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Diner RE, Allard SM, Gilbert JA. Host-associated microbes mitigate the negative impacts of aquatic pollution. mSystems 2024; 9:e0086824. [PMID: 39207151 PMCID: PMC11495061 DOI: 10.1128/msystems.00868-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Abstract
Pollution can negatively impact aquatic ecosystems, aquaculture operations, and recreational water quality. Many aquatic microbes can sequester or degrade pollutants and have been utilized for bioremediation. While planktonic and benthic microbes are well-studied, host-associated microbes likely play an important role in mitigating the negative impacts of aquatic pollution and represent an unrealized source of microbial potential. For example, aquatic organisms that thrive in highly polluted environments or concentrate pollutants may have microbiomes adapted to these selective pressures. Understanding microbe-pollutant interactions in sensitive and valuable species could help protect human well-being and improve ecosystem resilience. Investigating these interactions using appropriate experimental systems and overcoming methodological challenges will present novel opportunities to protect and improve aquatic systems. In this perspective, we review examples of how microbes could mitigate negative impacts of aquatic pollution, outline target study systems, discuss challenges of advancing this field, and outline implications in the face of global changes.
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Affiliation(s)
- Rachel E. Diner
- Department of Biological Sciences, University of Memphis, Memphis, Tennessee, USA
| | - Sarah M. Allard
- University of California, San Diego, Scripps Institution of Oceanography, La Jolla, California, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Jack A. Gilbert
- University of California, San Diego, Scripps Institution of Oceanography, La Jolla, California, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
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Wang Y, Deng M, Zhou S, Li L, Song K. Increasing fish production in recirculating aquaculture system by integrating a biofloc-worm reactor for protein recovery. WATER RESEARCH X 2024; 24:100246. [PMID: 39220625 PMCID: PMC11363497 DOI: 10.1016/j.wroa.2024.100246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/23/2024] [Accepted: 07/26/2024] [Indexed: 09/04/2024]
Abstract
Aquaculture, producing half of global fish production, offers a high-quality protein source for humans. Improving nitrogen use efficiency (NUE) through microbial protein recovery is crucial for increasing fish production and reducing environmental footprint. However, the poor palatability and high moisture content of microbial protein make its utilization challenging. Here, a biofloc-worm reactor was integrated into a recirculating aquaculture system (BW_RAS) for the first time to convert microbial protein into Tubificidae (Oligochaeta) biomass, which was used as direct feed for culturing fish. Batch experiments indicated that an aeration rate of 0.132 m3 L -1 h -1 and a worm density of 0.3 g cm-2 on the carrier were optimal for microbial biomass growth and worm predation, respectively. Compared to the biofloc reactor-based recirculating aquaculture system (B_RAS), the BW_RAS improved water quality, NUE, and fish production by 17.1 % during a 120-day aquaculture period. The abundance of heterotrophic aerobic denitrifier Deinococcus in BW_RAS was one order of magnitude higher than in B_RAS, while heterotrophic bacteria Mycobacterium was more abundant in B_RAS. Denitrifiers cooperated with organic matter degraders and nitrogen assimilation bacteria for protein recovery and gaseous nitrogen loss while competing with predatory bacteria. Function prediction and qPCR indicated greater aerobic respiration, nitrate assimilation, nitrification (AOB-amoA), and denitrification (napA, nirK, nirS, nosZI), but lower fermentation in BWR compared to BR. This study demonstrated that BW_RAS increased microbial protein production and aerobic nitrogen cycling through ongoing worm predation, further enhancing fish production to a commercially viable level.
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Affiliation(s)
- Yuren Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Lake and Watershed Science for Water Security, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Deng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Lake and Watershed Science for Water Security, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Shuni Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Lake and Watershed Science for Water Security, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Li
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Lake and Watershed Science for Water Security, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Kang Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Lake and Watershed Science for Water Security, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Liang Y, Liu H, Zhai S, Huang L, Huang W, Huang B, Xu J, Xiong J, Wang B. Effects of weaning American glass eels ( Anguilla rostrata) with the formula diet on intestinal microbiota and inflammatory cytokines genes expression. Heliyon 2023; 9:e16965. [PMID: 37346341 PMCID: PMC10279831 DOI: 10.1016/j.heliyon.2023.e16965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 04/27/2023] [Accepted: 06/02/2023] [Indexed: 06/23/2023] Open
Abstract
This study aimed to investigate the effects of weaning American glass eels (Anguilla rostrata) with the formula diet on intestinal microbiota and the expression of inflammatory cytokines genes. During the feeding trial, the control group (termed IF group) was fed with initial feed for 34 days, and the experimental group (termed FF group) was fed with initial feed for 30 days, and then weaned with the formula diet for 4 days. After feeding trial, intestines were subjected to microbiota analysis using 16S rDNA high-throughput sequencing, and expression of three inflammatory cytokines genes in gut were examined by qPCR. The results indicated that the species richness and diversity of intestinal microbiota exhibited significantly higher in FF group than that in IF group (P < 0.05). At the phylum level, the core intestinal microflora was the same for two groups. The most abundant phylum was Firmicutes in IF group, while it was Proteobacteria in FF group. Five genera were significantly higher in the IF group compared with the FF group, and Bacillus was the most major enriched biomarker at genus level. Nine genera were significantly higher in the FF group compared with the IF group, and Acidovorax was the most major enriched biomarker. Weaning from initial feeding diet to formula feeding diet enhanced the expression levels of TNF-α and IL-8, and there was no significant change in IL-1β expression between the two groups. These findings would be very useful to improve the diet formulation for weaning stage of American glass eels.
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Affiliation(s)
- Ying Liang
- Fisheries College, Jimei University, Xiamen, Fujian, 361021, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, Guangdong, 524088, China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, PR China, Xiamen, Fujian, 361021, China
- Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, PR China, Xiamen, Fujian, 361021, China
| | - Haizi Liu
- Fisheries College, Jimei University, Xiamen, Fujian, 361021, China
- Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, PR China, Xiamen, Fujian, 361021, China
| | - Shaowei Zhai
- Fisheries College, Jimei University, Xiamen, Fujian, 361021, China
- Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, PR China, Xiamen, Fujian, 361021, China
| | - Lixing Huang
- Fisheries College, Jimei University, Xiamen, Fujian, 361021, China
| | - Wenshu Huang
- Fisheries College, Jimei University, Xiamen, Fujian, 361021, China
- Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, PR China, Xiamen, Fujian, 361021, China
| | - Bei Huang
- Fisheries College, Jimei University, Xiamen, Fujian, 361021, China
- Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, PR China, Xiamen, Fujian, 361021, China
| | - Jisong Xu
- Fisheries College, Jimei University, Xiamen, Fujian, 361021, China
- Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, PR China, Xiamen, Fujian, 361021, China
| | - Jing Xiong
- Fisheries College, Jimei University, Xiamen, Fujian, 361021, China
- Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, PR China, Xiamen, Fujian, 361021, China
| | - Bei Wang
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, Guangdong, 524088, China
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Ayayee PA, Wesner JS, Ouellette SP. Geography, taxonomy, and ecological guild: Factors impacting freshwater macroinvertebrate gut microbiomes. Ecol Evol 2022; 12:e9663. [PMID: 36582772 PMCID: PMC9789321 DOI: 10.1002/ece3.9663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/25/2022] Open
Abstract
Despite their diversity, global distribution, and apparent effects on host biology, the rules of life that govern variation in microbiomes among host species remain unclear, particularly in freshwater organisms. In this study, we sought to assess whether geographic location, taxonomy (order, family, and genus), or functional feeding group (FFG) designations would best explain differences in the gut microbiome composition among macroinvertebrates sampled across 10 National Ecological Observatory Network's (NEON) freshwater stream sites in the United States. Subsequently, we compared the beta diversity of microbiomes among locations, taxonomy (order, family, and genus), and FFGs in a single statistical model to account for variation within the source microbial community and the types of macroinvertebrates sampled across locations. We determined significant differences in community composition among macroinvertebrate orders, families, genera, and FFGs. Differences in microbiome compositions were underscored by different bacterial ASVs that were differentially abundant among variables (four bacterial ASVs across the 10 NEON sites, 43 ASVs among the macroinvertebrate orders, and 18 bacterial ASVs differing among the five FFGs). Analyses of variations in microbiome composition using the Bray-Curtis distance matric revealed FFGs as the dominant source of variation (mean standard deviation of 0.8), followed by stream site (mean standard deviation of 0.5), and finally family and genus (mean standard deviation of 0.3 each). Our findings revealed a principal role for FFG classification in insect gut microbiome beta diversity with additional roles for geographic distribution and taxonomy.
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Affiliation(s)
- Paul A. Ayayee
- Department of BiologyUniversity of Nebraska at OmahaOmahaNebraskaUSA
| | - Jeff S. Wesner
- Department of BiologyUniversity of South DakotaVermillionSouth DakotaUSA
| | - Scot P. Ouellette
- Department of Pathology and Microbiology, College of MedicineUniversity of Nebraska Medical CenterOmahaNebraskaUSA
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Aryal B, Gurung R, Camargo AF, Fongaro G, Treichel H, Mainali B, Angove MJ, Ngo HH, Guo W, Puadel SR. Nitrous oxide emission in altered nitrogen cycle and implications for climate change. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 314:120272. [PMID: 36167167 DOI: 10.1016/j.envpol.2022.120272] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/28/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Natural processes and human activities play a crucial role in changing the nitrogen cycle and increasing nitrous oxide (N2O) emissions, which are accelerating at an unprecedented rate. N2O has serious global warming potential (GWP), about 310 times higher than that of carbon dioxide. The food production, transportation, and energy required to sustain a world population of seven billion have required dramatic increases in the consumption of synthetic nitrogen (N) fertilizers and fossil fuels, leading to increased N2O in air and water. These changes have radically disturbed the nitrogen cycle and reactive nitrogen species, such as nitrous oxide (N2O), and have impacted the climatic system. Yet, systematic and comprehensive studies on various underlying processes and parameters in the altered nitrogen cycle, and their implications for the climatic system are still lacking. This paper reviews how the nitrogen cycle has been disturbed and altered by anthropogenic activities, with a central focus on potential pathways of N2O generation. The authors also estimate the N2O-N emission mainly due to anthropogenic activities will be around 8.316 Tg N2O-N yr-1 in 2050. In order to minimize and tackle the N2O emissions and its consequences on the global ecosystem and climate change, holistic mitigation strategies and diverse adaptations, policy reforms, and public awareness are suggested as vital considerations. This study concludes that rapidly increasing anthropogenic perturbations, the identification of new microbial communities, and their role in mediating biogeochemical processes now shape the modern nitrogen cycle.
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Affiliation(s)
- Babita Aryal
- Naaya Aayam Multidisciplinary Institute, NAMI, University of Northampton, Jorpati, Kathmandu, Nepal
| | - Roshni Gurung
- Naaya Aayam Multidisciplinary Institute, NAMI, University of Northampton, Jorpati, Kathmandu, Nepal
| | - Aline F Camargo
- Federal University of Santa Catarina, Post-graduation Program in Biotechnology and Biosciences, Florianopólis, Brazil; Laboratory of Microbiology and Bioprocesses, Federal University of Fronteira Sul, Erechim, Brazil
| | - Gislaine Fongaro
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, 88040-900, Florianópolis, SC, Brazil
| | - Helen Treichel
- Laboratory of Microbiology and Bioprocesses, Federal University of Fronteira Sul, Erechim, Brazil
| | - Bandita Mainali
- School of Engineering and Mathematical Sciences, La Trobe University, Bendigo, VIC, 3550, Australia; School of Engineering, Macquarie University, Sydney, Australia
| | - Michael J Angove
- Department of Pharmacy and Biomedical Science, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Bendigo, VIC-3550, Australia
| | - Huu Hao Ngo
- Faculty of Engineering, University of Technology Sydney (UTS), PO Box 123, Broadway, NSW, 2007, Australia
| | - Wenshan Guo
- Faculty of Engineering, University of Technology Sydney (UTS), PO Box 123, Broadway, NSW, 2007, Australia
| | - Shukra Raj Puadel
- Department of Civil Engineering, Pulchowk Campus, Institute of Engineering, Tribhuwan University, Pulchowk, Lalitpur, 44700, Nepal; Department of Environmental Engineering, College of Science and Technology, Korea University, Sejong, Republic of Korea.
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Du S, Sun X, Zhang J, Lin D, Chen R, Cui Y, Xiang S, Wu Z, Ding T. Metagenome-Assembled Genomes Reveal Mechanisms of Carbohydrate and Nitrogen Metabolism of Schistosomiasis-Transmitting Vector Biomphalaria Glabrata. Microbiol Spectr 2022; 10:e0184321. [PMID: 35254167 PMCID: PMC9045156 DOI: 10.1128/spectrum.01843-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 02/04/2022] [Indexed: 12/11/2022] Open
Abstract
Biomphalaria glabrata transmits schistosomiasis mansoni which poses considerable risks to hundreds of thousands of people worldwide, and is widely used as a model organism for studies on the snail-schistosome relationship. Gut microbiota plays important roles in multiple aspects of host including development, metabolism, immunity, and even behavior; however, detailed information on the complete diversity and functional profiles of B. glabrata gut microbiota is still limited. This study is the first to reveal the gut microbiome of B. glabrata based on metagenome-assembled genome (MAG). A total of 28 gut samples spanning diet and age were sequenced and 84 individual microbial genomes with ≥ 70% completeness and ≤ 5% contamination were constructed. Bacteroidota and Proteobacteria were the dominant bacteria in the freshwater snail, unlike terrestrial organisms harboring many species of Firmicutes and Bacteroidota. The microbial consortia in B. glabrata helped in the digestion of complex polysaccharide such as starch, hemicellulose, and chitin for energy supply, and protected the snail from food poisoning and nitrate toxicity. Both microbial community and metabolism of B. glabrata were significantly altered by diet. The polysaccharide-degrading bacterium Chryseobacterium was enriched in the gut of snails fed with high-digestibility protein and high polysaccharide diet (HPHP). Notably, B. glabrata as a mobile repository can escalate biosafety issues regarding transmission of various pathogens such as Acinetobacter nosocomialis and Vibrio parahaemolyticus as well as multiple antibiotic resistance genes in the environment and to other organisms. IMPORTANCE The spread of aquatic gastropod Biomphalaria glabrata, an intermediate host of Schistosoma mansoni, exacerbates the burden of schistosomiasis disease worldwide. This study provides insights into the importance of microbiome for basic biological activities of freshwater snails, and offers a valuable microbial genome resource to fill the gap in the analysis of the snail-microbiota-parasite relationship. The results of this study clarified the reasons for the high adaptability of B. glabrata to diverse environments, and further illustrated the role of B. glabrata in accumulation of antibiotic resistance in the environment and spread of various pathogens. These findings have important implications for further exploration of the control of snail dissemination and schistosomiasis from a microbial perspective.
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Affiliation(s)
- Shuling Du
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Xi Sun
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, China
| | - Jingxiang Zhang
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Datao Lin
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, China
| | - Runzhi Chen
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Ying Cui
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Suoyu Xiang
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Zhongdao Wu
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, China
| | - Tao Ding
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, China
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Intrahabitat Differences in Bacterial Communities Associated with Corbicula fluminea in the Large Shallow Eutrophic Lake Taihu. Appl Environ Microbiol 2022; 88:e0232821. [PMID: 35285714 DOI: 10.1128/aem.02328-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The Asian clam Corbicula fluminea is a keystone zoobenthos in freshwater ecosystems. However, its associated microbiome is not well understood. We investigated the bacterial communities of this clam and its surrounding environment, including sediment and water simultaneously, in a large lake by means of 16S rRNA gene sequencing. Approximately two-thirds of the bacterial operational taxonomic units (OTUs) associated with clams were observed in the surrounding environment and mostly from particle-associated samples. The associated bacterial communities were site specific and more similar to environmental bacteria from the same site than those at other sites, suggesting a local environmental influence on host bacteria. However, the significant differences in bacterial diversities and compositions between the clam and the environment also indicated strong host selection pressure on bacteria from the surrounding environment. Bacteria affiliated with Firmicutes, Spirochaetes, Tenericutes, Bacteroidetes, Epsilonbacteraeota, Patescibacteria, and Fusobacteria were found to be significantly enriched in the clams in comparison to their local environment. Oligotyping analyses of the core-associated bacterial OTUs also demonstrated that most of the core OTUs had lower relative abundances and occurrence frequencies in environmental samples. The core bacterial OTUs were found to play an important role in maintaining the stability of the bacterial community network. These core bacteria included the two most abundant taxa Romboutsia and Paraclostridium with the potential function of fermenting polysaccharides for assisting host clams in food digestion. Overall, we demonstrate that clam-associated bacteria were spatially dynamic and site specific, which were mainly structured both by local environments and host selection. IMPORTANCE The Asian clam Corbicula fluminea is an important benthic clam in freshwater ecosystems due to its high population densities and high filtering efficiency for particulate organic matter. While the associated microbiota is believed to be vital for host living, our knowledge about the compositions, sources, and potential functions is still lacking. We found that C. fluminea offers a unique ecological niche for specific lake bacteria. We also observed high intrahabitat variation in the associated bacterial communities. Such variations were driven mainly by local environments, followed by host selection pressure. While the local microbes served as a source of the clam-associated bacteria, host selection resulted in enrichments of bacterial taxa with the potential for assisting the host in organic matter digestion. These results significantly advance our current understanding of the origins and ecological roles of the microbiota associated with a keynote clam in freshwater ecosystems.
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An Z, Gao D, Chen F, Wu L, Zhou J, Zhang Z, Dong H, Yin G, Han P, Liang X, Liu M, Hou L, Zheng Y. Crab bioturbation alters nitrogen cycling and promotes nitrous oxide emission in intertidal wetlands: Influence and microbial mechanism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:149176. [PMID: 34346369 DOI: 10.1016/j.scitotenv.2021.149176] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/16/2021] [Accepted: 07/17/2021] [Indexed: 06/13/2023]
Abstract
Intertidal wetlands provide important ecosystem functions by acting as nitrogen (N) cycling hotspots, which can reduce anthropogenic N loading from land to coastal waters. Benthic bioturbations are thought to play an important role in mediating N cycling in intertidal marshes. However, how the burrowing activity of benthos and their microbial symbionts affect N transformation and greenhouse gas nitrous oxide (N2O) emission remains unclear in these environments. Here, we show that bioturbation of crabs reshaped the structure of intertidal microbial communities and their N cycling function. Molecular analyses suggested that the microbially-driven N cycling might be accelerated by crab bioturbation, as the abundances of most of the N related functional genes were higher on the burrow wall than those in the surrounding bulk sediments, except for genes involved in N fixation, dissimilatory nitrate reduction to ammonium (DNRA), and N2O reduction, which were further confirmed by isotope-tracing experiments. Especially, the potential rates of the main N2O production pathways, nitrification and denitrification, were 2-3 times higher in the burrow wall sediments. However, even higher N2O emission rates (approximately 6 times higher) were observed in this unique microhabitat, which was due to a disproportionate increase in N2O production over N2O consumption driven by burrowing activity. In addition, the sources of N2O were also significantly affected by crab bioturbation, which increased the contribution of hydroxylamine oxidation pathway. This study reveals the mechanism through which benthic bioturbations mediate N cycling and highlights the importance of considering burrowing activity when evaluating the ecological function of intertidal wetlands.
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Affiliation(s)
- Zhirui An
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
| | - Dengzhou Gao
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Feiyang Chen
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Li Wu
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
| | - Jie Zhou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Zongxiao Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Hongpo Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Guoyu Yin
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
| | - Ping Han
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Min Liu
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China.
| | - Yanling Zheng
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China.
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9
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Yeh H, Skubel SA, Patel H, Cai Shi D, Bushek D, Chikindas ML. From Farm to Fingers: an Exploration of Probiotics for Oysters, from Production to Human Consumption. Probiotics Antimicrob Proteins 2021; 12:351-364. [PMID: 32056150 DOI: 10.1007/s12602-019-09629-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Oysters hold a unique place within the field of aquaculture as one of the only organisms that is regularly shipped live to be consumed whole and raw. The microbiota of oysters is capable of adapting to a wide range of environmental conditions within their dynamic estuarine environments; however, human aquaculture practices can challenge the resilience of this microbial community. Several discrete stages in oyster cultivation and market processing can cause disruption to the oyster microbiota, thus increasing the possibility of proliferation by pathogens and spoilage bacteria. These same pressure points offer the opportunity for the application of probiotics to help decrease disease occurrence in stocks, improve product yields, minimize the risk of shellfish poisoning, and increase product shelf life. This review provides a summary of the current knowledge on oyster microbiota, the impact of aquaculture upon this community, and the current status of oyster probiotic development. In response to this biotechnological gap, the authors highlight opportunities of highest potential impact within the aquaculture pipeline and propose a strategy for oyster-specific probiotic candidate development.
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Affiliation(s)
- Heidi Yeh
- Haskin Shellfish Research Laboratory, Rutgers State University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA.
| | - Sarah A Skubel
- Department of Plant Biology, Rutgers State University, New Brunswick, NJ, 08904, USA
| | - Harna Patel
- Department of Plant Biology, Rutgers State University, New Brunswick, NJ, 08904, USA
| | - Denia Cai Shi
- Department of Plant Biology, Rutgers State University, New Brunswick, NJ, 08904, USA
| | - David Bushek
- Haskin Shellfish Research Laboratory, Rutgers State University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA
| | - Michael L Chikindas
- Health Promoting Naturals Laboratory, School of Environmental and Biological Sciences, Rutgers State University, New Brunswick, NJ, 08904, USA.,Don State Technical University, Rostov-on-Don, 344002, Russia
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10
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Huang Y, Li W, Gao J, Wang F, Yang W, Han L, Lin D, Min B, Zhi Y, Grieger K, Yao J. Effect of microplastics on ecosystem functioning: Microbial nitrogen removal mediated by benthic invertebrates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:142133. [PMID: 32916494 DOI: 10.1016/j.scitotenv.2020.142133] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 06/11/2023]
Abstract
While ecotoxicological impacts of microplastics on aquatic organisms have started to be investigated recently, impacts on ecosystem functions mediated by benthic biota remain largely unknown. We investigated the effect of microplastics on nitrogen removal in freshwater sediments where microorganisms and benthic invertebrates (i.e., chironomid larvae) co-existed. Using microcosm experiments, sediments with and without invertebrate chironomid larvae were exposed to microplastics (polyethylene) at concentrations of 0, 0.1, and 1 wt%. After 28 days of exposure, the addition of microplastics or chironomid larvae promoted the growth of denitrifying and anammox bacteria, leading to increased total nitrogen removal, in both cases. However, in microcosms with chironomid larvae and microplastics co-existing, nitrogen removal was less than the sum of their individual effects, especially at microplastics concentration of 1 wt%, indicating an adverse effect on microbial nitrogen removal mediated by macroinvertebrates. This study reveals that the increasing concentration of microplastics entangled the nitrogen cycling mediated by benthic invertebrates in freshwater ecosystems. These findings highlight the pursuit of a comprehensive understanding of the impacts of microplastics on the functioning in freshwater ecosystems.
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Affiliation(s)
- Yuyue Huang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China
| | - Wei Li
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China
| | - Jie Gao
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China
| | - Fang Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China
| | - Wei Yang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China
| | - Le Han
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China
| | - Dunmei Lin
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China
| | - Bolin Min
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China
| | - Yue Zhi
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China; Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Khara Grieger
- Department of Applied Ecology, North Carolina State University, Raleigh, NC 27695, USA
| | - Jingmei Yao
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China; College of Environment and Ecology, Chongqing University, Chongqing 400045, PR China.
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11
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Timilsina A, Zhang C, Pandey B, Bizimana F, Dong W, Hu C. Potential Pathway of Nitrous Oxide Formation in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:1177. [PMID: 32849729 PMCID: PMC7412978 DOI: 10.3389/fpls.2020.01177] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/20/2020] [Indexed: 05/12/2023]
Abstract
Plants can produce and emit nitrous oxide (N2O), a potent greenhouse gas, into the atmosphere, and several field-based studies have concluded that this gas is emitted at substantial amounts. However, the exact mechanisms of N2O production in plant cells are unknown. Several studies have hypothesised that plants might act as a medium to transport N2O produced by soil-inhabiting microorganisms. Contrarily, aseptically grown plants and axenic algal cells supplied with nitrate (NO3) are reported to emit N2O, indicating that it is produced inside plant cells by some unknown physiological phenomena. In this study, the possible sites, mechanisms, and enzymes involved in N2O production in plant cells are discussed. Based on the experimental evidence from various studies, we determined that N2O can be produced from nitric oxide (NO) in the mitochondria of plants. NO, a signaling molecule, is produced through oxidative and reductive pathways in eukaryotic cells. During hypoxia and anoxia, NO3 in the cytosol is metabolised to produce nitrite (NO2), which is reduced to form NO via the reductive pathway in the mitochondria. Under low oxygen condition, NO formed in the mitochondria is further reduced to N2O by the reduced form of cytochrome c oxidase (CcO). This pathway is active only when cells experience hypoxia or anoxia, and it may be involved in N2O formation in plants and soil-dwelling animals, as reported previously by several studies. NO can be toxic at a high concentration. Therefore, the reduction of NO to N2O in the mitochondria might protect the integrity of the mitochondria, and thus, protect the cell from the toxicity of NO accumulation under hypoxia and anoxia. As NO3 is a major source of nitrogen for plants and all plants may experience hypoxic and anoxic conditions owing to soil environmental factors, a significant global biogenic source of N2O may be its formation in plants via the proposed pathway.
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Affiliation(s)
- Arbindra Timilsina
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Arbindra Timilsina, ; Chunsheng Hu,
| | - Chuang Zhang
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bikram Pandey
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Mountain Ecological Restoration and Bio-resource Utilization and Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Fiston Bizimana
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenxu Dong
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Chunsheng Hu
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Arbindra Timilsina, ; Chunsheng Hu,
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12
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The Effect of Chironomid Larvae on Nitrogen Cycling and Microbial Communities in Soft Sediments. WATER 2019. [DOI: 10.3390/w11091931] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The combination of biogeochemical methods and molecular techniques has the potential to uncover the black-box of the nitrogen (N) cycle in bioturbated sediments. Advanced biogeochemical methods allow the quantification of the process rates of different microbial processes, whereas molecular tools allow the analysis of microbial diversity (16S rRNA metabarcoding) and activity (marker genes and transcripts) in biogeochemical hot-spots such as the burrow wall or macrofauna guts. By combining biogeochemical and molecular techniques, we analyzed the role of tube-dwelling Chironomus plumosus (Insecta, Diptera) larvae on nitrification and nitrate reduction processes in a laboratory experiment with reconstructed sediments. We hypothesized that chironomid larvae stimulate these processes and host bacteria actively involved in N-cycling. Our results suggest that chironomid larvae significantly enhance the recycling of ammonium (80.5 ± 48.7 µmol m−2 h−1) and the production of dinitrogen (420.2 ± 21.4 µmol m−2 h−1) via coupled nitrification–denitrification and the consumption of water column nitrates. Besides creating oxygen microniches in ammonium-rich subsurface sediments via burrow digging and ventilation, chironomid larvae serve as hot-spots of microbial communities involved in N-cycling. The quantification of functional genes showed a significantly higher potential for microbial denitrification and nitrate ammonification in larvae as compared to surrounding sediments. Future studies may further scrutinize N transformation rates associated with intimate macrofaunal–bacteria associations.
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13
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Gárate M, Moseman-Valtierra S, Moen A. Potential nitrous oxide production by marine shellfish in response to warming and nutrient enrichment. MARINE POLLUTION BULLETIN 2019; 146:236-246. [PMID: 31426152 DOI: 10.1016/j.marpolbul.2019.06.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 06/10/2023]
Abstract
Bivalves facilitate microbial nitrogen cycling, which can produce nitrous oxide (N2O), a potent greenhouse gas. Potential N2O production by three marine bivalves (Mytilus edulis, Mercenaria mercenaria and Crassostrea virginica) was measured in the laboratory including responses to nitrogen (N) loading and/or warming over short-terms (up to 14 or 28 days). N additions (targeting 100 μM-N ammonium nitrate) or warming (22 °C) individually and in combination were applied with experimental controls (20 μM-N, 19 °C). N2O production rates were higher with N additions for all species, but warming lacked significant direct effects. Ammonium and nitrate concentrations varied but were consistent with nitrification as a potential N2O source for all bivalves. Highest N2O emissions (7.5 nmol N2O g-1 h-1) were from M. edulis under hypoxic conditions coincident with a drop in pH. Macro-epifauna on M. edulis did not significantly alter N2O production. Thus, under short-term hypoxic conditions, micro-organisms in M. edulis guts may be a particularly significant source of N2O.
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Affiliation(s)
- M Gárate
- Mass Audubon, 500 Walk Hill St, Boston, MA 02126
| | | | - A Moen
- URI Diving Safety Program, 215 South Ferry Road, Narragansett, RI 02882
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14
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Ray NE, Maguire TJ, Al-Haj AN, Henning MC, Fulweiler RW. Low Greenhouse Gas Emissions from Oyster Aquaculture. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:9118-9127. [PMID: 31295406 DOI: 10.1021/acs.est.9b02965] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Production of animal protein is associated with high greenhouse gas (GHG) emissions. Globally, oyster aquaculture is increasing as a way to meet growing demands for protein, yet its associated GHG-emissions are largely unknown. We quantified oyster aquaculture GHG-emissions from the three main constituents of GHG-release associated with terrestrial livestock production: fermentation in the animal gut, manure management, and fodder production. We found that oysters release no methane (CH4) and only negligible amounts of nitrous oxide (0.00012 ± 0.00004 μmol N2O gDW-1 hr-1) and carbon dioxide (3.556 ± 0.471 μmol CO2 gDW-1 hr-1). Further, sediment fluxes of N2O and CH4 were unchanged in the presence of oyster aquaculture, regardless of the length of time it had been in place. Sediment CO2 release was slightly stimulated between 4 and 6 years of aquaculture presence and then returned to baseline levels but was not significantly different between aquaculture and a control site when all ages of culture were pooled. There is no GHG-release from oyster fodder production. Considering the main drivers of GHG-release in terrestrial livestock systems, oyster aquaculture has less than 0.5% of the GHG-cost of beef, small ruminants, pork, and poultry in terms of CO2-equivalents per kg protein, suggesting that shellfish aquaculture may provide a a low GHG alternative for future animal protein production compared to land based sources. We estimate that if 10% of the protein from beef consumption in the United States was replaced with protein from oysters, the GHG savings would be equivalent to 10.8 million fewer cars on the road.
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Affiliation(s)
- Nicholas E Ray
- Department of Biology , Boston University , 5 Cummington Mall , Boston , Massachusetts 02215 , United States
| | - Timothy J Maguire
- Department of Biology , Boston University , 5 Cummington Mall , Boston , Massachusetts 02215 , United States
- Great Lakes Institute for Environmental Research , University of Windsor , Windsor , ON N9B 3P4 , Canada
| | - Alia N Al-Haj
- Department of Earth and Environment , Boston University , 685 Commonwealth Avenue , Boston , Massachusetts 02215 , United States
| | - Maria C Henning
- Department of Earth and Environment , Boston University , 685 Commonwealth Avenue , Boston , Massachusetts 02215 , United States
| | - Robinson W Fulweiler
- Department of Biology , Boston University , 5 Cummington Mall , Boston , Massachusetts 02215 , United States
- Department of Earth and Environment , Boston University , 685 Commonwealth Avenue , Boston , Massachusetts 02215 , United States
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15
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Dale H, Solan M, Lam P, Cunliffe M. Sediment microbial assemblage structure is modified by marine polychaete gut passage. FEMS Microbiol Ecol 2019; 95:5426820. [DOI: 10.1093/femsec/fiz047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/02/2019] [Indexed: 01/13/2023] Open
Affiliation(s)
- Harriet Dale
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
- Ocean and Earth Science, University of Southampton, Waterfront Campus, National Oceanography Centre, European Way, Southampton, SO14 3ZH, UK
| | - Martin Solan
- Ocean and Earth Science, University of Southampton, Waterfront Campus, National Oceanography Centre, European Way, Southampton, SO14 3ZH, UK
| | - Phyllis Lam
- Ocean and Earth Science, University of Southampton, Waterfront Campus, National Oceanography Centre, European Way, Southampton, SO14 3ZH, UK
| | - Michael Cunliffe
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
- Marine Biology and Ecology Research Group, School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth, PL4 8AA, UK
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16
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Hall SJ, Huber DP, Hughes RF. Invasion of Hawaiian rainforests by an introduced amphibian predator and N2-fixing tree increases soil N2O emissions. Ecosphere 2018. [DOI: 10.1002/ecs2.2416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Sharon J. Hall
- School of Life Sciences; Arizona State University; Tempe Arizona 85287-4501 USA
| | - David P. Huber
- Northwest Watershed Research Center; USDA-Agricultural Research Service; Boise Idaho 83712 USA
| | - R. Flint Hughes
- Institute for Pacific Islands Forestry; Pacific Southwest Research Station; USDA Forest Service; Hilo Hawaii 96720 USA
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17
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Methane fluxes from coastal sediments are enhanced by macrofauna. Sci Rep 2017; 7:13145. [PMID: 29030563 PMCID: PMC5640653 DOI: 10.1038/s41598-017-13263-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 09/22/2017] [Indexed: 11/08/2022] Open
Abstract
Methane and nitrous oxide are potent greenhouse gases (GHGs) that contribute to climate change. Coastal sediments are important GHG producers, but the contribution of macrofauna (benthic invertebrates larger than 1 mm) inhabiting them is currently unknown. Through a combination of trace gas, isotope, and molecular analyses, we studied the direct and indirect contribution of two macrofaunal groups, polychaetes and bivalves, to methane and nitrous oxide fluxes from coastal sediments. Our results indicate that macrofauna increases benthic methane efflux by a factor of up to eight, potentially accounting for an estimated 9.5% of total emissions from the Baltic Sea. Polychaetes indirectly enhance methane efflux through bioturbation, while bivalves have a direct effect on methane release. Bivalves host archaeal methanogenic symbionts carrying out preferentially hydrogenotrophic methanogenesis, as suggested by analysis of methane isotopes. Low temperatures (8 °C) also stimulate production of nitrous oxide, which is consumed by benthic denitrifying bacteria before it reaches the water column. We show that macrofauna contributes to GHG production and that the extent is dependent on lineage. Thus, macrofauna may play an important, but overlooked role in regulating GHG production and exchange in coastal sediment ecosystems.
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18
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Denitrification potential of the eastern oyster microbiome using a 16S rRNA gene based metabolic inference approach. PLoS One 2017; 12:e0185071. [PMID: 28934286 PMCID: PMC5608302 DOI: 10.1371/journal.pone.0185071] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 09/06/2017] [Indexed: 12/14/2022] Open
Abstract
The eastern oyster (Crassostrea virginica) is a foundation species providing significant ecosystem services. However, the roles of oyster microbiomes have not been integrated into any of the services, particularly nitrogen removal through denitrification. We investigated the composition and denitrification potential of oyster microbiomes with an approach that combined 16S rRNA gene analysis, metabolic inference, qPCR of the nitrous oxide reductase gene (nosZ), and N2 flux measurements. Microbiomes of the oyster digestive gland, the oyster shell, and sediments adjacent to the oyster reef were examined based on next generation sequencing (NGS) of 16S rRNA gene amplicons. Denitrification potentials of the microbiomes were determined by metabolic inferences using a customized denitrification gene and genome database with the paprica (PAthway PRediction by phylogenetIC plAcement) bioinformatics pipeline. Denitrification genes examined included nitrite reductase (nirS and nirK) and nitrous oxide reductase (nosZ), which was further subdivided by genotype into clade I (nosZI) or clade II (nosZII). Continuous flow through experiments measuring N2 fluxes were conducted with the oysters, shells, and sediments to compare denitrification activities. Paprica properly classified the composition of microbiomes, showing similar classification results from Silva, Greengenes and RDP databases. Microbiomes of the oyster digestive glands and shells were quite different from each other and from the sediments. The relative abundance of denitrifying bacteria inferred by paprica was higher in oysters and shells than in sediments suggesting that oysters act as hotspots for denitrification in the marine environment. Similarly, the inferred nosZI gene abundances were also higher in the oyster and shell microbiomes than in the sediment microbiome. Gene abundances for nosZI were verified with qPCR of nosZI genes, which showed a significant positive correlation (F1,7 = 14.7, p = 6.0x10-3, R2 = 0.68). N2 flux rates were significantly higher in the oyster (364.4 ± 23.5 μmol N-N2 m-2 h-1) and oyster shell (355.3 ± 6.4 μmol N-N2 m-2 h-1) compared to the sediment (270.5 ± 20.1 μmol N-N2 m-2 h-1). Thus, bacteria carrying nosZI genes were found to be an important denitrifier, facilitating nitrogen removal in oyster reefs. In addition, this is the first study to validate the use of 16S gene based metabolic inference as a method for determining microbiome function, such as denitrification, by comparing inference results with qPCR gene quantification and rate measurements.
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19
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Mehring AS, Cook PLM, Evrard V, Grant SB, Levin LA. Pollution-tolerant invertebrates enhance greenhouse gas flux in urban wetlands. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2017; 27:1852-1861. [PMID: 28482116 DOI: 10.1002/eap.1572] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 04/06/2017] [Accepted: 04/19/2017] [Indexed: 06/07/2023]
Abstract
One of the goals of urban ecology is to link community structure to ecosystem function in urban habitats. Pollution-tolerant wetland invertebrates have been shown to enhance greenhouse gas (GHG) flux in controlled laboratory experiments, suggesting that they may influence urban wetland roles as sources or sinks of GHG. However, it is unclear if their effects can be detected in highly variable conditions in a field setting. Here we use an extensive data set on carbon dioxide (CO2 ), methane (CH4 ), and nitrous oxide (N2 O) flux in sediment cores (n = 103) collected from 10 urban wetlands in Melbourne, Australia during summer and winter in order to test for invertebrate enhancement of GHG flux. We detected significant multiplicative enhancement effects of temperature, sediment carbon content, and invertebrate density on CH4 and CO2 flux. Each doubling in density of oligochaete worms or large benthic invertebrates (oligochaete worms and midge larvae) corresponded to ~42% and ~15% increases in average CH4 and CO2 flux, respectively. However, despite exceptionally high densities, invertebrates did not appear to enhance N2 O flux. This was likely due to fairly high organic carbon content in sediments (range 2.1-12.6%), and relatively low nitrate availability (median 1.96 μmol/L NO3- -N), which highlights the context-dependent nature of community structural effects on ecosystem function. The invertebrates enhancing GHG flux in this study are ubiquitous, and frequently dominate faunal communities in impaired aquatic ecosystems. Therefore, invertebrate effects on CO2 and CH4 flux may be common in wetlands impacted by urbanization, and urban wetlands may make greater contributions to the total GHG budgets of cities if the negative impacts of urbanization on wetlands are left unchecked.
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Affiliation(s)
- Andrew S Mehring
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, 92093, USA
| | - Perran L M Cook
- Water Studies Center, School of Chemistry, Monash University, Clayton, Victoria, 3800, Australia
| | - Victor Evrard
- Department of Environmental Sciences, University of Basel, Schönbeinstrasse 6, CH-4056, Basel, Switzerland
| | - Stanley B Grant
- Department of Civil and Environmental Engineering, Henry Samueli School of Engineering, University of California, Irvine, Irvine, California, 92697, USA
| | - Lisa A Levin
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, 92093, USA
- Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, La Jolla, California, 92093, USA
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20
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Welti N, Striebel M, Ulseth AJ, Cross WF, DeVilbiss S, Glibert PM, Guo L, Hirst AG, Hood J, Kominoski JS, MacNeill KL, Mehring AS, Welter JR, Hillebrand H. Bridging Food Webs, Ecosystem Metabolism, and Biogeochemistry Using Ecological Stoichiometry Theory. Front Microbiol 2017; 8:1298. [PMID: 28747904 PMCID: PMC5507128 DOI: 10.3389/fmicb.2017.01298] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 06/27/2017] [Indexed: 11/26/2022] Open
Abstract
Although aquatic ecologists and biogeochemists are well aware of the crucial importance of ecosystem functions, i.e., how biota drive biogeochemical processes and vice-versa, linking these fields in conceptual models is still uncommon. Attempts to explain the variability in elemental cycling consequently miss an important biological component and thereby impede a comprehensive understanding of the underlying processes governing energy and matter flow and transformation. The fate of multiple chemical elements in ecosystems is strongly linked by biotic demand and uptake; thus, considering elemental stoichiometry is important for both biogeochemical and ecological research. Nonetheless, assessments of ecological stoichiometry (ES) often focus on the elemental content of biota rather than taking a more holistic view by examining both elemental pools and fluxes (e.g., organismal stoichiometry and ecosystem process rates). ES theory holds the promise to be a unifying concept to link across hierarchical scales of patterns and processes in ecology, but this has not been fully achieved. Therefore, we propose connecting the expertise of aquatic ecologists and biogeochemists with ES theory as a common currency to connect food webs, ecosystem metabolism, and biogeochemistry, as they are inherently concatenated by the transfer of carbon, nitrogen, and phosphorous through biotic and abiotic nutrient transformation and fluxes. Several new studies exist that demonstrate the connections between food web ecology, biogeochemistry, and ecosystem metabolism. In addition to a general introduction into the topic, this paper presents examples of how these fields can be combined with a focus on ES. In this review, a series of concepts have guided the discussion: (1) changing biogeochemistry affects trophic interactions and ecosystem processes by altering the elemental ratios of key species and assemblages; (2) changing trophic dynamics influences the transformation and fluxes of matter across environmental boundaries; (3) changing ecosystem metabolism will alter the chemical diversity of the non-living environment. Finally, we propose that using ES to link nutrient cycling, trophic dynamics, and ecosystem metabolism would allow for a more holistic understanding of ecosystem functions in a changing environment.
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Affiliation(s)
- Nina Welti
- Department of Environmental and Biological Sciences, University of Eastern FinlandKuopio, Finland
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, AdelaideSA, Australia
| | - Maren Striebel
- Institute for Chemistry and Biology of the Marine Environment, University of OldenburgOldenburg, Germany
| | - Amber J. Ulseth
- Stream Biofilm and Ecosystem Research, Ecole Polytechnique Fédérale de LausanneLausanne, Switzerland
| | - Wyatt F. Cross
- Department of Ecology, Montana State University, BozemanMT, United States
| | - Stephen DeVilbiss
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, MilwaukeeWI, United States
| | - Patricia M. Glibert
- University of Maryland Center for Environmental Science, CambridgeMD, United States
| | - Laodong Guo
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, MilwaukeeWI, United States
| | - Andrew G. Hirst
- The Hirst Lab, Organismal Biology, School of Biological and Chemical Sciences, Queen Mary University of LondonLondon, United Kingdom
- Centre for Ocean Life, National Institute for Aquatic Resources, Technical University of DenmarkCopenhagen, Denmark
| | - Jim Hood
- Department of Evolution, Ecology, and Organismal Biology, Aquatic Ecology Laboratory, The Ohio State University, ColumbusOH, United States
| | - John S. Kominoski
- The Kominoski Lab, Department of Biological Sciences, Florida International University, MiamiFL, United States
| | - Keeley L. MacNeill
- Department of Ecology and Evolutionary Biology, Cornell University, IthacaNY, United States
| | - Andrew S. Mehring
- Scripps Institution of Oceanography, University of California, San Diego, La JollaCA, United States
| | - Jill R. Welter
- Department of Biology, St. Catherine University, MinneapolisMN, United States
| | - Helmut Hillebrand
- Institute for Chemistry and Biology of the Marine Environment, University of OldenburgOldenburg, Germany
- Helmholtz-Institute for Functional Marine BiodiversityOldenburg, Germany
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21
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Yasuda T, Waki M, Fukumoto Y, Hanajima D, Kuroda K, Suzuki K. Characterization of the denitrifying bacterial community in a full-scale rockwool biofilter for compost waste-gas treatment. Appl Microbiol Biotechnol 2017; 101:6779-6792. [DOI: 10.1007/s00253-017-8398-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/22/2017] [Accepted: 06/16/2017] [Indexed: 11/29/2022]
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Direct Nitrous Oxide Emission from the Aquacultured Pacific White Shrimp (Litopenaeus vannamei). Appl Environ Microbiol 2016; 82:4028-4034. [PMID: 27129966 DOI: 10.1128/aem.00396-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/21/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The Pacific white shrimp (Litopenaeus vannamei) is widely used in aquaculture, where it is reared at high stocking densities, temperatures, and nutrient concentrations. Here we report that adult L. vannamei shrimp emit the greenhouse gas nitrous oxide (N2O) at an average rate of 4.3 nmol N2O/individual × h, which is 1 to 2 orders of magnitude higher than previously measured N2O emission rates for free-living aquatic invertebrates. Dissection, incubation, and inhibitor experiments with specimens from a shrimp farm in Germany indicated that N2O is mainly produced in the animal's gut by microbial denitrification. Microsensor measurements demonstrated that the gut interior is anoxic and nearly neutral and thus is favorable for denitrification by ingested bacteria. Dinitrogen (N2) and N2O accounted for 64% and 36%, respectively, of the nitrogen gas flux from the gut, suggesting that the gut passage is too fast for complete denitrification to be fully established. Indeed, shifting the rearing water bacterial community, a diet component of shrimp, from oxic to anoxic conditions induced N2O accumulation that outlasted the gut passage time. Shrimp-associated N2O production was estimated to account for 6.5% of total N2O production in the shrimp farm studied here and to contribute to the very high N2O supersaturation measured in the rearing tanks (2,099%). Microbial N2O production directly associated with aquacultured animals should be implemented into life cycle assessments of seafood production. IMPORTANCE The most widely used shrimp species in global aquaculture, Litopenaeus vannamei, is shown to emit the potent greenhouse gas nitrous oxide (N2O) at a particularly high rate. Detailed experiments reveal that N2O is produced in the oxygen-depleted gut of the animal by bacteria that are part of the shrimp diet. Upon ingestion, these bacteria experience a shift from oxic to anoxic conditions and therefore switch their metabolism to the anaerobic denitrification process, which produces N2O as an intermediate and dinitrogen (N2) gas as an end product. The N2O/N2 production ratio is unusually high in the shrimp gut, because denitrification cannot be fully established during the short gut passage time of food-associated bacteria. Nitrous oxide emission directly mediated by L. vannamei contributes significantly to the overall N2O emission from aquaculture facilities.
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Hölker F, Vanni MJ, Kuiper JJ, Meile C, Grossart HP, Stief P, Adrian R, Lorke A, Dellwig O, Brand A, Hupfer M, Mooij WM, Nützmann G, Lewandowski J. Tube-dwelling invertebrates: tiny ecosystem engineers have large effects in lake ecosystems. ECOL MONOGR 2015. [DOI: 10.1890/14-1160.1] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Mehring AS, Kuehn KA, Thompson A, Pringle CM, Rosemond AD, First MR, Lowrance RR, Vellidis G. Leaf litter nutrient uptake in an intermittent blackwater river: influence of tree species and associated biotic and abiotic drivers. Funct Ecol 2015. [DOI: 10.1111/1365-2435.12399] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Kevin A. Kuehn
- Department of Biological Sciences University of Southern Mississippi Hattiesburg MS 39406 USA
| | - Aaron Thompson
- Department of Crop and Soil Sciences University of Georgia Athens GA 30602 USA
| | | | - Amy D. Rosemond
- Odum School of Ecology University of Georgia Athens GA30602 USA
| | - Matthew R. First
- Department of Geology and Geophysics Woods Hole Oceanographic Institution 221 Watson Woods Hole MA 02543 USA
| | - R Richard Lowrance
- United States Department of Agriculture‐Agricultural Research Service Southeast Watershed Research Lab Tifton GA31793 USA
| | - George Vellidis
- Department of Crop and Soil Sciences University of Georgia Athens GA 30602 USA
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Narrowe AB, Albuthi-Lantz M, Smith EP, Bower KJ, Roane TM, Vajda AM, Miller CS. Perturbation and restoration of the fathead minnow gut microbiome after low-level triclosan exposure. MICROBIOME 2015; 3:6. [PMID: 25815185 PMCID: PMC4374533 DOI: 10.1186/s40168-015-0069-6] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Accepted: 01/29/2015] [Indexed: 05/02/2023]
Abstract
BACKGROUND Triclosan is a widely used antimicrobial compound and emerging environmental contaminant. Although the role of the gut microbiome in health and disease is increasingly well established, the interaction between environmental contaminants and host microbiome is largely unexplored, with unknown consequences for host health. This study examined the effects of low, environmentally relevant levels of triclosan exposure on the fish gut microbiome. Developing fathead minnows (Pimephales promelas) were exposed to two low levels of triclosan over a 7-day exposure. Fish gastrointestinal tracts from exposed and control fish were harvested at four time points: immediately preceding and following the 7-day exposure and after 1 and 2 weeks of depuration. RESULTS A total of 103 fish gut bacterial communities were characterized by high-throughput sequencing and analysis of the V3-V4 region of the 16S rRNA gene. By measures of both alpha and beta diversity, gut microbial communities were significantly differentiated by exposure history immediately following triclosan exposure. After 2 weeks of depuration, these differences disappear. Independent of exposure history, communities were also significantly structured by time. This first detailed census of the fathead minnow gut microbiome shows a bacterial community that is similar in composition to those of zebrafish and other freshwater fish. Among the triclosan-resilient members of this host-associated community are taxa associated with denitrification in wastewater treatment, taxa potentially able to degrade triclosan, and taxa from an unstudied host-associated candidate division. CONCLUSIONS The fathead minnow gut microbiome is rapidly and significantly altered by exposure to low, environmentally relevant levels of triclosan, yet largely recovers from this short-term perturbation over an equivalently brief time span. These results suggest that even low-level environmental exposure to a common antimicrobial compound can induce significant short-term changes to the gut microbiome, followed by restoration, demonstrating both the sensitivity and resilience of the gut flora to challenges by environmental toxicants. This short-term disruption in a developing organism may have important long-term consequences for host health. The identification of multiple taxa not often reported in the fish gut suggests that microbial nitrogen metabolism in the fish gut may be more complex than previously appreciated.
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Affiliation(s)
- Adrienne B Narrowe
- />Department of Integrative Biology, University of Colorado Denver, Campus Box 171, PO Box 173364, Denver, CO 80217 USA
| | - Munira Albuthi-Lantz
- />Department of Integrative Biology, University of Colorado Denver, Campus Box 171, PO Box 173364, Denver, CO 80217 USA
| | - Erin P Smith
- />Department of Integrative Biology, University of Colorado Denver, Campus Box 171, PO Box 173364, Denver, CO 80217 USA
- />Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA 99164 USA
- />School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164 USA
| | - Kimberly J Bower
- />Department of Integrative Biology, University of Colorado Denver, Campus Box 171, PO Box 173364, Denver, CO 80217 USA
| | - Timberley M Roane
- />Department of Integrative Biology, University of Colorado Denver, Campus Box 171, PO Box 173364, Denver, CO 80217 USA
| | - Alan M Vajda
- />Department of Integrative Biology, University of Colorado Denver, Campus Box 171, PO Box 173364, Denver, CO 80217 USA
| | - Christopher S Miller
- />Department of Integrative Biology, University of Colorado Denver, Campus Box 171, PO Box 173364, Denver, CO 80217 USA
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Hu Z, Lee JW, Chandran K, Kim S, Brotto AC, Khanal SK. Effect of plant species on nitrogen recovery in aquaponics. BIORESOURCE TECHNOLOGY 2015; 188:92-8. [PMID: 25650140 DOI: 10.1016/j.biortech.2015.01.013] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 01/03/2015] [Accepted: 01/06/2015] [Indexed: 05/03/2023]
Abstract
Nitrogen transformations in aquaponics with different edible plant species, i.e., tomato (Lycopersicon esculentum) and pak choi (Brassica campestris L. subsp. chinensis) were systematically examined and compared. Results showed that nitrogen utilization efficiencies (NUE) of tomato- and pak choi-based aquaponic systems were 41.3% and 34.4%, respectively. The abundance of nitrifying bacteria in tomato-based aquaponics was 4.2-folds higher than that in pak choi-based aquaponics, primarily due to its higher root surface area. In addition, tomato-based aquaponics had better water quality than that of pak choi-based aquaponics. About 1.5-1.9% of nitrogen input were emitted to atmosphere as nitrous oxide (N2O) in tomato- and pak choi-based aquaponic systems, respectively, suggesting that aquaponics is a potential anthropogenic source of N2O emission. Overall, this is the first intensive study that examined the role plant species played in aquaponics, which could provide new strategy in designing and operating an aquaponic system.
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Affiliation(s)
- Zhen Hu
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan 250100, China
| | - Jae Woo Lee
- Department of Environmental Engineering, College of Science and Technology, Korea University, Sejong-ro 2511, Sejong 339-700, South Korea
| | - Kartik Chandran
- Department of Earth and Environmental Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, USA
| | - Sungpyo Kim
- Department of Environmental Engineering, College of Science and Technology, Korea University, Sejong-ro 2511, Sejong 339-700, South Korea
| | - Ariane Coelho Brotto
- Department of Earth and Environmental Engineering, Columbia University, 500 West 120th Street, New York, NY 10027, USA
| | - Samir Kumar Khanal
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
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Bai E, Li W, Li S, Sun J, Peng B, Dai W, Jiang P, Han S. Pulse increase of soil N2O emission in response to N addition in a temperate forest on Mt Changbai, northeast China. PLoS One 2014; 9:e102765. [PMID: 25079363 PMCID: PMC4117475 DOI: 10.1371/journal.pone.0102765] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 06/22/2014] [Indexed: 11/18/2022] Open
Abstract
Nitrogen (N) deposition has increased significantly globally since the industrial revolution. Previous studies on the response of gaseous emissions to N deposition have shown controversial results, pointing to the system-specific effect of N addition. Here we conducted an N addition experiment in a temperate natural forest in northeastern China to test how potential changes in N deposition alter soil N2O emission and its sources from nitrification and denitrification. Soil N2O emission was measured using closed chamber method and a separate incubation experiment using acetylene inhibition method was carried out to determine denitrification fluxes and the contribution of nitrification and denitrification to N2O emissions between Jul. and Oct. 2012. An NH4NO3 addition of 50 kg N/ha/yr significantly increased N2O and N2 emissions, but their "pulse emission" induced by N addition only lasted for two weeks. Mean nitrification-derived N2O to denitrification-derived N2O ratio was 0.56 in control plots, indicating higher contribution of denitrification to N2O emissions in the study area, and this ratio was not influenced by N addition. The N2O to (N2+N2O) ratio was 0.41-0.55 in control plots and was reduced by N addition at one sampling time point. Based on this short term experiment, we propose that N2O and denitrification rate might increase with increasing N deposition at least by the same fold in the future, which would deteriorate global warming problems.
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Affiliation(s)
- Edith Bai
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- * E-mail:
| | - Wei Li
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Shanlong Li
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Jianfei Sun
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Bo Peng
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Weiwei Dai
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Ping Jiang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Shijie Han
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
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Ecological roles and biotechnological applications of marine and intertidal microbial biofilms. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 146:163-205. [PMID: 24817086 DOI: 10.1007/10_2014_271] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
This review is a retrospective of ecological effects of bioactivities produced by biofilms of surface-dwelling marine/intertidal microbes as well as of the industrial and environmental biotechnologies developed exploiting the knowledge of biofilm formation. Some examples of significant interest pertaining to the ecological aspects of biofilm-forming species belonging to the Roseobacter clade include autochthonous bacteria from turbot larvae-rearing units with potential application as a probiotic as well as production of tropodithietic acid and indigoidine. Species of the Pseudoalteromonas genus are important examples of successful surface colonizers through elaboration of the AlpP protein and antimicrobial agents possessing broad-spectrum antagonistic activity against medical and environmental isolates. Further examples of significance comprise antiprotozoan activity of Pseudoalteromonas tunicata elicited by violacein, inhibition of fungal colonization, antifouling activities, inhibition of algal spore germination, and 2-n-pentyl-4-quinolinol production. Nitrous oxide, an important greenhouse gas, emanates from surface-attached microbial activity of marine animals. Marine and intertidal biofilms have been applied in the biotechnological production of violacein, phenylnannolones, and exopolysaccharides from marine and tropical intertidal environments. More examples of importance encompass production of protease, cellulase, and xylanase, melanin, and riboflavin. Antifouling activity of Bacillus sp. and application of anammox bacterial biofilms in bioremediation are described. Marine biofilms have been used as anodes and cathodes in microbial fuel cells. Some of the reaction vessels for biofilm cultivation reviewed are roller bottle, rotating disc bioreactor, polymethylmethacrylate conico-cylindrical flask, fixed bed reactor, artificial microbial mats, packed-bed bioreactors, and the Tanaka photobioreactor.
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Poulsen M, Kofoed MVW, Larsen LH, Schramm A, Stief P. Chironomus plumosus larvae increase fluxes of denitrification products and diversity of nitrate-reducing bacteria in freshwater sediment. Syst Appl Microbiol 2013; 37:51-9. [PMID: 24054696 DOI: 10.1016/j.syapm.2013.07.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 07/21/2013] [Accepted: 07/23/2013] [Indexed: 11/27/2022]
Abstract
Benthic invertebrates affect microbial processes and communities in freshwater sediment by enhancing sediment-water solute fluxes and by grazing on bacteria. Using microcosms, the effects of larvae of the widespread midge Chironomus plumosus on the efflux of denitrification products (N2O and N2+N2O) and the diversity and abundance of nitrate- and nitrous-oxide-reducing bacteria were investigated. Additionally, the diversity of actively nitrate- and nitrous-oxide-reducing bacteria was analyzed in the larval gut. The presence of larvae increased the total effluxes of N2O and N2+N2O up to 8.6- and 4.2-fold, respectively, which was mostly due to stimulation of sedimentary denitrification; incomplete denitrification in the guts accounted for up to 20% of the N2O efflux. Phylotype richness of the nitrate reductase gene narG was significantly higher in sediment with than without larvae. In the gut, 47 narG phylotypes were found expressed, which may contribute to higher phylotype richness in colonized sediment. In contrast, phylotype richness of the nitrous oxide reductase gene nosZ was unaffected by the presence of larvae and very few nosZ phylotypes were expressed in the gut. Gene abundance of neither narG, nor nosZ was different in sediments with and without larvae. Hence, C. plumosus increases activity and diversity, but not overall abundance of nitrate-reducing bacteria, probably by providing additional ecological niches in its burrow and gut.
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Affiliation(s)
- Morten Poulsen
- Department of Bioscience, Microbiology, Aarhus University, Ny Munkegade 114, 8000 Århus C, Denmark
| | - Michael V W Kofoed
- Department of Bioscience, Microbiology, Aarhus University, Ny Munkegade 114, 8000 Århus C, Denmark
| | - Lone H Larsen
- Department of Bioscience, Microbiology, Aarhus University, Ny Munkegade 114, 8000 Århus C, Denmark
| | - Andreas Schramm
- Department of Bioscience, Microbiology, Aarhus University, Ny Munkegade 114, 8000 Århus C, Denmark
| | - Peter Stief
- Department of Bioscience, Microbiology, Aarhus University, Ny Munkegade 114, 8000 Århus C, Denmark; Max-Planck-Institute for Marine Microbiology, Microsensor Group, Celsiusstraße 1, 28359 Bremen, Germany.
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Schreiber F, Wunderlin P, Udert KM, Wells GF. Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions, and novel technologies. Front Microbiol 2012; 3:372. [PMID: 23109930 PMCID: PMC3478589 DOI: 10.3389/fmicb.2012.00372] [Citation(s) in RCA: 149] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 09/28/2012] [Indexed: 12/20/2022] Open
Abstract
Nitrous oxide (N(2)O) is an environmentally important atmospheric trace gas because it is an effective greenhouse gas and it leads to ozone depletion through photo-chemical nitric oxide (NO) production in the stratosphere. Mitigating its steady increase in atmospheric concentration requires an understanding of the mechanisms that lead to its formation in natural and engineered microbial communities. N(2)O is formed biologically from the oxidation of hydroxylamine (NH(2)OH) or the reduction of nitrite (NO(-) (2)) to NO and further to N(2)O. Our review of the biological pathways for N(2)O production shows that apparently all organisms and pathways known to be involved in the catabolic branch of microbial N-cycle have the potential to catalyze the reduction of NO(-) (2) to NO and the further reduction of NO to N(2)O, while N(2)O formation from NH(2)OH is only performed by ammonia oxidizing bacteria (AOB). In addition to biological pathways, we review important chemical reactions that can lead to NO and N(2)O formation due to the reactivity of NO(-) (2), NH(2)OH, and nitroxyl (HNO). Moreover, biological N(2)O formation is highly dynamic in response to N-imbalance imposed on a system. Thus, understanding NO formation and capturing the dynamics of NO and N(2)O build-up are key to understand mechanisms of N(2)O release. Here, we discuss novel technologies that allow experiments on NO and N(2)O formation at high temporal resolution, namely NO and N(2)O microelectrodes and the dynamic analysis of the isotopic signature of N(2)O with quantum cascade laser absorption spectroscopy (QCLAS). In addition, we introduce other techniques that use the isotopic composition of N(2)O to distinguish production pathways and findings that were made with emerging molecular techniques in complex environments. Finally, we discuss how a combination of the presented tools might help to address important open questions on pathways and controls of nitrogen flow through complex microbial communities that eventually lead to N(2)O build-up.
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Affiliation(s)
- Frank Schreiber
- Department of Environmental Microbiology, Eawag - Swiss Federal Institute of Aquatic Science and Technology Dübendorf, Switzerland ; Department of Environmental Systems Sciences, Eidgenössische Technische Hochschule Zurich, Switzerland
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31
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Depkat-Jakob PS, Brown GG, Tsai SM, Horn MA, Drake HL. Emission of nitrous oxide and dinitrogen by diverse earthworm families from Brazil and resolution of associated denitrifying and nitrate-dissimilating taxa. FEMS Microbiol Ecol 2012; 83:375-91. [DOI: 10.1111/j.1574-6941.2012.01476.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 07/31/2012] [Accepted: 08/17/2012] [Indexed: 11/30/2022] Open
Affiliation(s)
| | | | - Siu M. Tsai
- Center for Nuclear Energy in Agriculture; University of São Paulo; São Paulo; Brazil
| | - Marcus A. Horn
- Department of Ecological Microbiology; University of Bayreuth; Bayreuth; Germany
| | - Harold L. Drake
- Department of Ecological Microbiology; University of Bayreuth; Bayreuth; Germany
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Heisterkamp IM, Schramm A, Larsen LH, Svenningsen NB, Lavik G, de Beer D, Stief P. Shell biofilm-associated nitrous oxide production in marine molluscs: processes, precursors and relative importance. Environ Microbiol 2012; 15:1943-55. [DOI: 10.1111/j.1462-2920.2012.02823.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Hu Z, Lee JW, Chandran K, Kim S, Khanal SK. Nitrous oxide (N2O) emission from aquaculture: a review. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:6470-80. [PMID: 22594516 DOI: 10.1021/es300110x] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Nitrous oxide (N(2)O) is an important greenhouse gas (GHG) which has a global warming potential 310 times that of carbon dioxide (CO(2)) over a hundred year lifespan. N(2)O is generated during microbial nitrification and denitrification, which are common in aquaculture systems. To date, few studies have been conducted to quantify N(2)O emission from aquaculture. Additionally, very little is known with respect to the microbial pathways through which N(2)O is formed in aquaculture systems. This review suggests that aquaculture can be an important anthropogenic source of N(2)O emission. The global N(2)O-N emission from aquaculture in 2009 is estimated to be 9.30 × 10(10) g, and will increase to 3.83 × 10(11)g which could account for 5.72% of anthropogenic N(2)O-N emission by 2030 if the aquaculture industry continues to increase at the present annual growth rate (about 7.10%). The possible mechanisms and various factors affecting N(2)O production are summarized, and two possible methods to minimize N(2)O emission, namely aquaponic and biofloc technology aquaculture, are also discussed. The paper concludes with future research directions.
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Affiliation(s)
- Zhen Hu
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
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Shell biofilm nitrification and gut denitrification contribute to emission of nitrous oxide by the invasive freshwater mussel Dreissena polymorpha (zebra mussel). Appl Environ Microbiol 2012; 78:4505-9. [PMID: 22492461 DOI: 10.1128/aem.00401-12] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nitrification in shell biofilms and denitrification in the gut of the animal accounted for N(2)O emission by Dreissena polymorpha (Bivalvia), as shown by gas chromatography and gene expression analysis. The mussel's ammonium excretion was sufficient to sustain N(2)O production and thus potentially uncouples invertebrate N(2)O production from environmental N concentrations.
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Ngugi DK, Brune A. Nitrate reduction, nitrous oxide formation, and anaerobic ammonia oxidation to nitrite in the gut of soil-feeding termites (Cubitermes and Ophiotermes spp.). Environ Microbiol 2011; 14:860-71. [PMID: 22118414 DOI: 10.1111/j.1462-2920.2011.02648.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Soil-feeding termites play important roles in the dynamics of carbon and nitrogen in tropical soils. Through the mineralization of nitrogenous humus components, their intestinal tracts accumulate enormous amounts of ammonia, and nitrate and nitrite concentrations are several orders of magnitude above those in the ingested soil. Here, we studied the metabolism of nitrate in the different gut compartments of two Cubitermes and one Ophiotermes species using (15)N isotope tracer analysis. Living termites emitted N(2) at rates ranging from 3.8 to 6.8 nmol h(-1) (g fresh wt.)(-1). However, in homogenates of individual gut sections, denitrification was restricted to the posterior hindgut, whereas nitrate ammonification occurred in all gut compartments and was the prevailing process in the anterior gut. Potential rates of nitrate ammonification for the entire intestinal tract were tenfold higher than those of denitrification, implying that ammonification is the major sink for ingested nitrate in the intestinal tract of soil-feeding termites. Because nitrate is efficiently reduced already in the anterior gut, reductive processes in the posterior gut compartments must be fuelled by an endogenous source of oxidized nitrogen species. Quite unexpectedly, we observed an anaerobic oxidation of (15)N-labelled ammonia to nitrite, especially in the P4 section, which is presumably driven by ferric iron; nitrification and anammox activities were not detected. Two of the termite species also emitted substantial amounts of N(2) O, ranging from 0.4 to 3.9 nmol h(-1) (g fresh wt.)(-1), providing direct evidence that soil-feeding termites are a hitherto unrecognized source of this greenhouse gas in tropical soils.
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Affiliation(s)
- David Kamanda Ngugi
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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36
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Freese HM, Schink B. Composition and stability of the microbial community inside the digestive tract of the aquatic crustacean Daphnia magna. MICROBIAL ECOLOGY 2011; 62:882-94. [PMID: 21667195 DOI: 10.1007/s00248-011-9886-8] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 05/29/2011] [Indexed: 05/03/2023]
Abstract
Small filter-feeding zooplankton organisms like the cladoceran Daphnia spp. are key members of freshwater food webs. Although several interactions between Daphnia and bacteria have been investigated, the importance of the microbial communities inside Daphnia guts has been studied only poorly so far. In the present study, we characterised the bacterial community composition inside the digestive tract of a laboratory-reared clonal culture of Daphnia magna using 16S rRNA gene libraries and terminal-restriction length polymorphism fingerprint analyses. In addition, the diversity and stability of the intestinal microbial community were investigated over time, with different food sources as well as under starvation stress and death, and were compared to the community in the cultivation water. The diversity of the Daphnia gut microbiota was low. The bacterial community consisted mainly of Betaproteobacteria (e.g. Limnohabitans sp.), few Gammaproteobacteria (e.g. Pseudomonas sp.) and Bacteroidetes that were related to facultatively anaerobic bacteria, but did not contain typical fermentative or obligately anaerobic gut bacteria. Rather, the microbiota was constantly dominated by Limnohabitans sp. which belongs to the Lhab-A1 tribe (previously called R-BT065 cluster) that is abundant in various freshwaters. Other bacterial groups varied distinctly even under constant cultivation conditions. Overall, the intestinal microbial community did not reflect the community in the surrounding cultivation water and clustered separately when analysed via the Additive Main Effects and Multiplicative Interaction model. In addition, the microbiota proved to be stable also when Daphnia were exposed to bacteria associated with a different food alga. After starvation, the community in the digestive tract was reduced to stable members. After death of the host animals, the community composition in the gut changed distinctly, and formerly undetected bacteria were activated. Our results suggest that the Daphnia microbiota consists mainly of an aerobic resident bacterial community which is indigenous to this habitat.
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Affiliation(s)
- Heike M Freese
- Department of Biology, Microbial Ecology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany.
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Grossart HP. Ecological consequences of bacterioplankton lifestyles: changes in concepts are needed. ENVIRONMENTAL MICROBIOLOGY REPORTS 2010; 2:706-14. [PMID: 23766274 DOI: 10.1111/j.1758-2229.2010.00179.x] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
In recent years, microbial ecology has developed from a peripheral discipline into a central field of microbiology. This change in state and perception is mainly driven by a rapid development of methods applied in the manifold fields related to microbial ecology. In biogeochemistry, for example, the use of high-resolution techniques such as FT-ICR-MS (Fourier transform ion cyclotron mass spectroscopy) has uncovered an enormous diversity and complexity of natural organic matter produced or degraded microbially either in dissolved or particulate forms. On the other hand, the introduction of high-throughput sequencing methods, such as 454 pyrosequencing, in combination with advances in bioinformatics allows for studying the bacterial diversity in natural samples circumventing cultivation dependent approaches. These new molecular tools enable in depth studies on single-cell genomes, distinct populations or even metacommunities. In combination with metatranscriptome and proteome studies it is for the first time possible to simultaneously unravel the structure and function of complex communities in situ. These technique-derived findings have, on the one hand, dramatically increased our knowledge on the vast diversity and complexity of bacterial habitats and, on the other hand, on phylogentic diversity and physiological responses of natural bacterial communities to their environment. However, until now microbial ecology is lacking an ecologically relevant species definition and useful tools for the identification of ecologically coherent taxa. Studies on intra- and interspecies interactions even with higher organisms demonstrate that bacteria can rapidly adapt to temporal and spatial changes in their environment. Aquatic bacteria have optimized and dramatically expanded their living space by efficient exploitation of organic matter point sources such as particles/aggregates and higher organisms. Although it is evident that particles/aggregates and organisms such as phytoplankton are 'hotspots' for microbial growth and transformation processes, it has not affected sampling strategies of aquatic microbial ecologists, who often focus solely on the free-living bacterial fractions and a priori exclude higher organisms by non-representative water sampling. Therefore, aquatic microbial ecologists have largely overlooked the fact that many aquatic bacteria may possess a complex lifestyle and frequently alternate between a free-living and a surface-associated stage. Here, I propose that modern concepts in aquatic microbial ecology should take into account the high chemical diversity and spatio-temporal variability of the bacterial environment. Interactions of aquatic bacteria with surfaces including living organisms are the key to understanding their physiological adaptations and population dynamics, as well as their contribution to biogeochemical cycles. New sampling strategies and theoretical concepts are needed in aquatic microbial ecology to access the whole spectrum of bacterial lifestyles and their ecological and evolutionary consequences.
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Affiliation(s)
- Hans-Peter Grossart
- Leibniz Institute of Freshwater Ecology and Inland Fishries, Alte Fischerhuette 2, D-16775 Stechlin, Germany
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Depkat-Jakob PS, Hilgarth M, Horn MA, Drake HL. Effect of earthworm feeding guilds on ingested dissimilatory nitrate reducers and denitrifiers in the alimentary canal of the earthworm. Appl Environ Microbiol 2010; 76:6205-14. [PMID: 20656855 PMCID: PMC2937516 DOI: 10.1128/aem.01373-10] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Accepted: 07/19/2010] [Indexed: 11/20/2022] Open
Abstract
The earthworm gut is an anoxic nitrous oxide (N(2)O)-emitting microzone in aerated soils. In situ conditions of the gut might stimulate ingested nitrate-reducing soil bacteria linked to this emission. The objective of this study was to determine if dissimilatory nitrate reducers and denitrifiers in the alimentary canal were affected by feeding guilds (epigeic [Lumbricus rubellus], anecic [Lumbricus terrestris], and endogeic [Aporrectodea caliginosa]). Genes and gene transcripts of narG (encodes a subunit of nitrate reductase and targets both dissimilatory nitrate reducers and denitrifiers) and nosZ (encodes a subunit of N(2)O reductase and targets denitrifiers) were detected in guts and soils. Gut-derived sequences were similar to those of cultured and uncultured soil bacteria and to soil-derived sequences obtained in this study. Gut-derived narG sequences and narG terminal restriction fragments (TRFs) were affiliated mainly with Gram-positive organisms (Actinobacteria). The majority of gut- and uppermost-soil-derived narG transcripts were affiliated with Mycobacterium (Actinobacteria). In contrast, narG sequences indicative of Gram-negative organisms (Proteobacteria) were dominant in mineral soil. Most nosZ sequences and nosZ TRFs were affiliated with Bradyrhizobium (Alphaproteobacteria) and uncultured soil bacteria. TRF profiles indicated that nosZ transcripts were more affected by earthworm feeding guilds than were nosZ genes, whereas narG transcripts were less affected by earthworm feeding guilds than were narG genes. narG and nosZ transcripts were different and less diverse in the earthworm gut than in mineral soil. The collective results indicate that dissimilatory nitrate reducers and denitrifiers in the earthworm gut are soil derived and that ingested narG- and nosZ-containing taxa were not uniformly stimulated in the guts of worms from different feeding guilds.
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Affiliation(s)
- Peter S. Depkat-Jakob
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Maik Hilgarth
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Marcus A. Horn
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Harold L. Drake
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
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Reyna L, Wunderlin DA, Genti-Raimondi S. Identification and quantification of a novel nitrate-reducing community in sediments of Suquía River basin along a nitrate gradient. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2010; 158:1608-1614. [PMID: 20045234 DOI: 10.1016/j.envpol.2009.12.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Revised: 12/01/2009] [Accepted: 12/06/2009] [Indexed: 05/28/2023]
Abstract
We evaluated the molecular diversity of narG gene from Suquía River sediments to assess the impact of the nitrate concentration and water quality on the composition and structure of the nitrate-reducing bacterial community. To this aim, a library of one of the six monitoring stations corresponding to the highest nitrate concentration was constructed and 118 narG clones were screened. Nucleotide sequences were associated to narG gene from alpha-, beta-, delta-, gammaproteobacteria and Thermus thermophilus. Remarkably, 18% of clones contained narG genes with less than 69% similarity to narG sequences available in databases. Thus, indicating the presence of nitrate-reducing bacteria with novel narG genes, which were quantified by real-time PCR. Results show a variable number of narG copies, ranging from less than 1.0 x 10(2) to 5.0 x 10(4) copies per ng of DNA, which were associated with a decreased water quality index monitored along the basin at different times.
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Affiliation(s)
- Luciana Reyna
- Universidad Nacional de Córdoba-CONICET, Facultad de Ciencias Químicas, Departamento de Bioquímica Clínica-CIBICI, Haya de la Torre y Medina Allende, Ciudad Universitaria, 5000 Córdoba, Argentina
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Santoro AE, Casciotti KL, Francis CA. Activity, abundance and diversity of nitrifying archaea and bacteria in the central California Current. Environ Microbiol 2010; 12:1989-2006. [PMID: 20345944 DOI: 10.1111/j.1462-2920.2010.02205.x] [Citation(s) in RCA: 187] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A combination of stable isotope and molecular biological approaches was used to determine the activity, abundance and diversity of nitrifying organisms in the central California Current. Using (15)NH(4)(+) incubations, nitrification was detectable in the upper water column down to 500 m; maximal rates were observed just below the euphotic zone. Crenarchaeal and betaproteobacterial ammonia monooxygenase subunit A genes (amoA), and 16S ribosomal RNA (rRNA) genes of Marine Group I Crenarchaeota and a putative nitrite-oxidizing genus, Nitrospina, were quantified using quantitative PCR. Crenarchaeal amoA abundance ranged from three to six genes ml(-1) in oligotrophic surface waters to > 8.7 x 10(4) genes ml(-1) just below the core of the California Current at 200 m depth. Bacterial amoA abundance was lower than archaeal amoA and ranged from below detection levels to 400 genes ml(-1). Nitrification rates were not directly correlated to bacterial or archaeal amoA abundance. Archaeal amoA and Marine Group I crenarchaeal 16S rRNA gene abundances were correlated with Nitrospina 16S rRNA gene abundance at all stations, indicating that similar factors may control the distribution of these two groups. Putatively shallow water-associated archaeal amoA types ('Cluster A') decreased in relative abundance with depth, while a deep water-associated amoA type ('Cluster B') increased with depth. Although some Cluster B amoA sequences were found in surface waters, expressed amoA gene sequences were predominantly from Cluster A. Cluster B amoA transcripts were detected between 100 and 500 m depths, suggesting an active role in ammonia oxidation in the mesopelagic. Expression of marine Nitrosospira-like bacterial amoA genes was detected throughout the euphotic zone down to 200 m. Natural abundance stable isotope ratios (delta(15)N and delta(18)O) in nitrate (NO(3)(-)) and nitrous oxide (N(2)O) were used to evaluate the importance of nitrification over longer time scales. Using an isotope mass balance model, we calculate that nitrification could produce between 0.45 and 2.93 micromol m(-2) day(-1) N(2)O in the central California Current, or approximately 1.5-4 times the local N(2)O flux from deep water.
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Affiliation(s)
- Alyson E Santoro
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA.
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Abstract
Background Microbial denitrification is not considered important in human-associated microbial communities. Accordingly, metabolic investigations of the microbial biofilm communities of human dental plaque have focused on aerobic respiration and acid fermentation of carbohydrates, even though it is known that the oral habitat is constantly exposed to nitrate (NO3-) concentrations in the millimolar range and that dental plaque houses bacteria that can reduce this NO3- to nitrite (NO2-). Results We show that dental plaque mediates denitrification of NO3- to nitric oxide (NO), nitrous oxide (N2O), and dinitrogen (N2) using microsensor measurements, 15N isotopic labelling and molecular detection of denitrification genes. In vivo N2O accumulation rates in the mouth depended on the presence of dental plaque and on salivary NO3- concentrations. NO and N2O production by denitrification occurred under aerobic conditions and was regulated by plaque pH. Conclusions Increases of NO concentrations were in the range of effective concentrations for NO signalling to human host cells and, thus, may locally affect blood flow, signalling between nerves and inflammatory processes in the gum. This is specifically significant for the understanding of periodontal diseases, where NO has been shown to play a key role, but where gingival cells are believed to be the only source of NO. More generally, this study establishes denitrification by human-associated microbial communities as a significant metabolic pathway which, due to concurrent NO formation, provides a basis for symbiotic interactions.
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Hoffmann F, Radax R, Woebken D, Holtappels M, Lavik G, Rapp HT, Schläppy ML, Schleper C, Kuypers MMM. Complex nitrogen cycling in the sponge Geodia barretti. Environ Microbiol 2009; 11:2228-43. [PMID: 19453700 DOI: 10.1111/j.1462-2920.2009.01944.x] [Citation(s) in RCA: 160] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Marine sponges constitute major parts of coral reefs and deep-water communities. They often harbour high amounts of phylogenetically and physiologically diverse microbes, which are so far poorly characterized. Many of these sponges regulate their internal oxygen concentration by modulating their ventilation behaviour providing a suitable habitat for both aerobic and anaerobic microbes. In the present study, both aerobic (nitrification) and anaerobic (denitrification, anammox) microbial processes of the nitrogen cycle were quantified in the sponge Geodia barretti and possible involved microbes were identified by molecular techniques. Nitrification rates of 566 nmol N cm(-3) sponge day(-1) were obtained when monitoring the production of nitrite and nitrate. In support of this finding, ammonia-oxidizing Archaea (crenarchaeotes) were found by amplification of the amoA gene, and nitrite-oxidizing bacteria of the genus Nitrospira were detected based on rRNA gene analyses. Incubation experiments with stable isotopes ((15)NO(3)(-) and (15)NH(4)(+)) revealed denitrification and anaerobic ammonium oxidation (anammox) rates of 92 nmol N cm(-3) sponge day(-1) and 3 nmol N cm(-3) sponge day(-1) respectively. Accordingly, sequences closely related to 'Candidatus Scalindua sorokinii' and 'Candidatus Scalindua brodae' were detected in 16S rRNA gene libraries. The amplification of the nirS gene revealed the presence of denitrifiers, likely belonging to the Betaproteobacteria. This is the first proof of anammox and denitrification in the same animal host, and the first proof of anammox and denitrification in sponges. The close and complex interactions of aerobic, anaerobic, autotrophic and heterotrophic microbial processes are fuelled by metabolic waste products of the sponge host, and enable efficient utilization and recirculation of nutrients within the sponge-microbe system. Since denitrification and anammox remove inorganic nitrogen from the environment, sponges may function as so far unrecognized nitrogen sinks in the ocean. In certain marine environments with high sponge cover, sponge-mediated nitrogen mineralization processes might even be more important than sediment processes.
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Affiliation(s)
- Friederike Hoffmann
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1,Bremen, Germany.
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