusmita Mohapatra
- Wetland Research and Training Centre, Chilika Development Authority, Barkul, Balugaon, 752030, Odisha, India
| | - Ji Yoon Kim
- Department of Integrated Biological Science, Pusan National University, Geumjeong-gu, 46241 Busan, South Korea
| | - Tapan K Adhya
- School of Biotechnology, KIIT University, Patia, Bhubaneswar, 751024, Odisha, India
| | - Vishakha Raina
- School of Biotechnology, KIIT University, Patia, Bhubaneswar, 751024, Odisha, India
| | - Mrutyunjay Suar
- School of Biotechnology, KIIT University, Patia, Bhubaneswar, 751024, Odisha, India
| | - Ajit K Pattnaik
- Wetland Research and Training Centre, Chilika Development Authority, Barkul, Balugaon, 752030, Odisha, India
| | - Gurdeep Rastogi
- Wetland Research and Training Centre, Chilika Development Authority, Barkul, Balugaon, 752030, Odisha, India.
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Distinct taxonomic and functional composition of soil microbiomes along the gradient forest-restinga-mangrove in southeastern Brazil. Antonie van Leeuwenhoek 2017; 111:101-114. [PMID: 28831604 DOI: 10.1007/s10482-017-0931-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 08/17/2017] [Indexed: 02/06/2023]
Abstract
Soil microorganisms play crucial roles in ecosystem functioning, and the central goal in microbial ecology studies is to elucidate which factors shape community structure. A better understanding of the relationship between microbial diversity, functions and environmental parameters would increase our ability to set conservation priorities. Here, the bacterial and archaeal community structure in Atlantic Forest, restinga and mangrove soils was described and compared based on shotgun metagenomics. We hypothesized that each distinct site would harbor a distinct taxonomic and functional soil community, which is influenced by environmental parameters. Our data showed that the microbiome is shaped by soil properties, with pH, base saturation, boron and iron content significantly correlated to overall community structure. When data of specific phyla were correlated to specific soil properties, we demonstrated that parameters such as boron, copper, sulfur, potassium and aluminum presented significant correlation with the most number of bacterial groups. Mangrove soil was the most distinct site and presented the highest taxonomic and functional diversity in comparison with forest and restinga soils. From the total 34 microbial phyla identified, 14 were overrepresented in mangrove soils, including several archaeal groups. Mangrove soils hosted a high abundance of sequences related to replication, survival and adaptation; forest soils included high numbers of sequences related to the metabolism of nutrients and other composts; while restinga soils included abundant genes related to the metabolism of carbohydrates. Overall, our finds show that the microbial community structure and functional potential were clearly different across the environmental gradient, followed by functional adaptation and both were related to the soil properties.
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Global Distribution Patterns and Pangenomic Diversity of the Candidate Phylum "Latescibacteria" (WS3). Appl Environ Microbiol 2017; 83:AEM.00521-17. [PMID: 28314726 DOI: 10.1128/aem.00521-17] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 03/11/2017] [Indexed: 01/01/2023] Open
Abstract
We investigated the global distribution patterns and pangenomic diversity of the candidate phylum "Latescibacteria" (WS3) in 16S rRNA gene as well as metagenomic data sets. We document distinct distribution patterns for various "Latescibacteria" orders in 16S rRNA gene data sets, with prevalence of orders sediment_1 in terrestrial, PBSIII_9 in groundwater and temperate freshwater, and GN03 in pelagic marine, saline-hypersaline, and wastewater habitats. Using a fragment recruitment approach, we identified 68.9 Mb of "Latescibacteria"-affiliated contigs in publicly available metagenomic data sets comprising 73,079 proteins. Metabolic reconstruction suggests a prevalent saprophytic lifestyle in all "Latescibacteria" orders, with marked capacities for the degradation of proteins, lipids, and polysaccharides predominant in plant, bacterial, fungal/crustacean, and eukaryotic algal cell walls. As well, extensive transport and central metabolic pathways for the metabolism of imported monomers were identified. Interestingly, genes and domains suggestive of the production of a cellulosome-e.g., protein-coding genes harboring dockerin I domains attached to a glycosyl hydrolase and scaffoldin-encoding genes harboring cohesin I and CBM37 domains-were identified in order PBSIII_9, GN03, and MSB-4E2 fragments recovered from four anoxic aquatic habitats; hence extending the cellulosomal production capabilities in Bacteria beyond the Gram-positive Firmicutes In addition to fermentative pathways, a complete electron transport chain with terminal cytochrome c oxidases Caa3 (for operation under high oxygen tension) and Cbb3 (for operation under low oxygen tension) were identified in PBSIII_9 and GN03 fragments recovered from oxygenated and partially/seasonally oxygenated aquatic habitats. Our metagenomic recruitment effort hence represents a comprehensive pangenomic view of this yet-uncultured phylum and provides insights broader than and complementary to those gained from genome recovery initiatives focusing on a single or few sampled environments.IMPORTANCE Our understanding of the phylogenetic diversity, metabolic capabilities, and ecological roles of yet-uncultured microorganisms is rapidly expanding. However, recent efforts mainly have been focused on recovering genomes of novel microbial lineages from a specific sampling site, rather than from a wide range of environmental habitats. To comprehensively evaluate the genomic landscape, putative metabolic capabilities, and ecological roles of yet-uncultured candidate phyla, efforts that focus on the recovery of genomic fragments from a wide range of habitats and that adequately sample the intraphylum diversity within a specific target lineage are needed. Here, we investigated the global distribution patterns and pangenomic diversity of the candidate phylum "Latescibacteria" Our results document the preference of specific "Latescibacteria" orders to specific habitats, the prevalence of plant polysaccharide degradation abilities within all "Latescibacteria" orders, the occurrence of all genes/domains necessary for the production of cellulosomes within three "Latescibacteria" orders (GN03, PBSIII_9, and MSB-4E2) in data sets recovered from anaerobic locations, and the identification of the components of an aerobic respiratory chain, as well as occurrence of multiple O2-dependent metabolic reactions in "Latescibacteria" orders GN03 and PBSIII_9 recovered from oxygenated habitats. The results demonstrate the value of phylocentric pangenomic surveys for understanding the global ecological distribution and panmetabolic abilities of yet-uncultured microbial lineages since they provide broader and more complementary insights than those gained from single-cell genomic and/or metagenomic-enabled genome recovery efforts focusing on a single sampling site.
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Barksdale SM, Hrifko EJ, van Hoek ML. Cathelicidin antimicrobial peptide from Alligator mississippiensis has antibacterial activity against multi-drug resistant Acinetobacter baumanii and Klebsiella pneumoniae. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 70:135-144. [PMID: 28089718 DOI: 10.1016/j.dci.2017.01.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/10/2017] [Accepted: 01/10/2017] [Indexed: 06/06/2023]
Abstract
Alligator mississippiensis (American alligator), a member of order Crocodilia, lives in bacteria-laden environments but is not often known to succumb to bacterial infections. Their serum has been shown to have antibacterial activity beyond that of human serum, and it is believed that this activity is partially due to cationic antimicrobial peptides (CAMPs). CAMPs are produced by many organisms as part of the innate immune system. CAMPs are attractive possible therapies against multi-drug resistant bacteria, such as those found in biofilm-infected war wounds, because they seldom cause genetic resistance in bacteria and are effective against antibiotic resistant bacteria. In this work, we identified, synthesized, and characterized a cathelicidin and two shorter fragments from the American alligator. We discovered the cathelicidin using Basic Local Alignment Search Tool (BLAST) alignment and by comparing A. mississippiensis expressed sequence tags (ESTs) with propeptide cathelicidins of other reptiles. We analyzed the structure using bioinformatics tools and circular dichroism and predicted that the full-length cathelicidin peptide has a mixed structure, with an N-terminal α-helix and a center Pro hinge. In minimal inhibitory concentration (MIC) assays, it was determined that the cathelicidin and the two shorter fragments have strong activity against multiple Gram-negative bacteria, including clinical isolates of multi-drug resistant (MDR) Acinetobacter baumannii and carbapenem-resistant Klebsiella pneumoniae. Using the ethidium bromide uptake assay, it was found that these peptides permeabilize the bacterial membrane and are less sensitive to salt inhibition than many other known CAMPs. The alligator cathelicidin peptides were not hemolytic against sheep red blood cells at 300 μg/ml and were not significantly cytotoxic against A549 human lung epithelial cells after 24 h exposure in 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assays. These alligator cathelicidin peptides have activity similar to other CAMPs from reptiles such as NA-CATH. It is possible that the alligator cathelicidins play an important role in the innate immune response of A. mississippiensis, similar to LL-37 in humans. In addition, due to their activities against MDR bacteria and lack of cytotoxicity, the AM-CATH peptides could be an attractive platform for further development as a potential therapeutic.
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Affiliation(s)
| | - Evelyn J Hrifko
- College of Science, George Mason University, Manassas, VA, USA
| | - Monique L van Hoek
- School of Systems Biology, George Mason University, Manassas, VA, USA; College of Science, George Mason University, Manassas, VA, USA; National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA, USA.
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Hu M, Ren H, Ren P, Li J, Wilson BJ, Tong C. Response of gaseous carbon emissions to low-level salinity increase in tidal marsh ecosystem of the Min River estuary, southeastern China. J Environ Sci (China) 2017; 52:210-222. [PMID: 28254041 DOI: 10.1016/j.jes.2016.05.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 05/19/2016] [Accepted: 05/20/2016] [Indexed: 06/06/2023]
Abstract
Although estuarine tidal marshes are important contributors to the emission of greenhouse gases into the atmosphere, the relationship between carbon dioxide (CO2), methane (CH4) emission, and environmental factors, with respect to estuarine marshes, has not been clarified thoroughly. This study investigated the crucial factors controlling the emission of CO2 and CH4 from a freshwater marsh and a brackish marsh located in a subtropical estuary in southeastern China, as well as their magnitude. The duration of the study period was November 2013 to October 2014. Relevant to both the field and incubation experiments, the CO2 and CH4 emissions from the two marshes showed pronounced seasonal variations. The CO2 and CH4 emissions from both marshes demonstrated significant positive correlations with the air/soil temperature (p<0.01), but negative correlations with the soil electrical conductivity and the pore water/tide water Cl- and SO42- (p<0.01). The results indicate no significant difference in the CO2 emissions between the freshwater and brackish marshes in the subtropical estuary, whereas there was a difference in the CH4 emissions between the two sites (p<0.01). Although future sea-level rise and saltwater intrusion could reduce the CH4 emissions from the estuarine freshwater marshes, these factors had little effect on the CO2 emissions with respect to an increase in salinity of less than 5‰. The findings of this study could have important implications for estimating the global warming contributions of estuarine marshes along differing salinity gradients.
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Affiliation(s)
- Minjie Hu
- School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China; Key Laboratory of Humid Sub-tropical Eco-geographical Process of Ministry of Education, Fujian Normal University, Fuzhou 350007, China; Research Centre of Wetlands in Subtropical Region, Fujian Normal University, Fuzhou 350007, China.
| | - Hongchang Ren
- School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China; Key Laboratory of Humid Sub-tropical Eco-geographical Process of Ministry of Education, Fujian Normal University, Fuzhou 350007, China; Research Centre of Wetlands in Subtropical Region, Fujian Normal University, Fuzhou 350007, China
| | - Peng Ren
- School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China; Key Laboratory of Humid Sub-tropical Eco-geographical Process of Ministry of Education, Fujian Normal University, Fuzhou 350007, China; Research Centre of Wetlands in Subtropical Region, Fujian Normal University, Fuzhou 350007, China
| | - Jiabing Li
- School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China; School of Environmental Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Benjamin J Wilson
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA.
| | - Chuan Tong
- School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China; Key Laboratory of Humid Sub-tropical Eco-geographical Process of Ministry of Education, Fujian Normal University, Fuzhou 350007, China; Research Centre of Wetlands in Subtropical Region, Fujian Normal University, Fuzhou 350007, China.
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Wang K, Ye X, Zhang H, Chen H, Zhang D, Liu L. Regional variations in the diversity and predicted metabolic potential of benthic prokaryotes in coastal northern Zhejiang, East China Sea. Sci Rep 2016; 6:38709. [PMID: 27917954 PMCID: PMC5137025 DOI: 10.1038/srep38709] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/11/2016] [Indexed: 12/21/2022] Open
Abstract
Knowledge about the drivers of benthic prokaryotic diversity and metabolic potential in interconnected coastal sediments at regional scales is limited. We collected surface sediments across six zones covering ~200 km in coastal northern Zhejiang, East China Sea and combined 16 S rRNA gene sequencing, community-level metabolic prediction, and sediment physicochemical measurements to investigate variations in prokaryotic diversity and metabolic gene composition with geographic distance and under local environmental conditions. Geographic distance was the most influential factor in prokaryotic β-diversity compared with major environmental drivers, including temperature, sediment texture, acid-volatile sulfide, and water depth, but a large unexplained variation in community composition suggested the potential effects of unmeasured abiotic/biotic factors and stochastic processes. Moreover, prokaryotic assemblages showed a biogeographic provincialism across the zones. The predicted metabolic gene composition similarly shifted as taxonomic composition did. Acid-volatile sulfide was strongly correlated with variation in metabolic gene composition. The enrichments in the relative abundance of sulfate-reducing bacteria and genes relevant with dissimilatory sulfate reduction were observed and predicted, respectively, in the Yushan area. These results provide insights into the relative importance of geographic distance and environmental condition in driving benthic prokaryotic diversity in coastal areas and predict specific biogeochemically-relevant genes for future studies.
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Affiliation(s)
- Kai Wang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Xiansen Ye
- Marine Environmental Monitoring Center of Ningbo, SOA, Ningbo, 315012, China
| | - Huajun Zhang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Heping Chen
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Faculty of Architectural, Civil Engineering and Environment, Ningbo University, Ningbo, 315211, China
| | - Demin Zhang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.,Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Lian Liu
- Marine Environmental Monitoring Center of Ningbo, SOA, Ningbo, 315012, China
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Bacterial community structure and function shift along a successional series of tidal flats in the Yellow River Delta. Sci Rep 2016; 6:36550. [PMID: 27824160 PMCID: PMC5099912 DOI: 10.1038/srep36550] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 10/18/2016] [Indexed: 11/19/2022] Open
Abstract
Coastal ecosystems play significant ecological and economic roles but are threatened and facing decline. Microbes drive various biogeochemical processes in coastal ecosystems. Tidal flats are critical components of coastal ecosystems; however, the structure and function of microbial communities in tidal flats are poorly understood. Here we investigated the seasonal variations of bacterial communities along a tidal flat series (subtidal, intertidal and supratidal flats) and the factors affecting the variations. Bacterial community composition and diversity were analyzed over four seasons by 16S rRNA genes using the Ion Torrent PGM platform. Bacterial community composition differed significantly along the tidal flat series. Bacterial phylogenetic diversity increased while phylogenetic turnover decreased from subtidal to supratidal flats. Moreover, the bacterial community structure differed seasonally. Canonical correspondence analysis identified salinity as a major environmental factor structuring the microbial community in the sediment along the successional series. Meanwhile, temperature and nitrite concentration were major drivers of seasonal microbial changes. Despite major compositional shifts, nitrogen, methane and energy metabolisms predicted by PICRUSt were inhibited in the winter. Taken together, this study indicates that bacterial community structure changed along the successional tidal flat series and provides new insights on the characteristics of bacterial communities in coastal ecosystems.
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Zhou J, Zhang R, Liu F, Yong X, Wu X, Zheng T, Jiang M, Jia H. Biogas production and microbial community shift through neutral pH control during the anaerobic digestion of pig manure. BIORESOURCE TECHNOLOGY 2016; 217:44-49. [PMID: 26944458 DOI: 10.1016/j.biortech.2016.02.077] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 02/17/2016] [Accepted: 02/19/2016] [Indexed: 06/05/2023]
Abstract
Laboratory-scale reactors, in which the pH could be auto-adjusted, were employed to investigate the mesophilic methane fermentation with pig manure (7.8% total solids) at pH 6.0, 7.0, and 8.0. Results showed that the performance of anaerobic digestion was strongly dependent on pH value. Biogas production and methane content at neutral pH 7.0 were significantly higher (16,607mL, 51.81%) than those at pH 6.0 (6916mL, 42.9%) and 8.0 (9739mL, 35.6%). Denaturing gradient gel electrophoresis fingerprinting and Shannon's index indicated that the samples contained highly diverse microbial communities. The major genus at pH 7.0 was Methanocorpusculum, compared with that was Methanosarcina at both pH 6.0 and 8.0. Our research revealed that cultures maintained at pH 7.0 could support increased biogas production, which has significant implications for the scale-up biogas engineering.
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Affiliation(s)
- Jun Zhou
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Rui Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Fenwu Liu
- Environmental Engineering Laboratory, College of Resource and Environment, Shanxi Agricultural University, Taigu 030801, China
| | - Xiaoyu Yong
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Xiayuan Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Tao Zheng
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Min Jiang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Honghua Jia
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China.
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Zhao F, Xu K. Biodiversity patterns of soil ciliates along salinity gradients. Eur J Protistol 2016; 53:1-10. [DOI: 10.1016/j.ejop.2015.12.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/11/2015] [Accepted: 12/19/2015] [Indexed: 10/22/2022]
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50
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Cúcio C, Engelen AH, Costa R, Muyzer G. Rhizosphere Microbiomes of European + Seagrasses Are Selected by the Plant, But Are Not Species Specific. Front Microbiol 2016; 7:440. [PMID: 27065991 PMCID: PMC4815253 DOI: 10.3389/fmicb.2016.00440] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/18/2016] [Indexed: 11/13/2022] Open
Abstract
Seagrasses are marine flowering plants growing in soft-body sediments of intertidal and shallow sub-tidal zones. They play an important role in coastal ecosystems by stabilizing sediments, providing food and shelter for animals, and recycling nutrients. Like other plants, seagrasses live intimately with both beneficial and unfavorable microorganisms. Although much is known about the microbiomes of terrestrial plants, little is known about the microbiomes of seagrasses. Here we present the results of a detailed study on the rhizosphere microbiome of seagrass species across the North-eastern Atlantic Ocean: Zostera marina, Zostera noltii, and Cymodocea nodosa. High-resolution amplicon sequencing of 16S rRNA genes showed that the rhizobiomes were significantly different from the bacterial communities of surrounding bulk sediment and seawater. Although we found no significant differences between the rhizobiomes of different seagrass species within the same region, those of seagrasses in different geographical locations differed strongly. These results strongly suggest that the seagrass rhizobiomes are shaped by plant metabolism, but not coevolved with their host. The core rhizobiome of seagrasses includes mostly bacteria involved in the sulfur cycle, thereby highlighting the importance of sulfur-related processes in seagrass ecosystems.
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Affiliation(s)
- Catarina Cúcio
- Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of AmsterdamAmsterdam, Netherlands
| | - Aschwin H. Engelen
- Marine Ecology and Evolution Research Group, Centro de Ciencias do Mar, Universidade do AlgarveFaro, Portugal
| | - Rodrigo Costa
- Microbial Ecology and Evolution Research Group, Centro de Ciencias do Mar, Universidade do AlgarveFaro, Portugal
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of AmsterdamAmsterdam, Netherlands
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