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Marín-Vindas C, Sebastián M, Ruiz-González C, Balagué V, Vega-Corrales L, Gasol JM. Shifts in bacterioplankton community structure between dry and wet seasons in a tropical estuary strongly affected by riverine discharge. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166104. [PMID: 37558065 DOI: 10.1016/j.scitotenv.2023.166104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 08/04/2023] [Accepted: 08/05/2023] [Indexed: 08/11/2023]
Abstract
Estuaries are among the most productive ecosystems in the world and are highly dynamic due to the interaction of freshwater and seawater, which results in strong spatial gradients in physico-chemical conditions. Bacterioplankton play a central role in these systems, driving the fluxes of carbon and energy, and being central for contaminant removal in human-impacted areas. Most studies on bacterioplankton dynamics have been carried out in temperate estuaries, and they show that salinity is a major factor driving bacterioplankton distribution. Tropical estuaries, although largely understudied, experience drastic variations in river discharge between the dry and the rainy seasons, influencing the spatial distribution of the salinity gradient and thus likely impacting bacterioplankton communities. Using Illumina sequencing of the 16S rRNA gene, here we studied bacterial communities from the Nicoya's Gulf (Costa Rica), a large tropical estuary characterized by high riverine discharge during the rainy season, to explore seasonal changes in the spatial distribution and connectivity of these communities along the Gulf. Our results show pronounced differences in bacterial diversity and community structure between seasons and zones within the estuary (the shallow upper Gulf, the middle zone and the lower zone, located in the marine end of the estuary). Bacterial communities from the different regions were more similar during the rainy season, suggesting a larger degree of microbial connectivity likely driven by the fast water circulation fueled by the riverine discharge. In the dry season, Enterobacteriales and Cyanobacteria dominated bacterial communities, whereas in the rainy season Alphaproteobacteria was the dominant group. These contrasting seasonal trends were consistent with the seasonal variations observed in bacterial assemblages during a year at a single station in the upper region of the Gulf. We conclude that the Gulf is highly dynamic in both the spatial and temporal scale and that bacterioplankton communities are strongly influenced by the riverine and tidal inputs during both seasons. This study sheds light on the sources of variability in the structure of bacterial communities in tropical estuarine systems, an understudied type of aquatic ecosystem, and sets the basis to design further comprehensive studies on their microbial diversity.
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Affiliation(s)
- Carolina Marín-Vindas
- Universidad Nacional, Escuela de Ciencias Biológicas, Heredia, Costa Rica; Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain.
| | - Marta Sebastián
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
| | - Clara Ruiz-González
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
| | - Vanessa Balagué
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
| | - Luis Vega-Corrales
- Universidad Nacional, Escuela de Ciencias Biológicas, Heredia, Costa Rica
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya, Spain
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Ansari MI, Calleja MLI, Silva L, Viegas M, Ngugi DK, Huete-Stauffer TM, Morán XAG. High-Frequency Variability of Bacterioplankton in Response to Environmental Drivers in Red Sea Coastal Waters. Front Microbiol 2022; 13:780530. [PMID: 35432231 PMCID: PMC9009512 DOI: 10.3389/fmicb.2022.780530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 03/03/2022] [Indexed: 11/13/2022] Open
Abstract
Autotrophic and heterotrophic bacterioplankton are essential to the biogeochemistry of tropical ecosystems. However, the processes that govern their dynamics are not well known. We provide here a high-frequency assessment of bacterial community dynamics and concurrent environmental factors in Red Sea coastal waters. Weekly sampling of surface samples during a full annual cycle at an enclosed station revealed high variability in ecological conditions, which reflected in changes of major bacterioplankton communities. Temperature varied between 23 and 34°C during the sampling period. Autotrophic (Synechococcus, 1.7–16.2 × 104 cells mL−1) and heterotrophic bacteria (1.6–4.3 × 105 cells mL−1) showed two maxima in abundance in spring and summer, while minima were found in winter and autumn. Heterotrophic cells with high nucleic acid content (HNA) peaked in July, but their contribution to the total cell counts (35–60%) did not show a clear seasonal pattern. Actively respiring cells (CTC+) contributed between 4 and 51% of the total number of heterotrophic bacteria, while live cells (with intact membrane) consistently accounted for over 90%. Sequenced 16S rRNA amplicons revealed a predominance of Proteobacteria in summer and autumn (>40%) and a smaller contribution in winter (21–24%), with members of the Alphaproteobacteria class dominating throughout the year. The contribution of the Flavobacteriaceae family was highest in winter (21%), while the Rhodobacteraceae contribution was lowest (6%). Temperature, chlorophyll-a, and dissolved organic carbon concentration were the environmental variables with the greatest effects on bacterial abundance and diversity patterns.
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Affiliation(s)
- Mohd Ikram Ansari
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Department of Biosciences, Integral University, Lucknow, India
- *Correspondence: Mohd Ikram Ansari, ; Xosé Anxelu G. Morán,
| | - Maria LI. Calleja
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Department of Climate Geochemistry, Max Planck Institute for Chemistry (MPIC), Mainz, Germany
| | - Luis Silva
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Miguel Viegas
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - David Kamanda Ngugi
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tamara Megan Huete-Stauffer
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Xosé Anxelu G. Morán
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Centro Oceanográfico de Gijón/Xixón (IEO, CSIC), Gijón/Xixón, Spain
- *Correspondence: Mohd Ikram Ansari, ; Xosé Anxelu G. Morán,
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Mai Y, Peng S, Lai Z, Wang X. Seasonal and inter-annual variability of bacterioplankton communities in the subtropical Pearl River Estuary, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:21981-21997. [PMID: 34775557 DOI: 10.1007/s11356-021-17449-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
It is widely recognized that environmental factors substantially influence on the seasonal and inter-annual variability of bacterioplankton communities, yet little is known about the seasonality of bacterioplankton communities in subtropical estuaries at longer-term time scales. Here, the bacterioplankton communities from the eight major outlets of the subtropical Pearl River Estuary were investigated across 3 years (2017-2019) using full-length 16S rRNA gene sequencing. Significant seasonal and inter-annual variation was observed in bacterioplankton community compositions across the 3 years (p < 0.05). In addition, the inferred functional composition of the communities varied with seasons, although not significantly, suggesting that functional redundancy existed among communities and across seasons that could help to cope with environmental changes. Five evaluated environmental parameters (temperature, salinity, pH, total dissolved solids (TDS), total phosphorus (TP)) were significantly correlated with community composition variation, while only three environmental parameters (temperature, pH, and TDS) were correlated with variation in inferred functional composition. Moreover, community composition tracked the seasonal temperature gradients, indicating that temperature was a key environmental factor that affected bacterioplankton community's variation along with seasonal succession patterns. Gammaproteobacteria and Alphaproteobacteria were the most dominant classes in the surface waters of Pearl River Estuary, and their members exhibited divergent responses to temperature changes, while several taxa within these group could be indicators of low and high temperatures that are associated with seasonal changes. These results strengthen our understanding of bacterioplankton community variation in association with temperature-dependent seasonal changes in subtropical estuarine ecosystems.
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Affiliation(s)
- Yongzhan Mai
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Songyao Peng
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Zini Lai
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China.
- Guangdong Provincial Key Laboratory of Aquatic Animal Immune Technology, Guangzhou, 510070, China.
| | - Xuesong Wang
- Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou), Guangzhou, 100 Xianlie Middle Road, 510070, China.
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4
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Hongxia M, Jingfeng F, Jiwen L, Zhiyi W, Yantao W, Dongwei L, Mengfei L, Tingting S, Yuan J, Huiling H, Jixue S. Full-length 16S rRNA gene sequencing reveals spatiotemporal dynamics of bacterial community in a heavily polluted estuary, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 275:116567. [PMID: 33578312 DOI: 10.1016/j.envpol.2021.116567] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 01/15/2021] [Accepted: 01/17/2021] [Indexed: 06/12/2023]
Abstract
Understanding the bacterial community structure of the river estuary could provide insights into the resident microorganisms in response to environmental pollution. In this study, the bacterial community structure of Liaohe Estuary was investigated using single-molecule real-time sequencing (SMRT). A total of 57 samples were collected and grouped according to habitat, space, season, and lifestyle. In seawater, regardless of whether it is particle-attached (PA) or free-living (FL) bacteria, the area with higher alpha diversity is the nearshore area in the dry season, while it is the midstream area in the wet season. The bacterial communities in sediment and seawater samples were different at the genus level in the nearshore area, and habitat type was the main factor. A marked difference in the bacterial community was observed in the dry season between different lifestyles but not in the wet season, which resulted from lifestyle transitions of bacterioplankton. Bacterial community varied spatially but not seasonally in sediment samples. In seawater, both FL and PA bacterial communities varied spatially during the wet season. Seasonal differences were only observed in FL bacterial community. Zn and sand were the principal determining factors of the bacterial community in the sediment, Cu and salinity were the main environmental factors for FL bacteria, and Cu, salinity, Zn and temperature were the main environmental factors for PA bacteria. Besides, the tide and nutrients were also the main drivers of the bacterial community in seawater. The indicative taxa, related to Cyanobium_PCC-6307, Pseudomonas and Vibrio, further evidenced the presence of possible bloom, crude oil and pathogen contamination. Overall, our results can contribute to the knowledge of the bacterial community and anthropogenic impacts on the Liaohe Estuary.
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Affiliation(s)
- Ming Hongxia
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Fan Jingfeng
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China.
| | - Liu Jiwen
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Wan Zhiyi
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Wang Yantao
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China; Dalian Ocean University, Dalian, 116023, China
| | - Li Dongwei
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China; Dalian Maritime University, Dalian, 116026, China
| | - Li Mengfei
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China; Dalian Ocean University, Dalian, 116023, China
| | - Shi Tingting
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Jin Yuan
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Huang Huiling
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China; Dalian Ocean University, Dalian, 116023, China
| | - Song Jixue
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
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Sanders-Smith R, Segovia BT, Forbes C, Hessing-Lewis M, Morien E, Lemay MA, O'Connor MI, Parfrey LW. Host-Specificity and Core Taxa of Seagrass Leaf Microbiome Identified Across Tissue Age and Geographical Regions. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.605304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The seagrass Zostera marina is a widespread foundational species in temperate coastal ecosystems that supports diverse communities of epiphytes and grazers. Bacteria link the production of seagrass to higher trophic levels and are thought to influence seagrass biology and health. Yet, we lack a clear understanding of the factors that structure the seagrass microbiome, or whether there is a consistent microbial community associated with seagrass that underpins functional roles. We sampled surface microbiome (epibiota) from new and old growth seagrass leaves and the surrounding seawater in eight meadows among four regions along the Central Coast of British Columbia, Canada to assess microbiome variability across space and as leaves age. We found that the seagrass leaf microbiome differs strongly from seawater. Microbial communities in new and old growth leaves are different from each other and from artificial seagrass leaves we deployed in one meadow. The microbiome on new leaves is less diverse and there is a small suite of core OTUs (operational taxonomic units) consistently present across regions. The overall microbial community for new leaves is more dispersed but with little regional differentiation, while the epiphytes on old leaves are regionally distinct. Many core OTUs on old leaves are commonly associated with marine biofilms. Together these observations suggest a stronger role for host filtering in new compared to old leaves, and a stronger influence of the environment and environmental colonization in old leaves. We found 11 core microbial taxa consistently present on old and new leaves and at very low relative abundance on artificial leaves and in the water column. These 11 taxa appear to be strongly associated with Z. marina. These core taxa may perform key functions important for the host such as detoxifying seagrass waste products, enhancing plant growth, and controlling epiphyte cover.
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Adyasari D, Hassenrück C, Montiel D, Dimova N. Microbial community composition across a coastal hydrological system affected by submarine groundwater discharge (SGD). PLoS One 2020; 15:e0235235. [PMID: 32598345 PMCID: PMC7323985 DOI: 10.1371/journal.pone.0235235] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/10/2020] [Indexed: 11/18/2022] Open
Abstract
Mobile Bay, the fourth largest estuary in the USA located in the northern Gulf of Mexico, is known for extreme hypoxia in the water column during dry season caused by NH4+-rich and anoxic submarine groundwater discharge (SGD). Nutrient dynamics in the coastal ecosystem point to potentially elevated microbial activities; however, little is known about microbial community composition and their functional roles in this area. In this study, we investigated microbial community composition, distribution, and metabolic prediction along the coastal hydrological compartment of Mobile Bay using 16S rRNA gene sequencing. We collected microbial samples from surface (river and bay water) and subsurface water (groundwater and coastal pore water from two SGD sites with peat and sandy lithology, respectively). Salinity was identified as the primary factor affecting the distribution of microbial communities across surface water samples, while DON and PO43- were the major predictor of community shift within subsurface water samples. Higher microbial diversity was found in coastal pore water in comparison to surface water samples. Gammaproteobacteria, Bacteroidia, and Oxyphotobacteria dominated the bacterial community. Among the archaea, methanogens were prevalent in the peat-dominated SGD site, while the sandy SGD site was characterized by a higher proportion of ammonia-oxidizing archaea. Cyanobium PCC-6307 and unclassified Thermodesulfovibrionia were identified as dominant taxa strongly associated with trends in environmental parameters in surface and subsurface samples, respectively. Microbial communities found in the groundwater and peat layer consisted of taxa known for denitrification and dissimilatory nitrate reduction to ammonium (DNRA). This finding suggested that microbial communities might also play a significant role in mediating nitrogen transformation in the SGD flow path and in affecting the chemical composition of SGD discharging to the water column. Given the ecological importance of microorganisms, further studies at higher taxonomic and functional resolution are needed to accurately predict chemical biotransformation processes along the coastal hydrological continuum, which influence water quality and environmental condition in Mobile Bay.
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Affiliation(s)
- Dini Adyasari
- Department of Biogeochemistry and Geology, Leibniz Centre for Tropical Marine Research, Bremen, Germany
| | - Christiane Hassenrück
- Department of Biogeochemistry and Geology, Leibniz Centre for Tropical Marine Research, Bremen, Germany
| | - Daniel Montiel
- Department of Geological Sciences, Coastal Hydrogeology Laboratory, University of Alabama, Alabama, AL, United States of America
- Geosyntec Consultants, Clearwater, FL, United States of America
| | - Natasha Dimova
- Department of Geological Sciences, Coastal Hydrogeology Laboratory, University of Alabama, Alabama, AL, United States of America
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Ortmann AC, Cobanli SE, Wohlgeschaffen G, Thamer P, McIntyre C, Mason J, King TL. Inorganic nutrients have a significant, but minimal, impact on a coastal microbial community's response to fresh diluted bitumen. MARINE POLLUTION BULLETIN 2019; 139:381-389. [PMID: 30686441 DOI: 10.1016/j.marpolbul.2019.01.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 01/02/2019] [Accepted: 01/06/2019] [Indexed: 06/09/2023]
Abstract
Microbes capable of degrading hydrocarbons in oil are present in low abundances in coastal waters, but quickly respond to oil following a spill. When estimating potential biodegradation rates in the laboratory, high concentrations of inorganic nutrients are often added to prevent nutrient limitation. In this study, we tested the short term response of coastal microbes to fresh diluted bitumen under varying nutrient conditions in a cold water regime. Total hydrocarbon concentrations changed minimally over five days; however, oil composition changed over time and the abundance of microbes increased in all treatments. Addition of phosphate, with or without nitrogen, resulted in rapid changes in community composition, but after three days treatments no longer differed. Nutrients were never depleted in any treatment suggesting that, even at low inorganic nutrient concentrations, microbial communities can quickly respond to hydrocarbons following a spill.
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Affiliation(s)
- Alice C Ortmann
- Center for Offshore Oil, Gas and Energy Research, Department of Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada.
| | - Susan E Cobanli
- Center for Offshore Oil, Gas and Energy Research, Department of Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada
| | - Gary Wohlgeschaffen
- Center for Offshore Oil, Gas and Energy Research, Department of Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada
| | - Peter Thamer
- Center for Offshore Oil, Gas and Energy Research, Department of Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada
| | - Claire McIntyre
- Center for Offshore Oil, Gas and Energy Research, Department of Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada
| | - Jennifer Mason
- Center for Offshore Oil, Gas and Energy Research, Department of Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada
| | - Thomas L King
- Center for Offshore Oil, Gas and Energy Research, Department of Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Drive, Dartmouth, NS B2Y 4A2, Canada
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8
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Easson CG, Lopez JV. Depth-Dependent Environmental Drivers of Microbial Plankton Community Structure in the Northern Gulf of Mexico. Front Microbiol 2019; 9:3175. [PMID: 30662434 PMCID: PMC6328475 DOI: 10.3389/fmicb.2018.03175] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 12/07/2018] [Indexed: 02/01/2023] Open
Abstract
The Gulf of Mexico (GoM) is a dynamic marine ecosystem influenced by multiple natural and anthropogenic processes and inputs, such as the intrusion of warm oligotrophic water via the Loop Current, freshwater and nutrient input by the Mississippi River, and hydrocarbon inputs via natural seeps and industrial spills. Microbial plankton communities are important to pelagic food webs including in the GoM but understanding the drivers of the natural dynamics of these passively distributed microorganisms can be challenging in such a large and heterogeneous system. As part of the DEEPEND consortium, we applied high throughput 16S rRNA sequencing to investigate the spatial and temporal dynamics of pelagic microbial plankton related to several environmental conditions during two offshore cruises in 2015. Our results show dramatic community shifts across depths, especially between photic and aphotic zones. Though we only have two time points within a single year, observed temporal shifts in microbial plankton communities were restricted to the seasonally influenced epipelagic zone (0-200 m), and appear mainly driven by changes in temperature. Environmental selection in microbial plankton communities was depth-specific, with variables such as turbidity, salinity, and abundance of photosynthetic taxa strongly correlating with community structure in the epipelagic zone, while variables such as oxygen and specific nutrient concentrations were correlated with community structure at deeper depths.
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Affiliation(s)
- Cole G. Easson
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, United States
| | - Jose V. Lopez
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, FL, United States
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Raut S, Polley HW, Fay PA, Kang S. Bacterial community response to a preindustrial-to-future CO 2 gradient is limited and soil specific in Texas Prairie grassland. GLOBAL CHANGE BIOLOGY 2018; 24:5815-5827. [PMID: 30230661 DOI: 10.1111/gcb.14453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 09/07/2018] [Indexed: 06/08/2023]
Abstract
Rising atmospheric CO2 concentration directly stimulates plant productivity and affects nutrient dynamics in the soil. However, the influence of CO2 enrichment on soil bacterial communities remains elusive, likely due to their complex interactions with a wide range of plant and soil properties. Here, we investigated the bacterial community response to a decade long preindustrial-to-future CO2 gradient (250-500 ppm) among three contrasting soil types using 16S rRNA gene amplicon sequencing. In addition, we examined the effect of seasonal variation and plant species composition on bacterial communities. We found that Shannon index (H') and Faith's phylogenetic diversity (PD) did not change in response to the CO2 gradient (R2 = 0.01, p > 0.05). CO2 gradient and season also had a negligible effect on overall community structure, although silty clay soil communities were better structured on a CO2 gradient (p < 0.001) among three soils. Similarly, CO2 gradient had no significant effect on the relative abundance of different phyla. However, we observed soil-specific variation of CO2 effects in a few individual families. For example, the abundance of Pirellulaceae family decreased linearly with CO2 gradient, but only in sandy loam soils. Conversely, the abundance of Micromonosporaceae and Gaillaceae families increased with CO2 gradient in clay soils. Soil water content (SWC) and nutrient properties were the key environmental constraints shaping bacterial community structure, one manifestation of which was a decline in bacterial diversity with increasing SWC. Furthermore, the impact of plant species composition on community structure was secondary to the strong influence of soil properties. Taken together, our findings indicate that bacterial communities may be largely unresponsive to indirect effects of CO2 enrichment through plants. Instead, bacterial communities are strongly regulated by edaphic conditions, presumably because soil differences create distinct environmental niches for bacteria.
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Affiliation(s)
- Swastika Raut
- Department of Biology, Baylor University, Waco, Texas
| | - Herbert W Polley
- Grassland, Soil and Water Research Laboratory, Department of Agriculture, Agricultural Research Service, Temple, Texas
| | - Philip A Fay
- Grassland, Soil and Water Research Laboratory, Department of Agriculture, Agricultural Research Service, Temple, Texas
| | - Sanghoon Kang
- Department of Biology, Baylor University, Waco, Texas
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10
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Ortmann AC, Brannock PM, Wang L, Halanych KM. River Flow Impacts Bacterial and Archaeal Community Structure in Surface Sediments in the Northern Gulf of Mexico. MICROBIAL ECOLOGY 2018; 76:941-953. [PMID: 29666882 DOI: 10.1007/s00248-018-1184-2] [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: 08/17/2017] [Accepted: 03/28/2018] [Indexed: 06/08/2023]
Abstract
Meiobenthic community structure in the northern Gulf of Mexico has been shown to be driven by geographical differences due to inshore-offshore gradients and location relative to river discharge. Samples collected along three transects spanning Mobile Bay, Alabama, showed significant differences in meiobenthic communities east of the bay compared to those sampled from the west. In contrast, analysis of bacterial and archaeal communities from the same sediment samples shows that the inshore-offshore gradient has minimal impact on their community structure. Significant differences in community structure were observed for Bacteria and Archaea between the east and west samples, but there was no difference in richness or diversity. Grouped by sediment type, higher richness was observed in silty samples compared to sandy samples. Significant differences were also observed among sediment types for community structure with bacteria communities in silty samples having more anaerobic sulfate reducers compared to aerobic heterotrophs, which had higher abundances in sandy sediments. This is likely due to increased organic matter in the silty sediments from the overlying river leading to low oxygen habitats. Most archaeal sequences represented poorly characterized high-level taxa, limiting interpretation of their distributions. Overlap between groups based on transect and sediment characteristics made determining which factor is more important in structuring bacterial and archaeal communities difficult. However, both factors are driven by discharge from the Mobile River. Although inshore-offshore gradients do not affect Bacteria or Archaea to the same extent as the meiobenthic communities, all three groups are strongly affected by sediment characteristics.
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Affiliation(s)
- Alice C Ortmann
- Department of Marine Sciences, University of South Alabama, Mobile, AL, 36688, USA.
- Dauphin Island Sea Lab, Dauphin Island, AL, 36528, USA.
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, NS, B2Y 4A2, Canada.
| | - Pamela M Brannock
- Department of Biological Science, Auburn University, Auburn, AL, 36849, USA
- Department of Biology, Rollins College, Winter Park, FL, 32789, USA
| | - Lei Wang
- Department of Marine Sciences, University of South Alabama, Mobile, AL, 36688, USA
- Dauphin Island Sea Lab, Dauphin Island, AL, 36528, USA
| | - Kenneth M Halanych
- Department of Biological Science, Auburn University, Auburn, AL, 36849, USA
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11
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Cai W, Li Y, Niu L, Zhang W, Wang C, Wang P, Meng F. New insights into the spatial variability of biofilm communities and potentially negative bacterial groups in hydraulic concrete structures. WATER RESEARCH 2017; 123:495-504. [PMID: 28689132 DOI: 10.1016/j.watres.2017.06.055] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 06/17/2017] [Accepted: 06/20/2017] [Indexed: 06/07/2023]
Abstract
The composition and distribution characteristics of bacterial communities in biofilms attached to hydraulic concrete structure (HCS) surfaces were investigated for the first time in four reservoirs in the middle and lower reaches of the Yangtze River Basin using 16S rRNA Miseq sequencing. High microbial diversity was found in HCS biofilms, and notable differences were observed in different types of HCS. Proteobacteria, Cyanobacteria and Chloroflexi were the predominant phyla, with respective relative abundances of 35.3%, 25.4% and 13.0%. The three most abundant genera were Leptolyngbya, Anaerolineaceae and Polynucleobacter. The phyla Beta-proteobacteria and Firmicutes and genus Lyngbya were predominant in CGP, whereas the phyla Cyanobacteria and Chloroflexi and genera Leptolyngbya, Anaerolinea and Polynucleobacter survived better in land walls and bank slopes. Dissolved oxygen, ammonia nitrogen and temperature were characterized as the main factors driving the bacterial community composition. The most abundant groups of metabolic functions were also identified as ammonia oxidizers, sulphate reducers, and dehalogenators. Additionally, functional groups related to biocorrosion were found to account for the largest proportion (14.0% of total sequences) in gate piers, followed by those in land walls (11.5%) and bank slopes (10.2%). Concrete gate piers were at the greatest risk of biocorrosion with the most abundant negative bacterial groups, especially for sulphate reducers. Thus, it should be paid high attention to the biocorrosion prevention of concrete gate piers. Overall, this study contributed to the optimization of microbial control and the improvement of the safety management for water conservation structures.
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Affiliation(s)
- Wei Cai
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, PR China.
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, PR China
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, PR China
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, PR China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, PR China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China
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12
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Segovia BT, Dias JD, Cabral AF, Meira BR, Lansac-Tôha FM, Lansac-Tôha FA, Bini LM, Velho LFM. Common and Rare Taxa of Planktonic Ciliates: Influence of Flood Events and Biogeographic Patterns in Neotropical Floodplains. MICROBIAL ECOLOGY 2017; 74:522-533. [PMID: 28386768 DOI: 10.1007/s00248-017-0974-2] [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: 12/12/2016] [Accepted: 03/24/2017] [Indexed: 06/07/2023]
Abstract
After much discussion about the cosmopolitan nature of microbes, the great issue nowadays is to identify at which spatial extent microorganisms may display biogeographic patterns and if temporal variation is important in altering those patterns. Here, planktonic ciliates were sampled from shallow lakes of four Neotropical floodplains, distributed over a spatial extent of ca. 3000 km, during high and low water periods, along with several abiotic and biotic variables potentially affecting the ciliate community. We found that common ciliate species were more associated with environmental gradients and rare species were more related to spatial variables; however, this pattern seemed to change depending on the temporal and spatial scales considered. Environmental gradients were more important in the high waters for both common and rare species. In low waters, common species continued to be mainly driven by environmental conditions, but rare species were more associated with the spatial component, suggesting dispersal limitation likely due to differences in dispersal ability and ecological tolerance of species. We also found that common and rare species were related to different environmental variables, suggesting different ecological niches. At the largest spatial extents, rare species showed clear biogeographic patterns.
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Affiliation(s)
- Bianca Trevizan Segovia
- Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (NUPELIA), Universidade Estadual de Maringá, Maringá, Paraná, Brazil.
| | - Juliana Déo Dias
- Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (NUPELIA), Universidade Estadual de Maringá, Maringá, Paraná, Brazil
| | - Adalgisa Fernanda Cabral
- Departamento de Ecologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Bianca Ramos Meira
- Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (NUPELIA), Universidade Estadual de Maringá, Maringá, Paraná, Brazil
| | - Fernando Miranda Lansac-Tôha
- Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (NUPELIA), Universidade Estadual de Maringá, Maringá, Paraná, Brazil
| | - Fabio Amodêo Lansac-Tôha
- Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (NUPELIA), Universidade Estadual de Maringá, Maringá, Paraná, Brazil
| | - Luis Mauricio Bini
- Departamento de Ecologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Luiz Felipe Machado Velho
- Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura (NUPELIA), Universidade Estadual de Maringá, Maringá, Paraná, Brazil
- Programa de Pós-Graduação em Tecnologias Limpas, Centro Universitário Cesumar - UniCesumar/Instituto Cesumar de Ciência, Tecnologia e Inovação (ICETI), Maringá, Paraná, Brazil
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13
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Brannock PM, Sharma J, Bik HM, Thomas WK, Halanych KM. Spatial and temporal variation of intertidal nematodes in the northern Gulf of Mexico after the Deepwater Horizon oil spill. MARINE ENVIRONMENTAL RESEARCH 2017; 130:200-212. [PMID: 28781067 DOI: 10.1016/j.marenvres.2017.07.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 06/19/2017] [Accepted: 07/05/2017] [Indexed: 06/07/2023]
Abstract
Nematodes are an abundant and diverse interstitial component of sedimentary habitats that have been reported to serve as important bioindicators. Though the 2010 Deepwater Horizon (DWH) disaster occurred 60 km offshore in the Gulf of Mexico (GOM) at a depth of 1525 m, oil rose to the surface and washed ashore, subjecting large segments of coastline in the northern GOM to contamination. Previous metabarcoding work shows intertidal nematode communities were negatively affected by the oil spill. Here we examine the subsequent recovery of nematode community structure at five sites along the Alabama coast over a two-year period. The latter part of the study (July 2011-July 2012) also included an examination of nematode vertical distribution in intertidal sediments. Results showed nematode composition within this region was more influenced by sample locality than time and depth. The five sampling sites were characterized by distinct nematode assemblages that varied by sampling dates. Nematode diversity decreased four months after the oil spill but increased after one year, returning to previous levels at all sites except Bayfront Park (BP). There was no significant difference among nematode assemblages in reference to vertical distribution. Although the composition of nematode assemblages changed, the feeding guilds they represented were not significantly different even though some variation was noted. Data from morphological observations integrated with metabarcoding data indicated similar spatial variation in nematode distribution patterns, indicating the potential of using these faster approaches to examine overall disturbance impact trends within communities. Heterogeneity of microhabitats in the intertidal zone indicates that future sampling and fine-scale studies of nematodes are needed to examine such anthropogenic effects.
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Affiliation(s)
- Pamela M Brannock
- Department of Biological Science, Auburn University, 101 Rouse Life Science Building, Auburn, AL 36849, USA.
| | - Jyotsna Sharma
- Department of Biology, University of Texas at San Antonio, TX 78249, USA
| | - Holly M Bik
- Hubbard Center for Genome Studies, University of New Hampshire, 35 Colovos Rd, Durham, NH 03824, USA; Department of Nematology, University of California, Riverside, CA 92521, USA
| | - W Kelley Thomas
- Hubbard Center for Genome Studies, University of New Hampshire, 35 Colovos Rd, Durham, NH 03824, USA
| | - Kenneth M Halanych
- Department of Biological Science, Auburn University, 101 Rouse Life Science Building, Auburn, AL 36849, USA.
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14
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Brannock PM, Wang L, Ortmann AC, Waits DS, Halanych KM. Genetic assessment of meiobenthic community composition and spatial distribution in coastal sediments along northern Gulf of Mexico. MARINE ENVIRONMENTAL RESEARCH 2016; 119:166-175. [PMID: 27299291 DOI: 10.1016/j.marenvres.2016.05.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 04/18/2016] [Accepted: 05/09/2016] [Indexed: 06/06/2023]
Abstract
Meiobenthic (meiofauna and micro-eukaryotes) organisms are important contributors to ecosystem functioning in aquatic environments through their roles in nutrient transport, sediment stability, and food web interactions. Despite their ecological importance, information pertaining to variation of these communities at various spatial and temporal scales is not widely known. Many studies in the Gulf of Mexico (GOM) have focused either on deep sea or continental shelf areas, while little attention has been paid to bays and coastal regions. Herein, we take a holistic approach by using high-throughput sequencing approaches to examine spatial variation in meiobenthic communities within Alabama bays and the coastal northern GOM region. Sediment samples were collected along three transects (Mississippi Sound: MS, FOCAL: FT, and Orange Beach: OB) from September 2010 to April 2012 and community composition was determined by metabarcoding the V9 hypervariable region of the nuclear18S rRNA gene. Results showed that Stramenopiles (diatoms), annelids, arthropods (copepods), and nematodes were the dominate groups within samples, while there was presence of other phyla throughout the dataset. Location played a larger role than time sampled in community composition. However, samples were collected over a short temporal scale. Samples clustered in reference to transect, with the most eastern transect (OB) having a distinct community composition in comparison to the other two transects (MS and FT). Communities also differed in reference to region (Bay versus Shelf). Bulk density and percent inorganic carbon were the only measured environmental factors that were correlated with community composition.
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Affiliation(s)
- Pamela M Brannock
- Department of Biological Sciences, Auburn University, 101 Rouse Life Science Building, Auburn, AL, 36849, USA.
| | - Lei Wang
- Department of Marine Sciences, University of South Alabama, 307 University Blvd, Mobile, AL, 36688, USA; Dauphin Island Sea Lab, 101B Bienville Blvd, Dauphin Island, AL, 36528, USA
| | - Alice C Ortmann
- Department of Marine Sciences, University of South Alabama, 307 University Blvd, Mobile, AL, 36688, USA; Dauphin Island Sea Lab, 101B Bienville Blvd, Dauphin Island, AL, 36528, USA
| | - Damien S Waits
- Department of Biological Sciences, Auburn University, 101 Rouse Life Science Building, Auburn, AL, 36849, USA
| | - Kenneth M Halanych
- Department of Biological Sciences, Auburn University, 101 Rouse Life Science Building, Auburn, AL, 36849, USA.
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15
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Cai W, Li Y, Wang P, Niu L, Zhang W, Wang C. Effect of the pollution level on the functional bacterial groups aiming at degrading bisphenol A and nonylphenol in natural biofilms of an urban river. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:15727-15738. [PMID: 27146525 DOI: 10.1007/s11356-016-6757-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 04/25/2016] [Indexed: 06/05/2023]
Abstract
Bisphenol A (BPA) and 4-nonylphenol (NP) are ubiquitous pollutants with estrogenic activity in aquatic environment and have attracted global concern due to their disruption of endocrine systems. This study investigated the spatial distribution characteristics of the bacterial groups involved in the degradation of BPA and NP within biofilms in an urban river using terminal restriction fragment length polymorphism based on 16S rRNA gene sequences. The effects of the pollution level and water parameters on these groups were also assessed. Hierarchical cluster analysis grouped the sampling sites into three clusters reflecting their varying nutrient pollution levels of relatively slight pollution (SP), moderate pollution (MP), and high pollution (HP) based on water quality data and Environmental Quality Standard for Surface Water of China (GB3838-2002). The BPA and NP concentration in river water ranged from 0.8 to 77.5 and 10.2 to 162.9 ng L(-1), respectively. Comamonadaceae, Pseudomonadaceae, Alcaligenaceae, Bacillaceae, Sphingomonadacea, Burkholderiaceae, and Rhizobiaceae were the dominant bacterial taxa involved in BPA and NP degradation, comprising an average of 9.8, 8.1, 7.6, 6.7, 6.2, 4.1, and 2.8 % of total sequences, respectively. The total abundance of these groups showed a slight upward trend and subsequently rapidly decreased with increasing pollution levels. The average proportion of Comamonadaceae in MP river sections was almost 1.5-2 times than that in SP or HP one. The distribution of functional groups was found related to environmental variables, especially pH, conductivity, ammonium nitrogen (NH3-N), and BPA. The abundance of Comamonadaceae and Rhizobiaceae was both closely related to higher values of pH and conductivity as well as lower concentrations of NP and BPA. Alcaligenaceae and Pseudomonadaceae were associated with higher concentrations of TP and CODMn and inversely correlated with DO concentration. This study might provide effective data on bacterial group changes in polluted urban rivers.
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Affiliation(s)
- Wei Cai
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, People's Republic of China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, People's Republic of China.
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, People's Republic of China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, People's Republic of China
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, People's Republic of China
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, People's Republic of China
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16
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Ortmann AC, Santos TTL. Spatial and temporal patterns in the Pelagibacteraceae across an estuarine gradient. FEMS Microbiol Ecol 2016; 92:fiw133. [PMID: 27387911 DOI: 10.1093/femsec/fiw133] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2016] [Indexed: 11/14/2022] Open
Abstract
Marine bacterial communities show strong spatial and seasonal patterns, often characterized by changes at high taxonomic levels. The Pelagibacteraceae are common members of bacterial communities, with well-documented biogeography at the subclade level. To identify patterns within the subclades, the abundance and diversity of Pelagibacteraceae were analyzed over a two-year period at four stations across an estuarine gradient. Pelagibacteraceae was the most abundant bacterial family, averaging 27% of the community, but varying from 1% to 57% in any one sample. Highest abundances were detected in autumn and winter. Pelagibacteraceae richness was lowest at the most inshore site, and highest in autumn and winter at all sites. Shannon diversity decreased in winter, when a few OTUs dominated the community. Dissolved oxygen, dissolved silicate and prokaryote abundance explained most of the variability in the Pelagibacteraceae communities, with salinity differentiating low salinity communities. The 10 most abundant OTUs included OTUs that varied across sites, with little seasonality as well as those with small site effects, but strong seasonal patterns indicating differences in the niches of individual OTUs. While salinity was important in structuring low salinity communities, higher salinity communities appear to be responding to additional environmental parameters including oxygen, nutrients and other organisms.
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Affiliation(s)
- Alice C Ortmann
- Department of Marine Sciences, University of South Alabama, Mobile, AL 36688, USA Dauphin Island Sea Lab, Dauphin Island, AL 36528, USA
| | - Thays T L Santos
- Department of Oceanography and Limnology, Federal University of Maranhao, CEP 65080-805, Sao Luis, MA, Brazil School of Marine Science, University of Maine, Orono, ME 04469, USA
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17
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Brannock PM, Ortmann AC, Moss AG, Halanych KM. Metabarcoding reveals environmental factors influencing spatio‐temporal variation in pelagic micro‐eukaryotes. Mol Ecol 2016; 25:3593-604. [DOI: 10.1111/mec.13709] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 04/06/2016] [Accepted: 05/22/2016] [Indexed: 01/16/2023]
Affiliation(s)
- Pamela M. Brannock
- Department of Biological Sciences Auburn University 101 Rouse Life Science Building Auburn AL 36849 USA
| | - Alice C. Ortmann
- Department of Marine Sciences University of South Alabama 307 University Blvd Mobile AL 36688 USA
- Dauphin Island Sea Lab 101B Bienville Blvd Dauphin Island AL 36528 USA
- Department of Fisheries and Ocean Canada Centre for Offshore Oil, Gas and Energy Research Bedford Institute of Oceanography Dartmouth B2Y 4A2 Canada
| | - Anthony G. Moss
- Department of Biological Sciences Auburn University 101 Rouse Life Science Building Auburn AL 36849 USA
| | - Kenneth M. Halanych
- Department of Biological Sciences Auburn University 101 Rouse Life Science Building Auburn AL 36849 USA
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18
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Bruder K, Malki K, Cooper A, Sible E, Shapiro JW, Watkins SC, Putonti C. Freshwater Metaviromics and Bacteriophages: A Current Assessment of the State of the Art in Relation to Bioinformatic Challenges. Evol Bioinform Online 2016; 12:25-33. [PMID: 27375355 PMCID: PMC4915788 DOI: 10.4137/ebo.s38549] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 04/03/2016] [Accepted: 04/10/2016] [Indexed: 12/30/2022] Open
Abstract
Advances in bioinformatics and sequencing technologies have allowed for the analysis of complex microbial communities at an unprecedented rate. While much focus is often placed on the cellular members of these communities, viruses play a pivotal role, particularly bacteria-infecting viruses (bacteriophages); phages mediate global biogeochemical processes and drive microbial evolution through bacterial grazing and horizontal gene transfer. Despite their importance and ubiquity in nature, very little is known about the diversity and structure of viral communities. Though the need for culture-based methods for viral identification has been somewhat circumvented through metagenomic techniques, the analysis of metaviromic data is marred with many unique issues. In this review, we examine the current bioinformatic approaches for metavirome analyses and the inherent challenges facing the field as illustrated by the ongoing efforts in the exploration of freshwater phage populations.
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Affiliation(s)
- Katherine Bruder
- Department of Biology, Loyola University Chicago, Chicago, IL, USA
| | - Kema Malki
- Department of Biology, Loyola University Chicago, Chicago, IL, USA
| | | | - Emily Sible
- Department of Biology, Loyola University Chicago, Chicago, IL, USA
| | - Jason W Shapiro
- Department of Biology, Loyola University Chicago, Chicago, IL, USA.; Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA
| | | | - Catherine Putonti
- Department of Biology, Loyola University Chicago, Chicago, IL, USA.; Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA.; Department of Computer Science, Loyola University Chicago, Chicago, IL, USA
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19
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Frank AH, Garcia JAL, Herndl GJ, Reinthaler T. Connectivity between surface and deep waters determines prokaryotic diversity in the North Atlantic Deep Water. Environ Microbiol 2016; 18:2052-63. [PMID: 26914787 PMCID: PMC4921061 DOI: 10.1111/1462-2920.13237] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 01/18/2016] [Indexed: 11/30/2022]
Abstract
To decipher the influence of depth stratification and surface provincialism on the dark ocean prokaryotic community composition, we sampled the major deep‐water masses in the eastern North Atlantic covering three biogeographic provinces. Their diversity was evaluated using ordination and canonical analysis of 454 pyrotag sequences. Variance partitioning suggested that 16% of the variation in the bacterial community composition was based on depth stratification while 9% of the variation was due to geographic location. General linear mixed effect models showed that the community of the subsurface waters was connected to the dark ocean prokaryotic communities in different biogeographic provinces. Cluster analysis indicated that some prokaryotic taxa are specific to distinct regions in bathypelagic water masses. Taken together, our data suggest that the dark ocean prokaryotic community composition of the eastern North Atlantic is primed by the formation and the horizontal transport of water masses.
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Affiliation(s)
- Alexander H Frank
- Department of Limnology and Bio-Oceanography, University of Vienna, Vienna, Austria
| | - Juan A L Garcia
- Department of Limnology and Bio-Oceanography, University of Vienna, Vienna, Austria
| | - Gerhard J Herndl
- Department of Limnology and Bio-Oceanography, University of Vienna, Vienna, Austria.,Department of Biological Oceanography, Royal Netherlands Institute for Sea Research, Texel, The Netherlands
| | - Thomas Reinthaler
- Department of Limnology and Bio-Oceanography, University of Vienna, Vienna, Austria
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20
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Cai W, Li Y, Wang P, Niu L, Zhang W, Wang C. Revealing the relationship between microbial community structure in natural biofilms and the pollution level in urban rivers: a case study in the Qinhuai River basin, Yangtze River Delta. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2016; 74:1163-1176. [PMID: 27642836 DOI: 10.2166/wst.2016.224] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
River pollution is one of the most challenging environmental issues, but the effect of river pollution levels on the biofilm communities has not been well-studied. Spatial and temporal distribution characteristics of environmental parameters and the biofilm communities were investigated in the Qinhuai River basin, Nanjing, China. Water samples were grouped into three clusters reflecting their varying pollution levels of relatively slight pollution, moderated pollution, and high pollution by hierarchical cluster analysis. In different clusters, the biofilm communities mainly differed in the proportion of Actinobacteria, Firmicutes, and Proteobacteria. As the dominant classes of Proteobacteria, Alpha-, Beta- and Gammaproteobacteria seemed to show an upward trend followed by a small fluctuation in the abundance with the escalation of water pollution level. Results of redundancy analysis demonstrated that temperature, total nitrogen to total phosphorus ratios (TN/TP) and concentrations of ammonia nitrogen (NH3-N) and TN were mainly responsible for the variation in bacterial community structure. The occurrences of Alpha-, Beta- and Gammaproteobacteria were closely associated with higher temperature, higher concentrations of NH3-N and TN and a lower TN/TP ratio. This study may provide a theoretical basis for the water pollution control and ecological restoration in urban rivers under different pollution levels.
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Affiliation(s)
- Wei Cai
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, China E-mail:
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, China E-mail:
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, China E-mail:
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, China E-mail:
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, China E-mail:
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, China E-mail:
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21
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Ling J, Zhang YY, Dong JD, Wang YS, Feng JB, Zhou WH. Spatial variations of bacterial community and its relationship with water chemistry in Sanya Bay, South China Sea as determined by DGGE fingerprinting and multivariate analysis. ECOTOXICOLOGY (LONDON, ENGLAND) 2015; 24:1486-1497. [PMID: 26013101 DOI: 10.1007/s10646-015-1492-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/15/2015] [Indexed: 06/04/2023]
Abstract
Bacteria play important roles in the structure and function of marine food webs by utilizing nutrients and degrading the pollutants, and their distribution are determined by surrounding water chemistry to a certain extent. It is vital to investigate the bacterial community's structure and identifying the significant factors by controlling the bacterial distribution in the paper. Flow cytometry showed that the total bacterial abundance ranged from 5.27 × 10(5) to 3.77 × 10(6) cells/mL. Molecular fingerprinting technique, denaturing gradient gel electrophoresis (DGGE) followed by DNA sequencing has been employed to investigate the bacterial community composition. The results were then interpreted through multivariate statistical analysis and tended to explain its relationship to the environmental factors. A total of 270 bands at 83 different positions were detected in DGGE profiles and 29 distinct DGGE bands were sequenced. The predominant bacteria were related to Phyla Protebacteria species (31 %, nine sequences), Cyanobacteria (37.9 %, eleven sequences) and Actinobacteria (17.2 %, five sequences). Other phylogenetic groups identified including Firmicutes (6.9 %, two sequences), Bacteroidetes (3.5 %, one sequences) and Verrucomicrobia (3.5 %, one sequences). Conical correspondence analysis was used to elucidate the relationships between the bacterial community compositions and environmental factors. The results showed that the spatial variations in the bacterial community composition was significantly related to phosphate (P = 0.002, P < 0.01), dissolved organic carbon (P = 0.004, P < 0.01), chemical oxygen demand (P = 0.010, P < 0.05) and nitrite (P = 0.016, P < 0.05). This study revealed the spatial variations of bacterial community and significant environmental factors driving the bacterial composition shift. These results may be valuable for further investigation on the functional microbial structure and expression quantitatively under the polluted environments in the world.
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Affiliation(s)
- Juan Ling
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Hainan Tropical Marine Biological Research Station, Sanya, 57200, China
| | - Yan-Ying Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Hainan Tropical Marine Biological Research Station, Sanya, 57200, China
| | - Jun-De Dong
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Hainan Tropical Marine Biological Research Station, Sanya, 57200, China.
| | - You-Shao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
| | - Jing-Bing Feng
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Hainan Tropical Marine Biological Research Station, Sanya, 57200, China
| | - Wei-Hua Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Hainan Tropical Marine Biological Research Station, Sanya, 57200, China
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22
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Ling J, Jiang YF, Wang YS, Dong JD, Zhang YY, Zhang YZ. Responses of bacterial communities in seagrass sediments to polycyclic aromatic hydrocarbon-induced stress. ECOTOXICOLOGY (LONDON, ENGLAND) 2015; 24:1517-1528. [PMID: 26048240 DOI: 10.1007/s10646-015-1493-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/15/2015] [Indexed: 06/04/2023]
Abstract
The seagrass meadows represent one of the highest productive marine ecosystems, and have the great ecological and economic values. Bacteria play important roles in energy flow, nutrient biogeochemical cycle and organic matter turnover in marine ecosystems. The seagrass meadows are experiencing a world-wide decline, and the pollution is one of the main reasons. Polycyclic aromatic hydrocarbons (PAHs) are thought be the most common. Bacterial communities in the seagrass Enhalus acoroides sediments were analyzed for their responses to PAHs induced stress. Dynamics of the composition and abundance of bacterial communities during the incubation period were explored by polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) and quantitative PCR assay, respectively. Both the incubation time and the PAHs concentration played significant roles in determining the microbial diversity, as reflected by the detected DGGE bands. Analysis of sequencing results showed that the Gammaproteobacteria were dominant in the seagrass sediments, accounting for 61.29 % of all sequenced bands. As PAHs could be used as carbon source for microbes, the species and diversity of the PAH-added groups (group 1 and 2) presented higher Shannon Wiener index than the group CK, with the group 1 showing the highest values almost through the same incubation stage. Patterns of changes in abundance of the three groups over the experiment time were quite different. The bacterial abundance of the group CK and group 2 decreased sharply from 4.15 × 10(11) and 6.37 × 10(11) to 1.17 × 10(10) and 1.07 × 10(10) copies/g from day 2 to 35, respectively while bacterial abundance of group 1 increased significantly from 1.59 × 10(11) copies/g at day 2 to 8.80 × 10(11) copies/g at day 7, and then dropped from day 14 till the end of the incubation. Statistical analysis (UMPGA and PCA) results suggested that the bacterial community were more likely to be affected by the incubation time than the concentration of the PAHs. This study provided the important information about dynamics of bacterial community under the PAHs stress and revealed the high bacterial diversity in sediments of E. acoroides. Investigation results also indicated that microbial community structure in the seagrass sediment were sensible to the PAHs induced stress, and may be used as potential indicators for the PAHs contamination.
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Affiliation(s)
- Juan Ling
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Hainan Tropical Marine Biological Research Station, Chinese Academy of Sciences, Sanya, 57200, China
| | - Yu-Feng Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Hainan Tropical Marine Biological Research Station, Chinese Academy of Sciences, Sanya, 57200, China
| | - You-Shao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
| | - Jun-De Dong
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Hainan Tropical Marine Biological Research Station, Chinese Academy of Sciences, Sanya, 57200, China.
| | - Yan-Ying Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Hainan Tropical Marine Biological Research Station, Chinese Academy of Sciences, Sanya, 57200, China
| | - Yuan-Zhou Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Hainan Tropical Marine Biological Research Station, Chinese Academy of Sciences, Sanya, 57200, China
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23
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Ortmann AC, Lu Y. Initial community and environment determine the response of bacterial communities to dispersant and oil contamination. MARINE POLLUTION BULLETIN 2015; 90:106-114. [PMID: 25487088 DOI: 10.1016/j.marpolbul.2014.11.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 11/02/2014] [Accepted: 11/10/2014] [Indexed: 06/04/2023]
Abstract
Bioremediation of seawater by natural bacterial communities is one potential response to coastal oil spills, but the success of the approach may vary, depending on geographical location, oil composition and the timing of spill. The short term response of coastal bacteria to dispersant, oil and dispersed oil was characterized using 16S rRNA gene tags in two mesocosm experiments conducted two months apart. Despite differences in the amount of oil-derived alkanes across the treatments and experiments, increases in the contributions of hydrocarbon degrading taxa and decreases in common estuarine bacteria were observed in response to dispersant and/or oil. Between the two experiments, the direction and rates of changes in particulate alkane concentrations differed, as did the magnitude of the bacterial response to oil and/or dispersant. Together, our data underscore large variability in bacterial responses to hydrocarbon pollutants, implying that bioremediation success varies with starting biological and environmental conditions.
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Affiliation(s)
- Alice C Ortmann
- Department of Marine Sciences, University of South Alabama, 307 University Blvd, Mobile, AL 36688, United States; Dauphin Island Sea Lab, 101B Bienville Blvd, Dauphin Island, AL 36528, United States.
| | - YueHan Lu
- Department of Geological Sciences, University of Alabama, Tuscaloosa, AL 35487, United States
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24
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Zhang Z, Wei J, Han X, Liang L, Yang Y, Meng H, Xu Y, Gao Z. The sesquiterpene biosynthesis and vessel-occlusion formation in stems of Aquilaria sinensis (Lour.) Gilg trees induced by wounding treatments without variation of microbial communities. Int J Mol Sci 2014; 15:23589-603. [PMID: 25530613 PMCID: PMC4284782 DOI: 10.3390/ijms151223589] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 11/28/2014] [Accepted: 12/04/2014] [Indexed: 11/16/2022] Open
Abstract
As widely recognized, agarwood formation in Aquilaria trees is induced by external wounding. Because agarwood usually harbors specific microbes, the function of microbes in agarwood formation has been debated for almost a century. In this study, two wounding methods, the burning-chisel-drilling method (BCD) and the whole-tree agarwood-inducing method (Agar-Wit), were used under the non-contamination of environmental microorganisms. After pyrosequencing the small rRNA subunits of the wounds induced by the BCD and Agar-Wit, no substantial variation was observed either in fungal and bacterial enrichment and diversity or in the relative abundances of taxa. By contrast, significant variations in fungal and bacterial communities were detected following the partial tree pruning (PTP)-wounding. The wound-induced sesquiterpene biosynthesis and vessel-occlusion formation, however, were found to be similar in all types of wounded trunks. We thus infer that wounding in the absence of variations in microbial communities may induce agarwood formation. This result does not support the long-standing notion that agarwood formation depends on microbes.
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Affiliation(s)
- Zheng Zhang
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China.
| | - Jianhe Wei
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China.
| | - Xiaomin Han
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China.
| | - Liang Liang
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China.
| | - Yun Yang
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medicinal Sciences and Peking Union Medical College, Wanning 571533, China.
| | - Hui Meng
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medicinal Sciences and Peking Union Medical College, Wanning 571533, China.
| | - Yanhong Xu
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China.
| | - Zhihui Gao
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China.
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