1
|
Williams J, Pettorelli N, Hartmann AC, Quinn RA, Plaisance L, O'Mahoney M, Meyer CP, Fabricius KE, Knowlton N, Ransome E. Decline of a distinct coral reef holobiont community under ocean acidification. MICROBIOME 2024; 12:75. [PMID: 38627822 PMCID: PMC11022381 DOI: 10.1186/s40168-023-01683-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 09/28/2023] [Indexed: 04/19/2024]
Abstract
BACKGROUND Microbes play vital roles across coral reefs both in the environment and inside and upon macrobes (holobionts), where they support critical functions such as nutrition and immune system modulation. These roles highlight the potential ecosystem-level importance of microbes, yet most knowledge of microbial functions on reefs is derived from a small set of holobionts such as corals and sponges. Declining seawater pH - an important global coral reef stressor - can cause ecosystem-level change on coral reefs, providing an opportunity to study the role of microbes at this scale. We use an in situ experimental approach to test the hypothesis that under such ocean acidification (OA), known shifts among macrobe trophic and functional groups may drive a general ecosystem-level response extending across macrobes and microbes, leading to reduced distinctness between the benthic holobiont community microbiome and the environmental microbiome. RESULTS We test this hypothesis using genetic and chemical data from benthic coral reef community holobionts sampled across a pH gradient from CO2 seeps in Papua New Guinea. We find support for our hypothesis; under OA, the microbiome and metabolome of the benthic holobiont community become less compositionally distinct from the sediment microbiome and metabolome, suggesting that benthic macrobe communities are colonised by environmental microbes to a higher degree under OA conditions. We also find a simplification and homogenisation of the benthic photosynthetic community, and an increased abundance of fleshy macroalgae, consistent with previously observed reef microbialisation. CONCLUSIONS We demonstrate a novel structural shift in coral reefs involving macrobes and microbes: that the microbiome of the benthic holobiont community becomes less distinct from the sediment microbiome under OA. Our findings suggest that microbialisation and the disruption of macrobe trophic networks are interwoven general responses to environmental stress, pointing towards a universal, undesirable, and measurable form of ecosystem changed. Video Abstract.
Collapse
Affiliation(s)
- Jake Williams
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Buckhurst Road, Ascot, SL5 7PY, UK
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Nathalie Pettorelli
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Aaron C Hartmann
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Robert A Quinn
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Laetitia Plaisance
- Laboratoire Evolution Et Diversité Biologique, CNRS/UPS, Toulouse, France
- National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013, USA
| | - Michael O'Mahoney
- National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013, USA
| | - Chris P Meyer
- National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013, USA
| | | | - Nancy Knowlton
- National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013, USA
| | - Emma Ransome
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Buckhurst Road, Ascot, SL5 7PY, UK.
| |
Collapse
|
2
|
Koepper S, Clark KF, McClure JT, Revie CW, Stryhn H, Thakur KK. Long-read sequencing reveals the shell microbiome of apparently healthy American lobsters Homarus americanus from Atlantic Canada. Front Microbiol 2023; 14:1245818. [PMID: 38029079 PMCID: PMC10658194 DOI: 10.3389/fmicb.2023.1245818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
The shell microbial community of lobsters-a key factor in the development of epizootic shell disease (ESD)-is still insufficiently researched in Atlantic Canada and many knowledge gaps remain. This study aimed to establish a baseline description and analysis of the shell microbiome of apparently healthy lobsters from four locations in the region. More than 180 lobster shell swab samples were collected from New Brunswick, Nova Scotia and Prince Edward Island (PEI). PacBio long-read 16S rDNA sequencing and bioinformatic analyses in QIIME2 identified the shell-associated bacteria. The shell microbiome of healthy lobsters consisted mainly of the bacterial classes Gammaproteobacteria, Saprospiria, Verrucomicrobiae, Alphaproteobacteria, Flavobacteriia, Acidimicrobiia and Planctomycetia. The microbial composition differed regionally and seasonally, with some classes showing decreased or increased relative abundances in the PEI samples as well as in the winter and spring samples in Nova Scotia. The core shell microbiome included potentially pathogenic as well as beneficial bacterial taxa, of which some were present only in certain regions. Bacterial taxa that have previously been associated with ESD were present on healthy lobsters in Atlantic Canada, but their frequency differed by location, sampling time, and moult stage. This study indicated that geographical and seasonal factors influenced the shell microbiome of apparently healthy lobsters more than host factors such as sex, size, and moult stage. Our results provide valuable reference microbial data from lobsters in a disease-free state.
Collapse
Affiliation(s)
- Svenja Koepper
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - K. Fraser Clark
- Department of Animal Sciences and Aquaculture, Faculty of Agriculture, Dalhousie University, Bible Hill, NS, Canada
| | - J. Trenton McClure
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Crawford W. Revie
- Department of Computer and Information Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Henrik Stryhn
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Krishna K. Thakur
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| |
Collapse
|
3
|
Arcadi E, Rizzo C, Calogero R, Sciutteri V, Fabiano F, Consoli P, Andaloro F, Romeo T. Microbial communities inhabiting shallow hydrothermal vents as sentinels of acidification processes. Front Microbiol 2023; 14:1233893. [PMID: 37727286 PMCID: PMC10505797 DOI: 10.3389/fmicb.2023.1233893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/09/2023] [Indexed: 09/21/2023] Open
Abstract
Introduction Shallow hydrothermal vents are considered natural laboratories to study the effects of acidification on biota, due to the consistent CO2 emissions with a consequent decrease in the local pH. Methods Here the microbial communities of water and sediment samples from Levante Bay (Vulcano Island) with different pH and redox conditions were explored by Next Generation Sequencing techniques. The taxonomic structure was elucidated and compared with previous studies from the same area in the last decades. Results and discussion The results revealed substantial shifts in the taxonomic structure of both bacterial and archaeal communities, with special relevance in the sediment samples, where the effects of external parameters probably act for a long time. The study demonstrates that microbial communities could be used as indicators of acidification processes, by shaping the entire biogeochemical balance of the ecosystem in response to stress factors. The study contributes to understanding how much these communities can tell us about future changes in marine ecosystems.
Collapse
Affiliation(s)
- Erika Arcadi
- Department of Biology and Evolution of Marine Organism, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
| | - Carmen Rizzo
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn–, Sicily Marine Centre, Messina, Italy
- Institute of Polar Sciences, National Research Council (CNR-ISP), Messina, Italy
| | - Rosario Calogero
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
| | - Valentina Sciutteri
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
| | - Francesco Fabiano
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn–, Sicily Marine Centre, Messina, Italy
| | - Pierpaolo Consoli
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
| | - Franco Andaloro
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
| | - Teresa Romeo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
- National Institute for Environmental Protection and Research, Milazzo, Italy
| |
Collapse
|
4
|
Wang C, Sun D, Junaid M, Xie S, Xu G, Li X, Tang H, Zou J, Zhou A. Effects of tidal action on the stability of microbiota, antibiotic resistance genes, and microplastics in the Pearl River Estuary, Guangzhou, China. CHEMOSPHERE 2023; 327:138485. [PMID: 36966930 DOI: 10.1016/j.chemosphere.2023.138485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/18/2023] [Accepted: 03/21/2023] [Indexed: 06/18/2023]
Abstract
In this study, the 16S rRNA gene amplicon sequencing technique was used to explore the microbial diversity and differences in the water environment of the Pearl River Estuary in Nansha District with various land use types such as the aquaculture area, industrial area, tourist area, agricultural plantation, and residential area. At the same time, the quantity, type, abundance, and distribution of two types of emerging environmental pollutants, antibiotic resistance genes (ARGs) and microplastics (MPs), are explored in the water samples from different functional areas. The results show that the dominant phyla in the five functional regions are Proteobacteria, Actinobacteria and Bacteroidetes, and the dominant genera are Hydrogenophaga, Synechococcus, Limnohabitans and Polynucleobacter. A total of 248 ARG subtypes were detected in the five regions, belonging to nine classes of ARGs (Aminoglycoside, Beta_Lactamase, Chlor, MGEs, MLSB, Multidrug, Sul, Tet, Van). Blue and white were the dominant MP colors in the five regions; 0.5-2 mm was the dominant MP size, and cellulose, rayon, and polyester comprised the highest proportion of the plastic polymers. This study provides the basis for understanding the environmental microbial distribution in estuaries and the prevention of environmental health risks from ARGs and microplastics.
Collapse
Affiliation(s)
- Chong Wang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
| | - Di Sun
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
| | - Muhammad Junaid
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
| | - Shaolin Xie
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
| | - Guohuan Xu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 16 510070, China.
| | - Xiang Li
- Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI C1A5T1, Canada.
| | - Huijuan Tang
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
| | - Jixing Zou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
| | - Aiguo Zhou
- Joint Laboratory of Guangdong Province and Hong Kong Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China; Canadian Food Inspection Agency, 93 Mount Edward Road, Charlottetown, PEI C1A5T1, Canada.
| |
Collapse
|
5
|
Banister RB, Schwarz MT, Fine M, Ritchie KB, Muller EM. Instability and Stasis Among the Microbiome of Seagrass Leaves, Roots and Rhizomes, and Nearby Sediments Within a Natural pH Gradient. MICROBIAL ECOLOGY 2022; 84:703-716. [PMID: 34596709 PMCID: PMC9622545 DOI: 10.1007/s00248-021-01867-9] [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: 11/11/2020] [Accepted: 09/10/2021] [Indexed: 05/10/2023]
Abstract
Seagrass meadows are hotspots of biodiversity with considerable economic and ecological value. The health of seagrass ecosystems is influenced in part by the makeup and stability of their microbiome, but microbiome composition can be sensitive to environmental change such as nutrient availability, elevated temperatures, and reduced pH. The objective of the present study was to characterize the bacterial community of the leaves, bulk samples of roots and rhizomes, and proximal sediment of the seagrass species Cymodocea nodosa along the natural pH gradient of Levante Bay, Vulcano Island, Italy. The bacterial community was determined by characterizing the 16S rRNA amplicon sequencing and analyzing the operational taxonomic unit classification of bacterial DNA within samples. Statistical analyses were used to explore how life-long exposure to different pH/pCO2 conditions may be associated with significant differences in microbial communities, dominant bacterial classes, and microbial diversity within each plant section and sediment. The microbiome of C. nodosa significantly differed among all sample types and site-specific differences were detected within sediment and root/rhizome microbial communities, but not the leaves. These results show that C. nodosa leaves have a consistent microbial community even across a pH range of 8.15 to 6.05. The ability for C. nodosa to regulate and maintain microbial structure may indicate a semblance of resilience within these vital ecosystems under projected changes in environmental conditions such as ocean acidification.
Collapse
Affiliation(s)
- Raymond B Banister
- Mote Marine Laboratory, Coral Health and Disease Program, Sarasota, FL, USA.
- Institute for Global Ecology, Florida Institute of Technology, 150, W University Blvd, Melbourne, FL, 32901, USA.
| | - Melbert T Schwarz
- Mote Marine Laboratory, Coral Health and Disease Program, Sarasota, FL, USA
| | - Maoz Fine
- The Goodman Faculty of Life Sciences, Bar-Ilan University, 52900, Ramat Gan, Israel
- The Interuniversity Institute for Marine Science, P.O.B. 469, 88103, Eilat, Israel
| | - Kim B Ritchie
- Department of Natural Sciences, University of South Carolina Beaufort, 801, Carteret St., Beaufort, SC, 29906, USA
| | - Erinn M Muller
- Mote Marine Laboratory, Coral Health and Disease Program, Sarasota, FL, USA
| |
Collapse
|
6
|
Su X, Yang X, Li H, Wang H, Wang Y, Xu J, Ding K, Zhu YG. Bacterial communities are more sensitive to ocean acidification than fungal communities in estuarine sediments. FEMS Microbiol Ecol 2021; 97:6207936. [PMID: 33792671 DOI: 10.1093/femsec/fiab058] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 03/30/2021] [Indexed: 12/13/2022] Open
Abstract
Ocean acidification (OA) in estuaries is becoming a global concern, and may affect microbial characteristics in estuarine sediments. Bacterial communities in response to acidification in this habitat have been well discussed; however, knowledge about how fungal communities respond to OA remains poorly understood. Here, we explored the effects of acidification on bacterial and fungal activities, structures and functions in estuarine sediments during a 50-day incubation experiment. Under acidified conditions, activities of three extracellular enzymes related to nutrient cycling were inhibited and basal respiration rates were decreased. Acidification significantly altered bacterial communities and their interactions, while weak alkalization had a minor impact on fungal communities. We distinguished pH-sensitive/tolerant bacteria and fungi in estuarine sediments, and found that only pH-sensitive/tolerant bacteria had strong correlations with sediment basal respiration activity. FUNGuild analysis indicated that animal pathogen abundances in sediment were greatly increased by acidification, while plant pathogens were unaffected. High-throughput quantitative PCR-based SmartChip analysis suggested that the nutrient cycling-related multifunctionality of sediments was reduced under acidified conditions. Most functional genes associated with nutrient cycling were identified in bacterial communities and their relative abundances were decreased by acidification. These new findings highlight that acidification in estuarine regions affects bacterial and fungal communities differently, increases potential pathogens and disrupts bacteria-mediated nutrient cycling.
Collapse
Affiliation(s)
- Xiaoxuan Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Xiaoru Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Hongtao Wang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China.,University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Yingmu Wang
- College of Civil Engineering, Fuzhou University, 2 Xueyuan Road, Fuzhou 350116, China
| | - Jianxin Xu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Kai Ding
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China.,University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.,State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing 100085, China
| |
Collapse
|
7
|
Ng JCY, Chiu JMY. Changes in biofilm bacterial communities in response to combined effects of hypoxia, ocean acidification and nutrients from aquaculture activity in Three Fathoms Cove. MARINE POLLUTION BULLETIN 2020; 156:111256. [PMID: 32510398 DOI: 10.1016/j.marpolbul.2020.111256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 05/04/2020] [Accepted: 05/07/2020] [Indexed: 06/11/2023]
Abstract
Anthropogenic nutrient enrichment results in hypoxia, ocean acidification and elevated nutrients (HOAN) in coastal environments throughout the world. Here, we examined the composition of biofilm bacterial communities from a nutrient-excessive fish farm with low dissolved oxygen (DO) and pH levels using 16S rRNA gene sequencing. HOAN was accompanied by higher bacterial diversity and richness, and resulted in an altered community composition than the control site. HOAN resulted in more Flavobacteriales, Rhizobiales, Epsilonproteobacteria and Vibrionales, but less Oceanospirillales and Alteromonadales. Photobacterium sp. and Vibrio sp. were mostly found to be exclusive to HOAN conditions, suggesting that HOAN could possibly proliferate the presence of these potential pathogens. Our study suggests the complexity of bacterial communities to hypoxia and acidification in response to increased nutrient loads, along with identities of nutrient, oxygen and pH-susceptible bacterial groups that are most likely affected under this ocean trend.
Collapse
Affiliation(s)
- Jenny C Y Ng
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Jill M Y Chiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.
| |
Collapse
|
8
|
Shi M, Li J, Zhou Q, Wang G, Zhang W, Zhang Z, Gao Y, Yan S. Interactions between elevated CO 2 levels and floating aquatic plants on the alteration of bacterial function in carbon assimilation and decomposition in eutrophic waters. WATER RESEARCH 2020; 171:115398. [PMID: 31874391 DOI: 10.1016/j.watres.2019.115398] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 12/09/2019] [Accepted: 12/14/2019] [Indexed: 06/10/2023]
Abstract
Elevated atmospheric CO2 concentration (eCO2) may have different effects on the bacterial community with regard to C assimilation and decomposition in eutrophic waters compared to that in fresh waters with intermediate levels of nutrients and oceans. Aquatic plant growth under eCO2 could further modify microbial activities associated with the C cycle in eutrophic waters. Therefore, there is an urgent need to further study how eCO2 and its interactions with the growth of aquatic plants affect the composition and function of the bacterial community involved in mediating the C cycle in eutrophic waters. Accordingly, we designed a microcosm experiment to investigate the effects of ambient and high CO2 concentrations on bacterial community composition and function in eutrophic waters with and without the growth of Eichhornia crassipes (Mart.) Solms. The results from 16S rRNA gene sequencing, function prediction, and q-PCR showed that eCO2 significantly increased the abundance of bacterial and functional genes involved in CO2 assimilation (photosynthetic bacteria; cbbL IA & IC, cbbL ID, cbbM, pufM) and C decomposition (Acidimicrobiia, Thermoleophilia, Gaiellales; ChiA), illustrating the functional enrichment with photoautotrophy, hydrocarbon degradation, cellulolysis, and aromatic hydrocarbon degradation. However, eCO2 decreased the abundance of some chemoautotrophic bacteria, including nitrifying bacteria (Nitrospirae, Nitrosomonadaceae). In contrast, the cultivation of E. crassipes decreased the abundance of photosynthetic bacteria but increased the abundance of bacteria involved in complex C decomposition associated with root exudates and degradation, e.g. Fibrobacteres, Sphingobacteriales, Sphingomonadales, and Rhizobiales. eCO2 and growth of E. crassipes had opposite effects on algal density in eutrophic waters, creating interactive effects that further decreased the diversity of the bacterial community and abundance of some CO2-assimilating bacteria with nitrifying characteristics (Nitrosomonadaceae) and some C-degrading bacteria (Fibrobacteres) with denitrifying properties (Flavobacteriaceae, Sphingomonadaceae, and Gemmobacter). Therefore, the interactions between aquatic plants and the bacterial community in eutrophic waters under eCO2 would be beneficial to the environment and help alleviate the greenhouse effect.
Collapse
Affiliation(s)
- Man Shi
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Jiangye Li
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Qi Zhou
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Guibin Wang
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Weiguo Zhang
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; Key Laboratory of Agricultural Environment on the Lower Yangtze River Plain, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, Jiangsu, China
| | - Zhenhua Zhang
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Yan Gao
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; Key Laboratory of Agricultural Environment on the Lower Yangtze River Plain, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, Jiangsu, China.
| | - Shaohua Yan
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China; Key Laboratory of Agricultural Environment on the Lower Yangtze River Plain, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, Jiangsu, China
| |
Collapse
|
9
|
Nelson KS, Baltar F, Lamare MD, Morales SE. Ocean acidification affects microbial community and invertebrate settlement on biofilms. Sci Rep 2020; 10:3274. [PMID: 32094391 PMCID: PMC7039980 DOI: 10.1038/s41598-020-60023-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 02/05/2020] [Indexed: 11/18/2022] Open
Abstract
Increased atmospheric CO2 is driving ocean acidification (OA), and potential changes in marine ecosystems. Research shows that both planktonic and benthic communities are affected, but how these changes are linked remains unresolved. Here we show experimentally that decreasing seawater pH (from pH 8.1 to 7.8 and 7.4) leads to reduced biofilm formation and lower primary producer biomass within biofilms. These changes occurred concurrently with a re-arrangement of the biofilm microbial communities. Changes suggest a potential shift from autotrophic to heterotrophic dominated biofilms in response to reduced pH. In a complimentary experiment, biofilms reared under reduced pH resulted in altered larval settlement for a model species (Galeolaria hystrix). These findings show that there is a potential cascade of impacts arising from OA effects on biofilms that may drive important community shifts through altered settlement patterns of benthic species.
Collapse
Affiliation(s)
- Katie S Nelson
- Department of Marine Science, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Federico Baltar
- Department of Marine Science, University of Otago, PO Box 56, Dunedin, 9054, New Zealand.,NIWA/University of Otago Research Centre for Oceanography, PO Box 56, Dunedin, 9054, New Zealand.,Department of Functional and Evolutionary Ecology, University of Vienna, A-1090, Vienna, Austria
| | - Miles D Lamare
- Department of Marine Science, University of Otago, PO Box 56, Dunedin, 9054, New Zealand. .,NIWA/University of Otago Research Centre for Oceanography, PO Box 56, Dunedin, 9054, New Zealand.
| | - Sergio E Morales
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin, 9054, New Zealand.
| |
Collapse
|
10
|
Hurtado-McCormick V, Kahlke T, Petrou K, Jeffries T, Ralph PJ, Seymour JR. Regional and Microenvironmental Scale Characterization of the Zostera muelleri Seagrass Microbiome. Front Microbiol 2019; 10:1011. [PMID: 31139163 PMCID: PMC6527750 DOI: 10.3389/fmicb.2019.01011] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/23/2019] [Indexed: 11/29/2022] Open
Abstract
Seagrasses are globally distributed marine plants that represent an extremely valuable component of coastal ecosystems. Like terrestrial plants, seagrass productivity and health are likely to be strongly governed by the structure and function of the seagrass microbiome, which will be distributed across a number of discrete microenvironments within the plant, including the phyllosphere, the endosphere and the rhizosphere, all different in physical and chemical conditions. Here we examined patterns in the composition of the microbiome of the seagrass Zostera muelleri, within six plant-associated microenvironments sampled across four different coastal locations in New South Wales, Australia. Amplicon sequencing approaches were used to characterize the diversity and composition of bacterial, microalgal, and fungal microbiomes and ultimately identify "core microbiome" members that were conserved across sampling microenvironments. Discrete populations of bacteria, microalgae and fungi were observed within specific seagrass microenvironments, including the leaves and roots and rhizomes, with "core" taxa found to persist within these microenvironments across geographically disparate sampling sites. Bacterial, microalgal and fungal community profiles were most strongly governed by intrinsic features of the different seagrass microenvironments, whereby microscale differences in community composition were greater than the differences observed between sampling regions. However, our results showed differing strengths of microbial preferences at the plant scale, since this microenvironmental variability was more pronounced for bacteria than it was for microalgae and fungi, suggesting more specific interactions between the bacterial consortia and the seagrass host, and potentially implying a highly specialized coupling between seagrass and bacterial metabolism and ecology. Due to their persistence within a given seagrass microenvironment, across geographically discrete sampling locations, we propose that the identified "core" microbiome members likely play key roles in seagrass physiology as well as the ecology and biogeochemistry of seagrass habitats.
Collapse
Affiliation(s)
| | - Tim Kahlke
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Katherina Petrou
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Thomas Jeffries
- School of Science and Health, Western Sydney University, Penrith, NSW, Australia
| | - Peter J. Ralph
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Justin Robert Seymour
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| |
Collapse
|
11
|
Zhang J, Chen M, Huang J, Guo X, Zhang Y, Liu D, Wu R, He H, Wang J. Diversity of the microbial community and cultivable protease-producing bacteria in the sediments of the Bohai Sea, Yellow Sea and South China Sea. PLoS One 2019; 14:e0215328. [PMID: 30973915 PMCID: PMC6459509 DOI: 10.1371/journal.pone.0215328] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 03/30/2019] [Indexed: 02/06/2023] Open
Abstract
The nitrogen (N) cycle is closely related to the stability of marine ecosystems. Microbial communities have been directly linked to marine N-cycling processes. However, systematic research on the bacterial community composition and diversity involved in N cycles in different seas is lacking. In this study, microbial diversity in the Bohai Sea (BHS), Yellow Sea (YS) and South China Sea (SCS) was surveyed by targeting the hypervariable V4 regions of the 16S rRNA gene using next-generation sequencing (NGS) technology. A total of 2,505,721 clean reads and 15,307 operational taxonomic units (OTUs) were obtained from 86 sediment samples from the three studied China seas. LEfSe analysis demonstrated that the SCS had more abundant microbial taxa than the BHS and YS. Diversity indices demonstrated that Proteobacteria and Planctomycetes were the dominant phyla in all three China seas. Canonical correspondence analysis (CCA) indicated that pH (P = 0.034) was the principal determining factors, while the organic matter content, depth and temperature had a minor correlated with the variations in sedimentary microbial community distribution. Cluster and functional analyses of microbial communities showed that chemoheterotrophic and aerobic chemoheterotrophic microorganisms widely exist in these three seas. Further research found that the cultivable protease-producing bacteria were mainly affiliated with the phyla Proteobacteria, Firmicutes and Bacteroidetes. It was very clear that Pseudoalteromonadaceae possessed the highest relative abundance in the three sea areas. The predominant protease-producing genera were Pseudoalteromonas and Bacillus. These results shed light on the differences in bacterial community composition, especially protease-producing bacteria, in these three China seas.
Collapse
Affiliation(s)
- Jiang Zhang
- School of Life Science, Central South University, Changsha, China
| | - Ming Chen
- Sanway Gene Technology Inc., Changsha, China
| | - Jiafeng Huang
- School of Life Science, Central South University, Changsha, China
| | - Xinwu Guo
- Sanway Gene Technology Inc., Changsha, China
| | - Yanjiao Zhang
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Dan Liu
- School of Life Science, Central South University, Changsha, China
| | - Ribang Wu
- School of Life Science, Central South University, Changsha, China
| | - Hailun He
- School of Life Science, Central South University, Changsha, China
- * E-mail: (HH); (GW)
| | - Jun Wang
- School of Life Science, Central South University, Changsha, China
- Sanway Gene Technology Inc., Changsha, China
- * E-mail: (HH); (GW)
| |
Collapse
|
12
|
Yu T, Chen Y. Effects of elevated carbon dioxide on environmental microbes and its mechanisms: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 655:865-879. [PMID: 30481713 DOI: 10.1016/j.scitotenv.2018.11.301] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/20/2018] [Accepted: 11/20/2018] [Indexed: 05/24/2023]
Abstract
Before the industrial revolution, the atmospheric CO2 concentration was 180-330 ppm; however, fossil-fuel combustion and forest destruction have led to increased atmospheric CO2 concentration. CO2 capture and storage is regarded as a promising strategy to prevent global warming and ocean acidification and to alleviate elevated atmospheric CO2 concentration, but the leakage of CO2 from storage system can lead to rapid acidification of the surrounding circumstance, which might cause negative influence on environmental microbes. The effects of elevated CO2 on microbes have been reported extensively, but the review regarding CO2 affecting different environmental microorganisms has never been done previously. Also, the mechanisms of CO2 affecting environmental microorganisms are usually contributed to the change of pH values, while the direct influences of CO2 on microorganisms were often neglected. This paper aimed to provide a systematic review of elevated CO2 affecting environmental microbes and its mechanisms. Firstly, the influences of elevated CO2 and potential leakage of CO2 from storage sites on community structures and diversity of different surrounding environmental microbes were assessed and compared. Secondly, the adverse impacts of CO2 on microbial growth, cell morphology and membranes, bacterial spores, and microbial metabolism were introduced. Then, based on biochemical principles and knowledge of microbiology and molecular biology, the fundamental mechanisms of the influences of carbon dioxide on environmental microbes were discussed from the aspects of enzyme activity, electron generation and transfer, and key gene and protein expressions. Finally, key questions relevant to the environmental effect of CO2 that need to be answered in the future were addressed.
Collapse
Affiliation(s)
- Tong Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
| |
Collapse
|
13
|
Molari M, Guilini K, Lins L, Ramette A, Vanreusel A. CO 2 leakage can cause loss of benthic biodiversity in submarine sands. MARINE ENVIRONMENTAL RESEARCH 2019; 144:213-229. [PMID: 30709637 DOI: 10.1016/j.marenvres.2019.01.006] [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: 08/20/2018] [Revised: 01/07/2019] [Accepted: 01/11/2019] [Indexed: 06/09/2023]
Abstract
One of the options to mitigate atmospheric CO2 increase is CO2 Capture and Storage in sub-seabed geological formations. Since predicting long-term storage security is difficult, different CO2 leakage scenarios and impacts on marine ecosystems require evaluation. Submarine CO2 vents may serve as natural analogues and allow studying the effects of CO2 leakage in a holistic approach. At the study site east of Basiluzzo Islet off Panarea Island (Italy), gas emissions (90-99% CO2) occur at moderate flows (80-120 L m-2 h-1). We investigated the effects of acidified porewater conditions (pHT range: 5.5-7.7) on the diversity of benthic bacteria and invertebrates by sampling natural sediments in three subsequent years and by performing a transplantation experiment with a duration of one year, respectively. Both multiple years and one year of exposure to acidified porewater conditions reduced the number of benthic bacterial operational taxonomic units and invertebrate species diversity by 30-80%. Reduced biodiversity at the vent sites increased the temporal variability in bacterial and nematode community biomass, abundance and composition. While the release from CO2 exposure resulted in a full recovery of nematode species diversity within one year, bacterial diversity remained affected. Overall our findings showed that seawater acidification, induced by seafloor CO2 emissions, was responsible for loss of diversity across different size-classes of benthic organisms, which reduced community stability with potential relapses on ecosystem resilience.
Collapse
Affiliation(s)
- Massimiliano Molari
- HGF-MPG Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, Germany.
| | - Katja Guilini
- Marine Biology Research Group, Department of Biology, Ghent University, Krijgslaan 281/S8, 9000, Ghent, Belgium
| | - Lidia Lins
- Marine Biology Research Group, Department of Biology, Ghent University, Krijgslaan 281/S8, 9000, Ghent, Belgium
| | - Alban Ramette
- HGF-MPG Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, Germany
| | - Ann Vanreusel
- Marine Biology Research Group, Department of Biology, Ghent University, Krijgslaan 281/S8, 9000, Ghent, Belgium
| |
Collapse
|
14
|
Li W, Lv X, Ruan J, Yu M, Song YB, Yu J, Dong M. Variations in Soil Bacterial Composition and Diversity in Newly Formed Coastal Wetlands. Front Microbiol 2019; 9:3256. [PMID: 30687257 PMCID: PMC6333922 DOI: 10.3389/fmicb.2018.03256] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 12/14/2018] [Indexed: 11/13/2022] Open
Abstract
Coastal ecosystems experience some of the most active land–ocean interactions in the world, and they are characterized by high primary productivity and biological diversity in the sediment. Given the roles of microorganisms in soil biogeochemical cycling and their multifaceted influence on soil ecosystems, it is critical to understand the variations and drivers of soil microbial communities across coastal ecosystems. Here, we studied soil bacterial community dynamics at different sites (from seawater to freshwater) in the Yellow River Delta, China. Bacterial community composition and diversity over four seasons were analyzed through 16S rRNA genes. Notably, the bacterial community near the ocean had the lowest alpha-diversity when compared with the other sites. No significant differences in bacterial communities among seasons were found, indicating that seasonal variation in temperature had little influence on bacterial community in the newly formed wetlands in the Yellow River Delta. Bacterial community structure changed substantially along the salinity gradient, revealing a clear ecological replacement along the gradual transformation gradient from freshwater to seawater environment. Redundancy analysis revealed that salinity was the main driver of variations in bacterial community structure and explained 17.5% of the variability. Our study provides a better understanding of spatiotemporally determined bacterial community dynamics in coastal ecosystems.
Collapse
Affiliation(s)
- Wenbing Li
- Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xiaofei Lv
- College of Quality and Safety Engineering, China Jiliang University, Hangzhou, China.,Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Junchao Ruan
- Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Miao Yu
- Institute for Advanced Study of Coastal Ecology, Ludong University, Yantai, China
| | - Yao-Bin Song
- Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Junbao Yu
- Institute for Advanced Study of Coastal Ecology, Ludong University, Yantai, China
| | - Ming Dong
- Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| |
Collapse
|
15
|
Louvado A, Coelho FJRC, Gomes H, Cleary DFR, Cunha Â, Gomes NCM. Independent and interactive effects of reduced seawater pH and oil contamination on subsurface sediment bacterial communities. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:32756-32766. [PMID: 30244446 DOI: 10.1007/s11356-018-3214-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 09/12/2018] [Indexed: 06/08/2023]
Abstract
Ocean acidification may exacerbate the environmental impact of oil hydrocarbon pollution by disrupting the core composition of the superficial (0-1 cm) benthic bacterial communities. However, at the subsurface sediments (approximately 5 cm below sea floor), the local biochemical characteristics and the superjacent sediment barrier may buffer these environmental changes. In this study, we used a microcosm experimental approach to access the independent and interactive effects of reduced seawater pH and oil contamination on the composition of subsurface benthic bacterial communities, at two time points, by 16S rRNA gene-based high-throughput sequencing. An in-depth taxa-specific variance analysis revealed that the independent effects of reduced seawater pH and oil contamination were significant predictors of changes in the relative abundance of some specific bacterial groups (e.g., Firmicutes, Rhizobiales, and Desulfobulbaceae). However, our results indicated that the overall microbial community structure was not affected by independent and interactive effects of reduced pH and oil contamination. This study provides evidence that bacterial communities inhabiting subsurface sediment may be less susceptible to the effects of oil contamination in a scenario of reduced seawater pH.
Collapse
Affiliation(s)
- António Louvado
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Francisco J R C Coelho
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Hélder Gomes
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Daniel F R Cleary
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Ângela Cunha
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Newton C M Gomes
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| |
Collapse
|
16
|
Batista D, Costa R, Carvalho AP, Batista WR, Rua CPJ, de Oliveira L, Leomil L, Fróes AM, Thompson FL, Coutinho R, Dobretsov S. Environmental conditions affect activity and associated microorganisms of marine sponges. MARINE ENVIRONMENTAL RESEARCH 2018; 142:59-68. [PMID: 30274716 DOI: 10.1016/j.marenvres.2018.09.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 08/09/2018] [Accepted: 09/19/2018] [Indexed: 06/08/2023]
Abstract
Changes in environmental conditions can influence sponges and their holobionts. The present study investigated the effect of upwelling and anthropogenic pollution on the bioactivity of marine sponges, microbial communities and functional genes, and composition of their chemical compounds. The species Dysidea etheria, Darwinella sp., Hymeniacidon heliophila and Tedania ignis were collected from areas with distinct influence of upwelling and low anthropogenic impact and from areas without influence of upwelling but affected by sewage and the port. In most cases, the same sponge species collected from areas with distinct environmental conditions had a different chemical composition, antifouling activity, composition and diversity of associated microorganisms. Antimicrobial, quorum sensing inhibitory and anti-larval activities of sponge extracts were more pronounced in the area without upwelling showing higher level of anthropogenic pollution. This study suggests that upwelling and anthropogenic pollution affect the chemical activity and holobiome composition of sponges.
Collapse
Affiliation(s)
- Daniela Batista
- Instituto de Estudos do Mar Almirante Paulo Moreira, Rua Kioto no 253, Praia dos Anjos, Arraial do Cabo, RJ, Brazil.
| | - Rafaela Costa
- Instituto de Estudos do Mar Almirante Paulo Moreira, Rua Kioto no 253, Praia dos Anjos, Arraial do Cabo, RJ, Brazil
| | - Ana Polycarpa Carvalho
- Instituto de Estudos do Mar Almirante Paulo Moreira, Rua Kioto no 253, Praia dos Anjos, Arraial do Cabo, RJ, Brazil
| | - William Romão Batista
- Instituto de Estudos do Mar Almirante Paulo Moreira, Rua Kioto no 253, Praia dos Anjos, Arraial do Cabo, RJ, Brazil
| | - Cintia P J Rua
- Instituto de Biologia e SAGE-COPPE, Universidade Federal do Rio de Janeiro, Ilha do Fundão s/n, Rio de Janeiro, RJ, Brazil
| | - Louisi de Oliveira
- Instituto de Biologia e SAGE-COPPE, Universidade Federal do Rio de Janeiro, Ilha do Fundão s/n, Rio de Janeiro, RJ, Brazil
| | - Luciana Leomil
- Instituto de Biologia e SAGE-COPPE, Universidade Federal do Rio de Janeiro, Ilha do Fundão s/n, Rio de Janeiro, RJ, Brazil
| | - Adriana M Fróes
- Instituto de Biologia e SAGE-COPPE, Universidade Federal do Rio de Janeiro, Ilha do Fundão s/n, Rio de Janeiro, RJ, Brazil
| | - Fabiano L Thompson
- Instituto de Biologia e SAGE-COPPE, Universidade Federal do Rio de Janeiro, Ilha do Fundão s/n, Rio de Janeiro, RJ, Brazil
| | - Ricardo Coutinho
- Instituto de Estudos do Mar Almirante Paulo Moreira, Rua Kioto no 253, Praia dos Anjos, Arraial do Cabo, RJ, Brazil
| | - Sergey Dobretsov
- Marine Science and Fisheries Department, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khoud 123. PO Box 34, Muscat, Oman; Center of Excellence in Marine Biotechnology, Sultan Qaboos University, Al-Khoud 123. PO Box 50, Muscat, Oman.
| |
Collapse
|
17
|
Hicks N, Liu X, Gregory R, Kenny J, Lucaci A, Lenzi L, Paterson DM, Duncan KR. Temperature Driven Changes in Benthic Bacterial Diversity Influences Biogeochemical Cycling in Coastal Sediments. Front Microbiol 2018; 9:1730. [PMID: 30190707 PMCID: PMC6115492 DOI: 10.3389/fmicb.2018.01730] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/11/2018] [Indexed: 11/13/2022] Open
Abstract
Marine sediments are important sites for global biogeochemical cycling, mediated by macrofauna and microalgae. However, it is the microorganisms that drive these key processes. There is strong evidence that coastal benthic habitats will be affected by changing environmental variables (rising temperature, elevated CO2), and research has generally focused on the impact on macrofaunal biodiversity and ecosystem services. Despite their importance, there is less understanding of how microbial community assemblages will respond to environmental changes. In this study, a manipulative mesocosm experiment was employed, using next-generation sequencing to assess changes in microbial communities under future environmental change scenarios. Illumina sequencing generated over 11 million 16S rRNA gene sequences (using a primer set biased toward bacteria) and revealed Bacteroidetes and Proteobacteria dominated the total bacterial community of sediment samples. In this study, the sequencing coverage and depth revealed clear changes in species abundance within some phyla. Bacterial community composition was correlated with simulated environmental conditions, and species level community composition was significantly influenced by the mean temperature of the environmental regime (p = 0.002), but not by variation in CO2 or diurnal temperature variation. Species level changes with increasing mean temperature corresponded with changes in NH4 concentration, suggesting there is no functional redundancy in microbial communities for nitrogen cycling. Marine coastal biogeochemical cycling under future environmental conditions is likely to be driven by changes in nutrient availability as a direct result of microbial activity.
Collapse
Affiliation(s)
- Natalie Hicks
- The Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom
| | - Xuan Liu
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Richard Gregory
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - John Kenny
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Anita Lucaci
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Luca Lenzi
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - David M. Paterson
- Sediment Ecology Research Group, School of Biology, Scottish Oceans Institute, University of St Andrews, Fife, United Kingdom
| | - Katherine R. Duncan
- The Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| |
Collapse
|
18
|
Huggett MJ, McMahon K, Bernasconi R. Future warming and acidification result in multiple ecological impacts to a temperate coralline alga. Environ Microbiol 2018; 20:2769-2782. [DOI: 10.1111/1462-2920.14113] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 03/15/2018] [Accepted: 03/19/2018] [Indexed: 11/27/2022]
Affiliation(s)
- Megan J. Huggett
- Centre for Marine Ecosystems Research, School of Science; Edith Cowan University, 270 Joondalup Dr; Joondalup WA 6027 Australia
- Centre for Ecosystem Management, School of Science, Edith Cowan University, 270 Joondalup Dr; Joondalup WA 6027 Australia
- School of Environmental and Life Sciences; The University of Newcastle; Ourimbah NSW 2258 Australia
| | - Kathryn McMahon
- Centre for Marine Ecosystems Research, School of Science; Edith Cowan University, 270 Joondalup Dr; Joondalup WA 6027 Australia
| | - Rachele Bernasconi
- Centre for Marine Ecosystems Research, School of Science; Edith Cowan University, 270 Joondalup Dr; Joondalup WA 6027 Australia
| |
Collapse
|
19
|
Minich JJ, Morris MM, Brown M, Doane M, Edwards MS, Michael TP, Dinsdale EA. Elevated temperature drives kelp microbiome dysbiosis, while elevated carbon dioxide induces water microbiome disruption. PLoS One 2018; 13:e0192772. [PMID: 29474389 PMCID: PMC5825054 DOI: 10.1371/journal.pone.0192772] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/30/2018] [Indexed: 01/23/2023] Open
Abstract
Global climate change includes rising temperatures and increased pCO2 concentrations in the ocean, with potential deleterious impacts on marine organisms. In this case study we conducted a four-week climate change incubation experiment, and tested the independent and combined effects of increased temperature and partial pressure of carbon dioxide (pCO2), on the microbiomes of a foundation species, the giant kelp Macrocystis pyrifera, and the surrounding water column. The water and kelp microbiome responded differently to each of the climate stressors. In the water microbiome, each condition caused an increase in a distinct microbial order, whereas the kelp microbiome exhibited a reduction in the dominant kelp-associated order, Alteromondales. The water column microbiomes were most disrupted by elevated pCO2, with a 7.3 fold increase in Rhizobiales. The kelp microbiome was most influenced by elevated temperature and elevated temperature in combination with elevated pCO2. Kelp growth was negatively associated with elevated temperature, and the kelp microbiome showed a 5.3 fold increase Flavobacteriales and a 2.2 fold increase alginate degrading enzymes and sulfated polysaccharides. In contrast, kelp growth was positively associated with the combination of high temperature and high pCO2 'future conditions', with a 12.5 fold increase in Planctomycetales and 4.8 fold increase in Rhodobacteriales. Therefore, the water and kelp microbiomes acted as distinct communities, where the kelp was stabilizing the microbiome under changing pCO2 conditions, but lost control at high temperature. Under future conditions, a new equilibrium between the kelp and the microbiome was potentially reached, where the kelp grew rapidly and the commensal microbes responded to an increase in mucus production.
Collapse
Affiliation(s)
- Jeremiah J. Minich
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - Megan M. Morris
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - Matt Brown
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - Michael Doane
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - Matthew S. Edwards
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | | | - Elizabeth A. Dinsdale
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| |
Collapse
|
20
|
Molari M, Guilini K, Lott C, Weber M, de Beer D, Meyer S, Ramette A, Wegener G, Wenzhöfer F, Martin D, Cibic T, De Vittor C, Vanreusel A, Boetius A. CO 2 leakage alters biogeochemical and ecological functions of submarine sands. SCIENCE ADVANCES 2018; 4:eaao2040. [PMID: 29441359 PMCID: PMC5810613 DOI: 10.1126/sciadv.aao2040] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 01/05/2018] [Indexed: 06/08/2023]
Abstract
Subseabed CO2 storage is considered a future climate change mitigation technology. We investigated the ecological consequences of CO2 leakage for a marine benthic ecosystem. For the first time with a multidisciplinary integrated study, we tested hypotheses derived from a meta-analysis of previous experimental and in situ high-CO2 impact studies. For this, we compared ecological functions of naturally CO2-vented seafloor off the Mediterranean island Panarea (Tyrrhenian Sea, Italy) to those of nonvented sands, with a focus on biogeochemical processes and microbial and faunal community composition. High CO2 fluxes (up to 4 to 7 mol CO2 m-2 hour-1) dissolved all sedimentary carbonate, and comigration of silicate and iron led to local increases of microphytobenthos productivity (+450%) and standing stocks (+300%). Despite the higher food availability, faunal biomass (-80%) and trophic diversity were substantially lower compared to those at the reference site. Bacterial communities were also structurally and functionally affected, most notably in the composition of heterotrophs and microbial sulfate reduction rates (-90%). The observed ecological effects of CO2 leakage on submarine sands were reproduced with medium-term transplant experiments. This study assesses indicators of environmental impact by CO2 leakage and finds that community compositions and important ecological functions are permanently altered under high CO2.
Collapse
Affiliation(s)
- Massimiliano Molari
- HGF-MPG (Helmholtz Gemeinschaft Deutscher Forschungszenten–Max Planck Gesellschaft) Joint Research Group on Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Katja Guilini
- Marine Biology Research Group, Department of Biology, Ghent University, Ghent, Belgium
| | - Christian Lott
- HYDRA Institute for Marine Sciences, Elba Field Station, Via del Forno 80, 57034 Campo nell’Elba (LI), Italy
| | - Miriam Weber
- HGF-MPG (Helmholtz Gemeinschaft Deutscher Forschungszenten–Max Planck Gesellschaft) Joint Research Group on Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- HYDRA Institute for Marine Sciences, Elba Field Station, Via del Forno 80, 57034 Campo nell’Elba (LI), Italy
| | - Dirk de Beer
- Microsensor Group, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Stefanie Meyer
- HGF-MPG (Helmholtz Gemeinschaft Deutscher Forschungszenten–Max Planck Gesellschaft) Joint Research Group on Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Alban Ramette
- HGF-MPG (Helmholtz Gemeinschaft Deutscher Forschungszenten–Max Planck Gesellschaft) Joint Research Group on Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Gunter Wegener
- HGF-MPG (Helmholtz Gemeinschaft Deutscher Forschungszenten–Max Planck Gesellschaft) Joint Research Group on Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University Bremen, 28359 Bremen, Germany
| | - Frank Wenzhöfer
- HGF-MPG (Helmholtz Gemeinschaft Deutscher Forschungszenten–Max Planck Gesellschaft) Joint Research Group on Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- HGF-MPG Joint Research Group on Deep Sea Ecology and Technology, Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | - Daniel Martin
- Centre d’Estudis Avançats de Blanes (CEAB), Consejo Superior de Investigaciones Científicas (CSIC), Blanes, Girona, Catalunya, Spain
| | - Tamara Cibic
- Sezione di Oceanografia, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale–OGS, I-34151 Trieste, Italy
| | - Cinzia De Vittor
- Sezione di Oceanografia, Istituto Nazionale di Oceanografia e di Geofisica Sperimentale–OGS, I-34151 Trieste, Italy
| | - Ann Vanreusel
- Marine Biology Research Group, Department of Biology, Ghent University, Ghent, Belgium
| | - Antje Boetius
- HGF-MPG (Helmholtz Gemeinschaft Deutscher Forschungszenten–Max Planck Gesellschaft) Joint Research Group on Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University Bremen, 28359 Bremen, Germany
- HGF-MPG Joint Research Group on Deep Sea Ecology and Technology, Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| |
Collapse
|
21
|
Danovaro R, Corinaldesi C, Dell'Anno A, Rastelli E. Potential impact of global climate change on benthic deep-sea microbes. FEMS Microbiol Lett 2018; 364:4553516. [PMID: 29045616 DOI: 10.1093/femsle/fnx214] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/12/2017] [Indexed: 11/12/2022] Open
Abstract
Benthic deep-sea environments are the largest ecosystem on Earth, covering ∼65% of the Earth surface. Microbes inhabiting this huge biome at all water depths represent the most abundant biological components and a relevant portion of the biomass of the biosphere, and play a crucial role in global biogeochemical cycles. Increasing evidence suggests that global climate changes are affecting also deep-sea ecosystems, both directly (causing shifts in bottom-water temperature, oxygen concentration and pH) and indirectly (through changes in surface oceans' productivity and in the consequent export of organic matter to the seafloor). However, the responses of the benthic deep-sea biota to such shifts remain largely unknown. This applies particularly to deep-sea microbes, which include bacteria, archaea, microeukaryotes and their viruses. Understanding the potential impacts of global change on the benthic deep-sea microbial assemblages and the consequences on the functioning of the ocean interior is a priority to better forecast the potential consequences at global scale. Here we explore the potential changes in the benthic deep-sea microbiology expected in the coming decades using case studies on specific systems used as test models.
Collapse
Affiliation(s)
- Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy.,Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Cinzia Corinaldesi
- Department of Sciences and Engineering of Materials, Environment and Urbanistics, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Antonio Dell'Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Eugenio Rastelli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy.,Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| |
Collapse
|
22
|
Brown NEM, Milazzo M, Rastrick SPS, Hall-Spencer JM, Therriault TW, Harley CDG. Natural acidification changes the timing and rate of succession, alters community structure, and increases homogeneity in marine biofouling communities. GLOBAL CHANGE BIOLOGY 2018; 24:e112-e127. [PMID: 28762601 DOI: 10.1111/gcb.13856] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 07/14/2017] [Indexed: 06/07/2023]
Abstract
Ocean acidification may have far-reaching consequences for marine community and ecosystem dynamics, but its full impacts remain poorly understood due to the difficulty of manipulating pCO2 at the ecosystem level to mimic realistic fluctuations that occur on a number of different timescales. It is especially unclear how quickly communities at various stages of development respond to intermediate-scale pCO2 change and, if high pCO2 is relieved mid-succession, whether past acidification effects persist, are reversed by alleviation of pCO2 stress, or are worsened by departures from prior high pCO2 conditions to which organisms had acclimatized. Here, we used reciprocal transplant experiments along a shallow water volcanic pCO2 gradient to assess the importance of the timing and duration of high pCO2 exposure (i.e., discrete events at different stages of successional development vs. continuous exposure) on patterns of colonization and succession in a benthic fouling community. We show that succession at the acidified site was initially delayed (less community change by 8 weeks) but then caught up over the next 4 weeks. These changes in succession led to homogenization of communities maintained in or transplanted to acidified conditions, and altered community structure in ways that reflected both short- and longer-term acidification history. These community shifts are likely a result of interspecific variability in response to increased pCO2 and changes in species interactions. High pCO2 altered biofilm development, allowing serpulids to do best at the acidified site by the end of the experiment, although early (pretransplant) negative effects of pCO2 on recruitment of these worms were still detectable. The ascidians Diplosoma sp. and Botryllus sp. settled later and were more tolerant to acidification. Overall, transient and persistent acidification-driven changes in the biofouling community, via both past and more recent exposure, could have important implications for ecosystem function and food web dynamics.
Collapse
Affiliation(s)
- Norah E M Brown
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Marco Milazzo
- DiSTeM, CoNISMa, University of Palermo, Palermo, Italy
| | - Samuel P S Rastrick
- Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, UK
- Institute of Marine Research, Bergen, Norway
| | - Jason M Hall-Spencer
- Marine Biology and Ecology Research Centre, University of Plymouth, Plymouth, UK
- Shimoda Marine Research Centre, Tsukuba University, Tsukuba, Japan
| | | | - Christopher D G Harley
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Muller EM, Fine M, Ritchie KB. The stable microbiome of inter and sub-tidal anemone species under increasing pCO 2. Sci Rep 2016; 6:37387. [PMID: 27876762 PMCID: PMC5120257 DOI: 10.1038/srep37387] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 10/28/2016] [Indexed: 01/18/2023] Open
Abstract
Increasing levels of pCO2 within the oceans will select for resistant organisms such as anemones, which may thrive under ocean acidification conditions. However, increasing pCO2 may alter the bacterial community of marine organisms, significantly affecting the health status of the host. A pH gradient associated with a natural volcanic vent system within Levante Bay, Vulcano Island, Italy, was used to test the effects of ocean acidification on the bacterial community of two anemone species in situ, Anemonia viridis and Actinia equina using 16 S rDNA pyrosequencing. Results showed the bacterial community of the two anemone species differed significantly from each other primarily because of differences in the Gammaproteobacteria and Epsilonproteobacteria abundances. The bacterial communities did not differ within species among sites with decreasing pH except for A. viridis at the vent site (pH = 6.05). In addition to low pH, the vent site contains trace metals and sulfide that may have influenced the bacteria community of A. viridis. The stability of the bacterial community from pH 8.1 to pH 7.4, coupled with previous experiments showing the lack of, or beneficial changes within anemones living under low pH conditions indicates that A. viridis and A. equina will be winners under future ocean acidification scenarios.
Collapse
Affiliation(s)
| | - Maoz Fine
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
- The Interuniversity Institute of Marine Science in Eilat, P.O.B. 469 Eilat 88103, Israel
| | - Kim B. Ritchie
- Mote Marine Laboratory, Sarasota, FL 34236, USA
- The University of South Carolina, Beaufort SC 29902, USA
| |
Collapse
|
25
|
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.
Collapse
|
26
|
Borrero-Santiago AR, Carbú M, DelValls TÁ, Riba I. CO2 leaking from sub-seabed storage: Responses of two marine bacteria strains. MARINE ENVIRONMENTAL RESEARCH 2016; 121:2-8. [PMID: 27255122 DOI: 10.1016/j.marenvres.2016.05.018] [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: 09/23/2015] [Revised: 05/16/2016] [Accepted: 05/23/2016] [Indexed: 06/05/2023]
Abstract
Carbon capture and storage (CCS) in stable geological locations is one of the options to mitigate the negative effects of global warming produced by the increase in CO2 concentrations in the atmosphere. A CO2 leak is one of the risks associated with this strategy. Marine bacteria attached to the sediment may be affected by an acidification event. Responses of two marine strains (Roseobacter sp. CECT 7117 and Pseudomonas litoralis CECT 7670) were assessed under different scenarios using a range of pH values (7.8, 7, 6.5, 6, and 5.5) to mimic a CO2 leak. A CO2 injection system was used to simulate an escape from a stable sub-seabed. Growth rate (μ), cell number, inhibition of Relative Inhibitory Effect (RI CO2) and inhibited population were analysed as endpoints. P. litoralis showed more sensitivity to high CO2 concentrations than Roseobacter sp. Our results highlight the diversity and resistance in marine bacteria and their capacity to adapt under a stressful CO2 leakage.
Collapse
Affiliation(s)
- A R Borrero-Santiago
- Departamento de Química-Física, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, UNESCO/UNITWIN WiCoP, Campus de Excelencia Internacional del Mar (CEIMAR), Polígono Río San Pedro s/n, Puerto Real, 11510 Cádiz, Spain.
| | - M Carbú
- Departamento de Biomedicina, Biotecnología y Salud Pública, Laboratorio de Microbiología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Polígono Río San Pedro s/n, Puerto Real, 11510 Cádiz, Spain
| | - T Á DelValls
- Departamento de Química-Física, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, UNESCO/UNITWIN WiCoP, Campus de Excelencia Internacional del Mar (CEIMAR), Polígono Río San Pedro s/n, Puerto Real, 11510 Cádiz, Spain
| | - I Riba
- Departamento de Química-Física, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, UNESCO/UNITWIN WiCoP, Campus de Excelencia Internacional del Mar (CEIMAR), Polígono Río San Pedro s/n, Puerto Real, 11510 Cádiz, Spain
| |
Collapse
|
27
|
Borrero-Santiago AR, DelValls TA, Riba I. Carbon Capture and Storage (CCS): Risk assessment focused on marine bacteria. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2016; 131:157-163. [PMID: 27107627 DOI: 10.1016/j.ecoenv.2016.04.020] [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: 09/24/2015] [Revised: 03/02/2016] [Accepted: 04/14/2016] [Indexed: 06/05/2023]
Abstract
Carbon capture and storage (CCS) is one of the options to mitigate the negative effects of the climate change. However, this strategy may have associated some risks such as CO2 leakages due to an escape from the reservoir. In this context, marine bacteria have been underestimated. In order to figure out the gaps and the lack of knowledge, this work summarizes different studies related to the potential effects on the marine bacteria associated with an acidification caused by a CO2 leak from CSS. An improved integrated model for risk assessment is suggested as a tool based on the rapid responses of bacterial community. Moreover, this contribution proposes a strategy for laboratory protocols using Pseudomona stanieri (CECT7202) as a case of study and analyzes the response of the strain under different CO2 conditions. Results showed significant differences (p≤0.05) under six diluted enriched medium and differences about the days in the exponential growth phase. Dilution 1:10 (Marine Broth 2216 with seawater) was selected as an appropriate growth medium for CO2 toxicity test in batch cultures. This work provide an essential and a complete tool to understand and develop a management strategy to improve future works related to possible effects produced by potential CO2 leaks.
Collapse
Affiliation(s)
- A R Borrero-Santiago
- Departamento de Química Física. Facultad de Ciencias Del Mar y Ambientales, Universidad de Cádiz. Grupo de Contaminación de sistemas acuáticos. UNESCO/UNITWIN Wicop. Polígono Río San Pedro s/n, Puerto Real, 11510 Cádiz, Spain.
| | - T A DelValls
- Departamento de Química Física. Facultad de Ciencias Del Mar y Ambientales, Universidad de Cádiz. Grupo de Contaminación de sistemas acuáticos. UNESCO/UNITWIN Wicop. Polígono Río San Pedro s/n, Puerto Real, 11510 Cádiz, Spain
| | - I Riba
- Departamento de Química Física. Facultad de Ciencias Del Mar y Ambientales, Universidad de Cádiz. Grupo de Contaminación de sistemas acuáticos. UNESCO/UNITWIN Wicop. Polígono Río San Pedro s/n, Puerto Real, 11510 Cádiz, Spain
| |
Collapse
|
28
|
Coelho FJRC, Cleary DFR, Costa R, Ferreira M, Polónia ARM, Silva AMS, Simões MMQ, Oliveira V, Gomes NCM. Multitaxon activity profiling reveals differential microbial response to reduced seawater pH and oil pollution. Mol Ecol 2016; 25:4645-59. [DOI: 10.1111/mec.13779] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 07/25/2016] [Indexed: 12/25/2022]
Affiliation(s)
| | - Daniel F. R. Cleary
- Department of Biology & CESAM; University of Aveiro; Campus de Santiago 3810-193 Aveiro Portugal
| | - Rodrigo Costa
- Centre of Marine Sciences (CCMAR); University of Algarve; Faro 8005-139 Algarve Portugal
- Institute for Bioengineering and Biosciences; Department of Bioengineering; Instituto Superior Técnico; Universidade de Lisboa; 1049-001 Lisbon Portugal
| | - Marina Ferreira
- Department of Biology & CESAM; University of Aveiro; Campus de Santiago 3810-193 Aveiro Portugal
| | - Ana R. M. Polónia
- Department of Biology & CESAM; University of Aveiro; Campus de Santiago 3810-193 Aveiro Portugal
| | - Artur M. S. Silva
- Department of Chemistry & QOPNA; University of Aveiro; Campus Universitário de Santiago Aveiro Portugal
| | - Mário M. Q. Simões
- Department of Chemistry & QOPNA; University of Aveiro; Campus Universitário de Santiago Aveiro Portugal
| | - Vanessa Oliveira
- Department of Biology & CESAM; University of Aveiro; Campus de Santiago 3810-193 Aveiro Portugal
| | - Newton C. M. Gomes
- Department of Biology & CESAM; University of Aveiro; Campus de Santiago 3810-193 Aveiro Portugal
| |
Collapse
|
29
|
Hassenrück C, Fink A, Lichtschlag A, Tegetmeyer HE, de Beer D, Ramette A. Quantification of the effects of ocean acidification on sediment microbial communities in the environment: the importance of ecosystem approaches. FEMS Microbiol Ecol 2016; 92:fiw027. [PMID: 26887661 PMCID: PMC4828923 DOI: 10.1093/femsec/fiw027] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/31/2015] [Accepted: 02/08/2016] [Indexed: 12/14/2022] Open
Abstract
To understand how ocean acidification (OA) influences sediment microbial communities, naturally CO2-rich sites are increasingly being used as OA analogues. However, the characterization of these naturally CO2-rich sites is often limited to OA-related variables, neglecting additional environmental variables that may confound OA effects. Here, we used an extensive array of sediment and bottom water parameters to evaluate pH effects on sediment microbial communities at hydrothermal CO2 seeps in Papua New Guinea. The geochemical composition of the sediment pore water showed variations in the hydrothermal signature at seep sites with comparable pH, allowing the identification of sites that may better represent future OA scenarios. At these sites, we detected a 60% shift in the microbial community composition compared with reference sites, mostly related to increases in Chloroflexi sequences. pH was among the factors significantly, yet not mainly, explaining changes in microbial community composition. pH variation may therefore often not be the primary cause of microbial changes when sampling is done along complex environmental gradients. Thus, we recommend an ecosystem approach when assessing OA effects on sediment microbial communities under natural conditions. This will enable a more reliable quantification of OA effects via a reduction of potential confounding effects.
Collapse
Affiliation(s)
- Christiane Hassenrück
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Artur Fink
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Anna Lichtschlag
- National Oceanography Centre, University of Southampton Waterfront Campus, European Way, Southampton SO14 3ZH, UK
| | - Halina E Tegetmeyer
- Center for Biotechnology, Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Dirk de Beer
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Alban Ramette
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany Institute of Social and Preventive Medicine, Bern University, Finkenhubelweg 11, 3012 Bern, Switzerland
| |
Collapse
|
30
|
Ruff SE, Kuhfuss H, Wegener G, Lott C, Ramette A, Wiedling J, Knittel K, Weber M. Methane Seep in Shallow-Water Permeable Sediment Harbors High Diversity of Anaerobic Methanotrophic Communities, Elba, Italy. Front Microbiol 2016; 7:374. [PMID: 27065954 PMCID: PMC4814501 DOI: 10.3389/fmicb.2016.00374] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 03/08/2016] [Indexed: 11/13/2022] Open
Abstract
The anaerobic oxidation of methane (AOM) is a key biogeochemical process regulating methane emission from marine sediments into the hydrosphere. AOM is largely mediated by consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB), and has mainly been investigated in deep-sea sediments. Here we studied methane seepage at four spots located at 12 m water depth in coastal, organic carbon depleted permeable sands off the Island of Elba (Italy). We combined biogeochemical measurements, sequencing-based community analyses and in situ hybridization to investigate the microbial communities of this environment. Increased alkalinity, formation of free sulfide and nearly stoichiometric methane oxidation and sulfate reduction rates up to 200 nmol g-1 day-1 indicated the predominance of sulfate-coupled AOM. With up to 40 cm thickness the zones of AOM activity were unusually large and occurred in deeper sediment horizons (20–50 cm below seafloor) as compared to diffusion-dominated deep-sea seeps, which is likely caused by advective flow of pore water due to the shallow water depth and permeability of the sands. Hydrodynamic forces also may be responsible for the substantial phylogenetic and unprecedented morphological diversity of AOM consortia inhabiting these sands, including the clades ANME-1a/b, ANME-2a/b/c, ANME-3, and their partner bacteria SEEP-SRB1a and SEEP-SRB2. High microbial dispersal, the availability of diverse energy sources and high habitat heterogeneity might explain that the emission spots shared few microbial taxa, despite their physical proximity. Although the biogeochemistry of this shallow methane seep was very different to that of deep-sea seeps, their key functional taxa were very closely related, which supports the global dispersal of key taxa and underlines strong selection by methane as the predominant energy source. Mesophilic, methane-fueled ecosystems in shallow-water permeable sediments may comprise distinct microbial habitats due to their unique biogeochemical and physical characteristics. To link AOM phylotypes with seep habitats and to enable future meta-analyses we thus propose that seep environment ontology needs to be further specified.
Collapse
Affiliation(s)
- S Emil Ruff
- Department for Molecular Ecology, Max Planck Institute for Marine MicrobiologyBremen, Germany; HGF MPG Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine MicrobiologyBremen, Germany
| | - Hanna Kuhfuss
- Department for Molecular Ecology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Gunter Wegener
- HGF MPG Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine MicrobiologyBremen, Germany; MARUM Center for Marine Environmental Sciences, University of BremenBremen, Germany
| | - Christian Lott
- HYDRA Institute for Marine Sciences, Elba Field Station Campo nell'Elba, Italy
| | - Alban Ramette
- HGF MPG Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Johanna Wiedling
- HYDRA Institute for Marine Sciences, Elba Field StationCampo nell'Elba, Italy; Department of Biogeochemistry, Max Planck Institute for Marine MicrobiologyBremen, Germany
| | - Katrin Knittel
- Department for Molecular Ecology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Miriam Weber
- HYDRA Institute for Marine Sciences, Elba Field StationCampo nell'Elba, Italy; Department of Biogeochemistry, Max Planck Institute for Marine MicrobiologyBremen, Germany
| |
Collapse
|
31
|
Hassenrück C, Hofmann LC, Bischof K, Ramette A. Seagrass biofilm communities at a naturally CO2 -rich vent. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:516-25. [PMID: 25727314 PMCID: PMC4677816 DOI: 10.1111/1758-2229.12282] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 02/20/2015] [Indexed: 05/25/2023]
Abstract
Seagrass meadows are a crucial component of tropical marine reef ecosystems. Seagrass plants are colonized by a multitude of epiphytic organisms that contribute to broadening the ecological role of seagrasses. To better understand how environmental changes like ocean acidification might affect epiphytic assemblages, the microbial community composition of the epiphytic biofilm of Enhalus acroides was investigated at a natural CO2 vent in Papua New Guinea using molecular fingerprinting and next-generation sequencing of 16S and 18S rRNA genes. Both bacterial and eukaryotic epiphytes formed distinct communities at the CO2 -impacted site compared with the control site. This site-related CO2 effect was also visible in the succession pattern of microbial epiphytes. We further found an increased relative sequence abundance of bacterial types associated with coral diseases at the CO2 -impacted site (Fusobacteria, Thalassomonas), whereas eukaryotes such as certain crustose coralline algae commonly related to healthy reefs were less diverse. These trends in the epiphytic community of E. acroides suggest a potential role of seagrasses as vectors of coral pathogens and may support previous predictions of a decrease in reef health and prevalence of diseases under future ocean acidification scenarios.
Collapse
MESH Headings
- Aquatic Organisms/microbiology
- Bacteria/classification
- Bacteria/genetics
- Biofilms/growth & development
- Biota
- Carbon Dioxide/metabolism
- DNA, Algal/chemistry
- DNA, Algal/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA-Directed DNA Polymerase
- Eukaryota/classification
- Eukaryota/genetics
- Hydrocharitaceae/microbiology
- Papua New Guinea
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 18S/genetics
- Sequence Analysis, DNA
Collapse
Affiliation(s)
- Christiane Hassenrück
- HGF MPG Group for Deep-Sea Ecology and Technology, Max Planck Institute for Marine MicrobiologyCelsiusstrasse 1, Bremen, 28359, Germany
| | - Laurie C Hofmann
- BreMarE, FB 02, University of BremenLeobener Str. NW2, Bremen, 28359, Germany
| | - Kai Bischof
- BreMarE, FB 02, University of BremenLeobener Str. NW2, Bremen, 28359, Germany
| | - Alban Ramette
- HGF MPG Group for Deep-Sea Ecology and Technology, Max Planck Institute for Marine MicrobiologyCelsiusstrasse 1, Bremen, 28359, Germany
| |
Collapse
|