1
|
Moncada C, Arnosti C, Brüwer JD, de Beer D, Amann R, Knittel K. Niche separation in bacterial communities and activities in porewater, loosely attached, and firmly attached fractions in permeable surface sediments. THE ISME JOURNAL 2024; 18:wrae159. [PMID: 39115410 PMCID: PMC11368169 DOI: 10.1093/ismejo/wrae159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/26/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024]
Abstract
Heterotrophic microbes are central to organic matter degradation and transformation in marine sediments. Currently, most investigations of benthic microbiomes do not differentiate between processes in the porewater and on the grains and, hence, only show a generalized picture of the community. This limits our understanding of the structure and functions of sediment microbiomes. To address this problem, we fractionated sandy surface sediment microbial communities from a coastal site in Isfjorden, Svalbard, into cells associated with the porewater, loosely attached to grains, and firmly attached to grains; we found dissimilar bacterial communities and metabolic activities in these fractions. Most (84%-89%) of the cells were firmly attached, and this fraction comprised more anaerobes, such as sulfate reducers, than the other fractions. The porewater and loosely attached fractions (3% and 8%-13% of cells, respectively) had more aerobic heterotrophs. These two fractions generally showed a higher frequency of dividing cells, polysaccharide (laminarin) hydrolysis rates, and per-cell O2 consumption than the firmly attached cells. Thus, the different fractions occupy distinct niches within surface sediments: the firmly attached fraction is potentially made of cells colonizing areas on the grain that are protected from abrasion, but might be more diffusion-limited for organic matter and electron acceptors. In contrast, the porewater and loosely attached fractions are less resource-limited and have faster growth. Their cell numbers are kept low possibly through abrasion and exposure to grazers. Differences in community composition and activity of these cell fractions point to their distinct roles and contributions to carbon cycling within surface sediments.
Collapse
Affiliation(s)
- Chyrene Moncada
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Carol Arnosti
- Department of Earth, Marine, and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Jan D Brüwer
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Dirk de Beer
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Katrin Knittel
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| |
Collapse
|
2
|
Gusmão ACB, Peres FV, Paula FS, Pellizari VH, Kolm HE, Signori CN. Microbial communities in the deep-sea sediments of the South São Paulo Plateau, Southwestern Atlantic Ocean. Int Microbiol 2023; 26:1041-1051. [PMID: 37093322 DOI: 10.1007/s10123-023-00358-w] [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] [Received: 02/14/2023] [Revised: 03/30/2023] [Accepted: 04/06/2023] [Indexed: 04/25/2023]
Abstract
Microbial communities play a key role in the ocean, acting as primary producers, nutrient recyclers, and energy providers. The São Paulo Plateau is a region located on the southeastern coast of Brazil within economic importance, due to its oil and gas reservoirs. With this focus, this study examined the diversity and composition of microbial communities in marine sediments located at three oceanographic stations in the southern region of São Paulo Plateau using the HOV Shinkai 6500 in 2013. The 16S rRNA gene was sequenced using the universal primers (515F and 926R) by the Illumina Miseq platform. The taxonomic compositions of samples recovered from SP3 station were markedly distinct from those obtained from SP1 and SP2. Although all three stations exhibited a high abundance of Gammaproteobacteria (> 15%), this taxon dominated more than 90% of composition of the A and C sediment layers at SP3. The highest abundance of the archaeal class Nitrososphaeria was presented at SP1, mainly at layer C (~ 21%), being absent at SP3 station. The prediction of chemoheterotrophy and fermentation as important microbial functions was supported by the data. Additionally, other metabolic pathways related to the cycles of nitrogen, carbon and sulfur were also predicted. The core microbiome analysis comprised only two ASVs. Our study contributes to a better understanding of microbial communities in an economically important little-explored region. This is the third microbiological survey in plateau sediments and the first focused on the southern region.
Collapse
Affiliation(s)
- Ana Carolina Bercini Gusmão
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça Do Oceanográfico, 191. CEP: 05508-120, São Paulo, Brazil.
| | - Francielli Vilela Peres
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça Do Oceanográfico, 191. CEP: 05508-120, São Paulo, Brazil
| | - Fabiana S Paula
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça Do Oceanográfico, 191. CEP: 05508-120, São Paulo, Brazil
| | - Vivian Helena Pellizari
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça Do Oceanográfico, 191. CEP: 05508-120, São Paulo, Brazil
| | - Hedda Elisabeth Kolm
- Department of Oceanography, Center for Marine Studies, Federal University of Paraná, Pontal do Paraná, Brazil
| | - Camila Negrão Signori
- Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, Praça Do Oceanográfico, 191. CEP: 05508-120, São Paulo, Brazil
| |
Collapse
|
3
|
Jia R, Li P, Chen C, Liu L, Li ZH. Shellfish-algal systems as important components of fisheries carbon sinks: Their contribution and response to climate change. ENVIRONMENTAL RESEARCH 2023; 224:115511. [PMID: 36801235 DOI: 10.1016/j.envres.2023.115511] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/30/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
In the context of global climate change, ocean acidification and warming are becoming increasingly serious. Adding carbon sinks in the ocean is an important part of efforts to mitigate climate change. Many researchers have proposed the concept of a fisheries carbon sink. Shellfish-algal systems are among the most important components of fisheries carbon sinks, but there has been limited research on the impact of climate change on shellfish-algal carbon sequestration systems. This review assesses the impact of global climate change on shellfish-algal carbon sequestration systems and provides a rough estimate of the global shellfish-algal carbon sink capacity. This review evaluates the impact of global climate change on shellfish-algal carbon sequestration systems. We review relevant studies that have examined the effects of climate change on such systems from multiple levels, perspectives, and species. There is an urgent need for more realistic and comprehensive studies given expectations about the future climate. Such studies should provide a better understanding of the mechanisms by which the carbon cycle function of marine biological carbon pumps may be affected in realistic future environmental conditions and the patterns of interaction between climate change and ocean carbon sinks.
Collapse
Affiliation(s)
- Ruolan Jia
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Ping Li
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Chengzhuang Chen
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Ling Liu
- Marine College, Shandong University, Weihai, Shandong, 264209, China
| | - Zhi-Hua Li
- Marine College, Shandong University, Weihai, Shandong, 264209, China.
| |
Collapse
|
4
|
Zhang W, Zhou P, Pan S, Li Y, Lin L, Niu L, Wang L, Zhang H. The role of microbial communities on primary producers in aquatic ecosystems: Implications in turbidity stress resistance. ENVIRONMENTAL RESEARCH 2022; 215:114353. [PMID: 36116492 DOI: 10.1016/j.envres.2022.114353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 06/15/2023]
Abstract
Expanding the stress tolerance and adaptation potential of primary producers is of importance for the restoration and management of aquatic ecosystems. Microorganisms have been reported to mediate improved resistance toward different abiotic stresses of primary producers in terrestrial and marine ecosystems. However, it is not clear about the role of microbial communities in the turbidity resistance of primary producers, when aquatic ecosystems are under turbidity pressure. In this study, key microbes and the action path which enhance turbidity tolerance of primary producers were recognized by mesocosm and various multivariate statistical methods. Remarkable decrease of the biomass of primary producers was found with the increase of turbidity. Significant differences in microbial community under different turbidity pressure were recognized and key microbes which may expand the turbidity tolerance of primary producers were further identified. Rhodobacter and Rhodoferax were selected as key microbes by the investigation of keystone species in the microbial ecological network and significant discriminant taxa under different turbidity stress. The action path for microbial communities to help primary producers cope with turbidity pressure was found through structural equation model, and in which the increase of key microbes may expand the turbidity tolerance of primary producers through enhancing the microbial loop. The results may provide a new insight for aquatic ecosystems to resist turbidity stress, and provide a theoretical basis for the management and restoration of aquatic ecosystems.
Collapse
Affiliation(s)
- Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Pengcheng Zhou
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Shenyang Pan
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China.
| | - Li Lin
- Key Lab of Basin Water Resource and Eco-Environmental Science in Hubei Province, Basin Water Environmental Research Department, Changjiang River Scientific Research Institute, Huangpu Road #23, Wuhan, 430010, PR China.
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| |
Collapse
|
5
|
Patchy Blooms and Multifarious Ecotypes of Labyrinthulomycetes Protists and Their Implication in Vertical Carbon Export in the Pelagic Eastern Indian Ocean. Microbiol Spectr 2022; 10:e0014422. [PMID: 35502912 PMCID: PMC9241719 DOI: 10.1128/spectrum.00144-22] [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] [Indexed: 11/20/2022] Open
Abstract
Labyrinthulomycetes protists are an important heterotrophic component of microeukaryotes in the world’s oceans, but their distribution patterns and ecological roles are poorly understood in pelagic waters. This study employed flow cytometry and high-throughput sequencing to characterize the abundance, diversity, and community structure of Labyrinthulomycetes in the pelagic Eastern Indian Ocean. The total Labyrinthulomycetes abundance varied much more among stations than did the abundance of prokaryotic plankton, reaching over 1,000 cells mL−1 at a few “bloom” stations. The total Labyrinthulomycetes abundance did not decline with depth throughout the whole water column (5 to 2,000 m) like the abundance of prokaryotic plankton did, and the Labyrinthulomycetes average projected biomass over all samples was higher than that of the prokaryotic plankton. However, Labyrinthulomycetes diversity showed obvious vertical variations, with richness, Shannon diversity, and evenness greatest in the upper epipelagic, lower epipelagic, and deep waters, respectively. Many abundant phylotypes were detected across multiple water layers, which aligned with the constant vertical Labyrinthulomycetes biomass, suggesting potential sinking and contribution to the biological pump. Hierarchical clustering revealed distinct ecotypes partitioning by vertical distribution patterns, suggesting their differential roles in the carbon cycle and storage processes. Particularly, most phylotypes showed patchy distributions (occurring in only few samples) as previously found in the coastal waters, but they were less associated with the Labyrinthulomycetes blooms than the prevalent phylotypes. Overall, this study revealed distinct patterns of Labyrinthulomycetes ecotypes and shed light on their importance in the pelagic ocean carbon cycling and sequestration relative to that of the prokaryotic plankton. IMPORTANCE While prokaryotic heterotrophic plankton are well accepted as major players in oceanic carbon cycling, the ecological distributions and functions of their microeukaryotic counterparts in the pelagic ocean remain largely unknown. This study focused on an important group of heterotrophic (mainly osmotrophic) protistan microbes, the Labyrinthulomycetes, whose biomass can surpass that of the prokaryotic plankton in many marine ecosystems, including the bathypelagic ocean. We found patchy horizontal but persistent vertical abundance profiles of the Labyrinthulomycetes protists in the pelagic waters of the Eastern Indian Ocean, which were distinct from the spatial patterns of the prokaryotic plankton. Moreover, multiple Labyrinthulomycetes ecotypes with distinct vertical patterns were detected and, based on the physiologic, metabolic, and genomic understanding of their cultivated relatives, were inferred to play multifaceted key roles in the carbon cycle and sequestration, particularly as contributors to the vertical carbon export from the surface to the dark ocean, i.e., the biological pump.
Collapse
|
6
|
Cherabier P, Ferrière R. Eco-evolutionary responses of the microbial loop to surface ocean warming and consequences for primary production. THE ISME JOURNAL 2022; 16:1130-1139. [PMID: 34864820 PMCID: PMC8940968 DOI: 10.1038/s41396-021-01166-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 11/19/2021] [Accepted: 11/26/2021] [Indexed: 11/09/2022]
Abstract
Predicting the response of ocean primary production to climate warming is a major challenge. One key control of primary production is the microbial loop driven by heterotrophic bacteria, yet how warming alters the microbial loop and its function is poorly understood. Here we develop an eco-evolutionary model to predict the physiological response and adaptation through selection of bacterial populations in the microbial loop and how this will impact ecosystem function such as primary production. We find that the ecophysiological response of primary production to warming is driven by a decrease in regenerated production which depends on nutrient availability. In nutrient-poor environments, the loss of regenerated production to warming is due to decreasing microbial loop activity. However, this ecophysiological response can be opposed or even reversed by bacterial adaptation through selection, especially in cold environments: heterotrophic bacteria with lower bacterial growth efficiency are selected, which strengthens the "link" behavior of the microbial loop, increasing both new and regenerated production. In cold and rich environments such as the Arctic Ocean, the effect of bacterial adaptation on primary production exceeds the ecophysiological response. Accounting for bacterial adaptation through selection is thus critically needed to improve models and projections of the ocean primary production in a warming world.
Collapse
Affiliation(s)
- Philippe Cherabier
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Université Paris Sciences et Lettres, CNRS, INSERM, Paris, 75005, France.
| | - Régis Ferrière
- grid.462036.5Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Université Paris Sciences et Lettres, CNRS, INSERM, Paris, 75005 France ,grid.134563.60000 0001 2168 186XDepartment of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ 85721 USA ,grid.134563.60000 0001 2168 186XInternational Research Laboratory for Interdisciplinary Global Environmental Studies (iGLOBES), CNRS, ENS-PSL University, University of Arizona, Tucson, AZ 85721 USA
| |
Collapse
|
7
|
Ge Z, Li QP, Yang W, Liu X, Wu Z. Transparent exopolymer particle dynamics along a shelf-to-sea gradient and impacts on the regional carbon cycle. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 808:152117. [PMID: 34863747 DOI: 10.1016/j.scitotenv.2021.152117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/28/2021] [Accepted: 11/27/2021] [Indexed: 06/13/2023]
Abstract
Transparent exopolymer particles (TEPs) have drawn extensive attention in recent decades due to their crucial role in the biogeochemical and ecological processes of the ocean. However, TEP distribution and fluxes are relatively less addressed in the shelf-seas, where its variability can be affected by not only biology but also complex physical dynamics. Here, we present a comprehensive study of TEP from the coast to the basin (12 sampling sites) of the northern South China Sea (NSCS). We found a large TEP variability from 0.6 to 78.6 μg Xeq. L-1 with higher levels in the coastal waters than the offshore epipelagic waters and the deep waters. In addition, the spatial distribution of TEP was significantly correlated to the cross-shelf change of temperature, salinity, and chlorophyll-a, revealing the complex physical-biogeochemical controls on TEP variability. We found the TEP dynamics nearshore largely influenced by the sedimentation and transportation of TEP-rich aggregates from the river plume. The contribution of TEP to particulate organic carbon (POC) increased gradually when approaching the shore from the sea, suggesting an elevated role of TEP in the coastal carbon cycle. Finally, a good correlation of particle-attached bacteria (PAB) with TEP but not POC revealed a preferential utilization of TEP by PAB. Thus, TEP may play an essential role in the recycling of carbon and nitrogen in the shelf-sea. These findings are crucial for understanding of the TEP dynamics under a changing environment and the associated impacts on the oceanic carbon cycle.
Collapse
Affiliation(s)
- Zaiming Ge
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qian P Li
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.
| | - Weifeng Yang
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Xin Liu
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Zhengchao Wu
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| |
Collapse
|
8
|
Montero P, Gutiérrez MH, Daneri G, Jacob B. The Effect of Salmon Food-Derived DOM and Glacial Melting on Activity and Diversity of Free-Living Bacterioplankton in Chilean Patagonian Fjords. Front Microbiol 2022; 12:772900. [PMID: 35087485 PMCID: PMC8787161 DOI: 10.3389/fmicb.2021.772900] [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: 09/08/2021] [Accepted: 12/07/2021] [Indexed: 11/17/2022] Open
Abstract
Fjord ecosystems cycle and export significant amounts of carbon and appear to be extremely sensitive to climate change and anthropogenic perturbations. To identify patterns of microbial responses to ongoing natural and human-derived changes in the fjords of Chilean Patagonia, we examined the effect of organic enrichment associated with salmon aquaculture and freshening produced by glacial melting on bacterial production (BP), extracellular enzymatic activity (EEA), and community diversity of free-living bacterioplankton. We assayed the effects of salmon food-derived dissolved organic matter (SF-DOM) and meltwaters through microcosm experiments containing waters from Puyuhuapi Fjord and the proglacial fjords of the Southern Patagonia Icefield, respectively. Rates of BP and EEA were 2 times higher in the presence of SF-DOM than in controls, whereas the addition of autochthonous organic matter derived from diatoms (D-DOM) resulted in rates of BP and EEA similar to those measured in the controls. The addition of SF-DOM also reduced species richness and abundance of a significant fraction of the representative taxa of bacterioplankton of Puyuhuapi Fjord. In the proglacial fjords, bacterioplankton diversity was reduced in areas more heavily influenced by meltwaters and was accompanied by moderate positive changes in BP and EEA. Our findings strongly suggest that SF-DOM is highly reactive, promoting enhanced rates of microbial activity while could be influencing the diversity of bacterioplankton communities in Patagonian fjords with a strong salmon farming activity. These findings challenge the traditional view of phytoplankton production as the primary source of labile DOM that fuels heterotrophic activity in coastal ecosystems impacted by anthropogenic organic enrichment. Given the intensive local production of salmon, we analyze the significance of this emerging source of rich "allochthonous" organic substrates for autotrophic/heterotrophic balance, carbon exportation, and hypoxia in Patagonian fjords. The effect of human DOM enrichment can be enhanced in proglacial fjords, where progressive glacial melting exerts additional selective pressure on bacterioplankton diversity.
Collapse
Affiliation(s)
- Paulina Montero
- Centro de Investigación en Ecosistemas de la Patagonia (CIEP), Coyhaique, Chile
- Center for Oceanographic Research COPAS Sur-Austral and COPAS COASTAL, Universidad de Concepción, Concepción, Chile
| | - Marcelo H. Gutiérrez
- Center for Oceanographic Research COPAS Sur-Austral and COPAS COASTAL, Universidad de Concepción, Concepción, Chile
- Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile
| | - Giovanni Daneri
- Centro de Investigación en Ecosistemas de la Patagonia (CIEP), Coyhaique, Chile
- Center for Oceanographic Research COPAS Sur-Austral and COPAS COASTAL, Universidad de Concepción, Concepción, Chile
| | - Bárbara Jacob
- Centro de Investigación en Ecosistemas de la Patagonia (CIEP), Coyhaique, Chile
| |
Collapse
|
9
|
Jo T, Minamoto T. Complex interactions between environmental DNA (eDNA) state and water chemistries on eDNA persistence suggested by meta-analyses. Mol Ecol Resour 2021; 21:1490-1503. [PMID: 33580561 DOI: 10.1111/1755-0998.13354] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 11/28/2022]
Abstract
Understanding the processes of environmental DNA (eDNA) persistence and degradation is essential to determine the spatiotemporal scale of eDNA signals and accurately estimate species distribution. The effects of environmental factors on eDNA persistence have previously been examined; however, the influence of the physiochemical and molecular states of eDNA on its persistence is not completely understood. Here, we performed meta-analyses including 26 previously published papers on the estimation of first-order eDNA decay rate constants, and assessed the effects of filter pore size, DNA fragment size, target gene, and environmental conditions on eDNA decay rates. Almost all supported models included the interactions between the filter pore size and water temperature, between the target gene and water temperature, and between the target gene and water source, implying the influence of complex interactions between the eDNA state and environmental conditions on eDNA persistence. These findings were generally consistent with the results of a reanalysis of a previous tank experiment which measured the time-series changes in marine fish eDNA concentrations in multiple size fractions after fish removal. Our results suggest that the mechanism of eDNA persistence and degradation cannot be fully understood without knowing not only environmental factors but also cellular and molecular states of eDNA in water. Further verification of the relationship between eDNA state and persistence is required by obtaining more information on eDNA persistence in various experimental and environmental conditions, which will enhance our knowledge on eDNA persistence and support our findings.
Collapse
Affiliation(s)
- Toshiaki Jo
- Graduate School of Human Development and Environment, Kobe University Kobe City, Hyogo, Japan.,Research Fellow of Japan Society for the Promotion of Science, Tokyo, Japan
| | - Toshifumi Minamoto
- Graduate School of Human Development and Environment, Kobe University Kobe City, Hyogo, Japan
| |
Collapse
|
10
|
Undaria pinnatifida exudates trigger shifts in seawater chemistry and microbial communities from Atlantic Patagonian coasts. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02471-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
11
|
Xue CX, Liu J, Lea-Smith DJ, Rowley G, Lin H, Zheng Y, Zhu XY, Liang J, Ahmad W, Todd JD, Zhang XH. Insights into the Vertical Stratification of Microbial Ecological Roles across the Deepest Seawater Column on Earth. Microorganisms 2020; 8:microorganisms8091309. [PMID: 32867361 PMCID: PMC7565560 DOI: 10.3390/microorganisms8091309] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 08/19/2020] [Accepted: 08/26/2020] [Indexed: 12/18/2022] Open
Abstract
The Earth's oceans are a huge body of water with physicochemical properties and microbial community profiles that change with depth, which in turn influences their biogeochemical cycling potential. The differences between microbial communities and their functional potential in surface to hadopelagic water samples are only beginning to be explored. Here, we used metagenomics to investigate the microbial communities and their potential to drive biogeochemical cycling in seven different water layers down the vertical profile of the Challenger Deep (0-10,500 m) in the Mariana Trench, the deepest natural point in the Earth's oceans. We recovered 726 metagenome-assembled genomes (MAGs) affiliated to 27 phyla. Overall, biodiversity increased in line with increased depth. In addition, the genome size of MAGs at ≥4000 m layers was slightly larger compared to those at 0-2000 m. As expected, surface waters were the main source of primary production, predominantly from Cyanobacteria. Intriguingly, microbes conducting an unusual form of nitrogen metabolism were identified in the deepest waters (>10,000 m), as demonstrated by an enrichment of genes encoding proteins involved in dissimilatory nitrate to ammonia conversion (DNRA), nitrogen fixation and urea transport. These likely facilitate the survival of ammonia-oxidizing archaea α lineage, which are typically present in environments with a high ammonia concentration. In addition, the microbial potential for oxidative phosphorylation and the glyoxylate shunt was enhanced in >10,000 m waters. This study provides novel insights into how microbial communities and their genetic potential for biogeochemical cycling differs through the Challenger deep water column, and into the unique adaptive lifestyle of microbes in the Earth's deepest seawater.
Collapse
Affiliation(s)
- Chun-Xu Xue
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (C.-X.X.); (J.L.); (Y.Z.); (X.-Y.Z.); (J.L.); (W.A.)
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Jiwen Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (C.-X.X.); (J.L.); (Y.Z.); (X.-Y.Z.); (J.L.); (W.A.)
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - David J. Lea-Smith
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (D.J.L.-S.); (G.R.); (J.D.T.)
| | - Gary Rowley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (D.J.L.-S.); (G.R.); (J.D.T.)
| | - Heyu Lin
- School of Earth Sciences, University of Melbourne, Parkville, VIC 3010, Australia;
| | - Yanfen Zheng
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (C.-X.X.); (J.L.); (Y.Z.); (X.-Y.Z.); (J.L.); (W.A.)
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Xiao-Yu Zhu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (C.-X.X.); (J.L.); (Y.Z.); (X.-Y.Z.); (J.L.); (W.A.)
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Jinchang Liang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (C.-X.X.); (J.L.); (Y.Z.); (X.-Y.Z.); (J.L.); (W.A.)
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Waqar Ahmad
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (C.-X.X.); (J.L.); (Y.Z.); (X.-Y.Z.); (J.L.); (W.A.)
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Jonathan D. Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (D.J.L.-S.); (G.R.); (J.D.T.)
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (C.-X.X.); (J.L.); (Y.Z.); (X.-Y.Z.); (J.L.); (W.A.)
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266100, China
- Correspondence:
| |
Collapse
|
12
|
Regulation of Microbial Activity Rates by Organic Matter in the Ross Sea during the Austral Summer 2017. Microorganisms 2020; 8:microorganisms8091273. [PMID: 32825597 PMCID: PMC7569985 DOI: 10.3390/microorganisms8091273] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/14/2020] [Accepted: 08/18/2020] [Indexed: 11/16/2022] Open
Abstract
The active prokaryotic communities proliferate in the ecosystems of the Antarctic Ocean, participating in biogeochemical cycles and supporting higher trophic levels. They are regulated by several environmental and ecological forcing, such as the characteristics of the water masses subjected to global warming and particulate organic matter (POM). During summer 2017, two polynyas in the Ross Sea were studied to evaluate key-microbiological parameters (the proteasic, glucosidasic, and phosphatasic activities, the microbial respiratory rates, the prokaryotic abundance and biomass) in relation to quantitative and qualitative characteristics of POM. Results showed significant differences in the epipelagic layer between two macro-areas (Terra Nova Bay and Ross Sea offshore area). Proteins and carbohydrates were metabolized rapidly in the offshore area (as shown by turnover times), due to high enzymatic activities in this zone, indicating fresh and labile organic compounds. The lower quality of POM in Terra Nova Bay, as shown by the higher refractory fraction, led to an increase in the turnover times of proteins and carbohydrates. Salinity was the physical constraint that played a major role in the distribution of POM and microbial activities in both areas.
Collapse
|
13
|
Physiological Profiling and Functional Diversity of Groundwater Microbial Communities in a Municipal Solid Waste Landfill Area. WATER 2019. [DOI: 10.3390/w11122624] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The disposal of municipal solid wastes in landfills represents a major threat for aquifer environments at the global scale. The aim of this study was to explore how groundwater geochemical characteristics can influence the microbial community functioning and the potential degradation patterns of selected organic substrates in response to different levels of landfill-induced alterations. Groundwaters collected from a landfill area were monitored by assessing major physical-chemical parameters and the microbiological contamination levels (total coliforms and fecal indicators—Colilert-18). The aquatic microbial community was further characterized by flow cytometry and Biolog EcoPlatesTM assay. Three groundwater conditions (i.e., pristine, mixed, and altered) were identified according to their distinct geochemical profiles. The altered groundwaters showed relatively higher values of organic matter concentration and total cell counts, along with the presence of fecal indicator bacteria, in comparison to samples from pristine and mixed conditions. The kinetic profiles of the Biolog substrate degradation showed that the microbial community thriving in altered conditions was relatively more efficient in metabolizing a larger number of organic substrates, including those with complex molecular structures. We concluded that the assessment of physiological profiling and functional diversity at the microbial community level could represent a supportive tool to understand the potential consequences of the organic contamination of impacted aquifers, thus complementing the current strategies for groundwater management.
Collapse
|
14
|
Li Y, Sun LL, Sun YY, Cha QQ, Li CY, Zhao DL, Song XY, Wang M, McMinn A, Chen XL, Zhang YZ, Qin QL. Extracellular Enzyme Activity and Its Implications for Organic Matter Cycling in Northern Chinese Marginal Seas. Front Microbiol 2019; 10:2137. [PMID: 31608022 PMCID: PMC6755343 DOI: 10.3389/fmicb.2019.02137] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/30/2019] [Indexed: 01/23/2023] Open
Abstract
Extracellular enzymes, initiating the degradation of organic macromolecules, are important functional components of marine ecosystems. Measuring in situ seawater extracellular enzyme activity (EEA) can provide fundamental information for understanding the biogeochemical cycling of organic matter in the ocean. Here we investigate the patterns of EEA and the major factors affecting the seawater EEA of Chinese marginal seas. The geographic distribution of EEA along a latitudinal transect was examined and found to be associated with dissolved organic carbon. Compared with offshore waters, inshore waters had higher enzyme activity. All the tested substrates were hydrolyzed at different rates and phosphatase, β-glucosidase and protease contributed greatly to summed hydrolysis rates. For any particular enzyme activity, the contribution of dissolved to total EEA was strongly heterogenous between stations. Comparisons of hydrolysis rates of the polymers and their corresponding oligomers suggest that molecule size does not necessarily limit the turnover of marine organic matter. In addition, several typical enzyme-producing clades, such as Bacteroidetes, Planctomycetes, Chloroflexi, Roseobacter, Alteromonas, and Pseudoalteromonas, were detected in the in situ environments. These enzyme-producing clades may be responsible for the production of different enzymes. Overall, each enzyme was found to flexibly respond to environmental conditions and were linked to microbial community composition. It is likely that this activity will profoundly affect organic matter cycling in the Chinese marginal seas.
Collapse
Affiliation(s)
- Yi Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Lin-Lin Sun
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Yuan-Yuan Sun
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Qian-Qian Cha
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Chun-Yang Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Dian-Li Zhao
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiao-Yan Song
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Min Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China.,College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| |
Collapse
|
15
|
Jo T, Arimoto M, Murakami H, Masuda R, Minamoto T. Particle Size Distribution of Environmental DNA from the Nuclei of Marine Fish. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:9947-9956. [PMID: 31328917 DOI: 10.1021/acs.est.9b02833] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Environmental DNA (eDNA) analyses have enabled a more efficient surveillance of species distribution and composition than conventional methods. However, the characteristics and dynamics of eDNA (e.g., origin, state, transport, and fate) remain unknown. This is especially limited for the eDNA derived from nuclei (nu-eDNA), which has recently been used in eDNA analyses. Here, we compared the particle size distribution (PSD) of nu-eDNA from Japanese Jack Mackerel (Trachurus japonicus) with that of mt-eDNA (eDNA derived from mitochondria) reported in previous studies. We repeatedly sampled rearing water from the tanks under multiple temperatures and fish biomass levels, and quantified the copy numbers of size-fractioned nu-eDNA. We found that the concentration of nu-eDNA was higher than that of mt-eDNA at 3-10 μm size fraction. Moreover, at the 0.8-3 μm and 0.4-0.8 μm size fractions, eDNA concentrations of both types increased with higher temperature and their degradation tended to be suppressed. These results imply that the production of eDNA from large to small size fractions could buffer the degradation of small-sized eDNA, which could improve its persistence in water. Our findings will contribute to refine the difference between nu- and mt-eDNA properties, and assist eDNA analyses as an efficient tool for the conservation of aquatic species.
Collapse
Affiliation(s)
- Toshiaki Jo
- Graduate School of Human Development and Environment , Kobe University , 3-11 Tsurukabuto , Nada-ku, Kobe City , Hyogo 657-8501 , Japan
- Research Fellow of Japan Society for the Promotion of Science , 5-3-1 Kojimachi , Chiyoda-ku, Tokyo , 102-0083 , Japan
| | - Mio Arimoto
- Faculty of Human Development , Kobe University , 3-11 Tsurukabuto , Nada-ku, Kobe City , Hyogo 657-8501 , Japan
| | - Hiroaki Murakami
- Maizuru Fisheries Research Station, Field Science Education and Research Center , Kyoto University , Maizuru , Kyoto 625-0086 , Japan
| | - Reiji Masuda
- Maizuru Fisheries Research Station, Field Science Education and Research Center , Kyoto University , Maizuru , Kyoto 625-0086 , Japan
| | - Toshifumi Minamoto
- Graduate School of Human Development and Environment , Kobe University , 3-11 Tsurukabuto , Nada-ku, Kobe City , Hyogo 657-8501 , Japan
| |
Collapse
|
16
|
Selfish, sharing and scavenging bacteria in the Atlantic Ocean: a biogeographical study of bacterial substrate utilisation. ISME JOURNAL 2018; 13:1119-1132. [PMID: 30531893 PMCID: PMC6474216 DOI: 10.1038/s41396-018-0326-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 11/06/2018] [Accepted: 11/23/2018] [Indexed: 12/12/2022]
Abstract
Identifying the roles played by individual heterotrophic bacteria in the degradation of high molecular weight (HMW) substrates is critical to understanding the constraints on carbon cycling in the ocean. At five sites in the Atlantic Ocean, we investigated the processing of organic matter by tracking changes in microbial community composition as HMW polysaccharides were enzymatically hydrolysed over time. During this investigation, we discovered that a considerable fraction of heterotrophic bacteria uses a newly-identified ‘selfish’ mode of substrate processing. We therefore additionally examined the balance of individual substrate utilisation mechanisms at different locations by linking individual microorganisms to distinct substrate utilisation mechanisms. Through FISH and uptake of fluorescently-labelled polysaccharides, ‘selfish’ organisms were identified as belonging to the Bacteroidetes, Planctomycetes and Gammaproteobacteria. ‘Sharing’ (extracellular enzyme producing) and ‘scavenging’ (non-enzyme producing) organisms predominantly belonged to the Alteromonadaceae and SAR11 clades, respectively. The extent to which individual mechanisms prevail depended on the initial population structure of the bacterial community at a given location and time, as well as the growth rate of specific bacteria. Furthermore, the same substrate was processed in different ways by different members of a pelagic microbial community, pointing to significant follow-on effects for carbon cycling.
Collapse
|
17
|
Haro-Moreno JM, López-Pérez M, de la Torre JR, Picazo A, Camacho A, Rodriguez-Valera F. Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment. MICROBIOME 2018; 6:128. [PMID: 29991350 PMCID: PMC6040077 DOI: 10.1186/s40168-018-0513-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/02/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND The photic zone of aquatic habitats is subjected to strong physicochemical gradients. To analyze the fine-scale variations in the marine microbiome, we collected seven samples from a single offshore location in the Mediterranean at 15 m depth intervals during a period of strong stratification, as well as two more samples during the winter when the photic water column was mixed. We were able to recover 94 new metagenome-assembled genomes (MAGs) from these metagenomes and examine the distribution of key marine microbes within the photic zone using metagenomic recruitment. RESULTS Our results showed significant differences in the microbial composition of different layers within the stratified photic water column. The majority of microorganisms were confined to discreet horizontal layers of no more than 30 m (stenobathic). Only a few such as members of the SAR11 clade appeared at all depths (eurybathic). During the winter mixing period, only some groups of bloomers such as Pseudomonas were favored. Although most microbes appeared in both seasons, some groups like the SAR116 clade and some Bacteroidetes and Verrucomicrobia seemed to disappear during the mixing period. Furthermore, we found that some microbes previously considered seasonal (e.g., Archaea or Actinobacteria) were living in deeper layers within the photic zone during the stratification period. A strong depth-related specialization was detected, not only at the taxonomic level but also at the functional level, even within the different clades, for the manipulation and uptake of specific polysaccharides. Rhodopsin sequences (green or blue) also showed narrow depth distributions that correlated with the taxonomy of the microbe in which they were found but not with depth. CONCLUSIONS Although limited to a single location in the Mediterranean, this study has profound implications for our understanding of how marine microbial communities vary with depth within the photic zone when stratified. Our results highlight the importance of collecting samples at different depths in the water column when comparing seasonal variations and have important ramifications for global marine studies that most often take samples from only one single depth. Furthermore, our perspective and approaches (metagenomic assembly and recruitment) are broadly applicable to other metagenomic studies.
Collapse
Affiliation(s)
- Jose M Haro-Moreno
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan de Alicante, 03550, Alicante, Spain
| | - Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan de Alicante, 03550, Alicante, Spain
| | - José R de la Torre
- Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA
| | - Antonio Picazo
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Burjassot, E-46100, Valencia, Spain
| | - Antonio Camacho
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Burjassot, E-46100, Valencia, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan de Alicante, 03550, Alicante, Spain.
| |
Collapse
|
18
|
Liu Q, Fang J, Li J, Zhang L, Xie BB, Chen XL, Zhang YZ. Depth-Resolved Variations of Cultivable Bacteria and Their Extracellular Enzymes in the Water Column of the New Britain Trench. Front Microbiol 2018; 9:135. [PMID: 29467744 PMCID: PMC5808245 DOI: 10.3389/fmicb.2018.00135] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 01/22/2018] [Indexed: 01/26/2023] Open
Abstract
Marine microorganisms and their extracellular enzymes (ECEs) play an important role in the remineralization of organic material by hydrolyzing high-molecular-weight substrates to sizes sufficiently small to be transported through cell membrane, yet the diversity of the enzyme-producing bacteria and the types of ECEs involved in the degradation process are largely unknown. In this work, we investigated the diversity of cultivable bacteria and their ECEs and the potential activities of aminopeptidase in the water column at eight different depths of the New Britain Trench. There was a great diversity of cultivable bacteria and ECEs, and depth appears an important driver of the diversity. The 16S rRNA sequence analysis revealed that the cultivable bacteria were affiliated mostly with the phyla Proteobacteria and Actinobacteria, and the predominant genera were Pseudoalteromonas (62.7%) and Halomonas (17.3%). Moreover, 70.7% of the isolates were found to produce hydrolytic zone on casein and gelatin plates, in which Pseudoalteromonas was the predominant group, exhibiting relatively high protease production. Inhibitor analysis showed that the extracellular proteases from the isolated bacteria were serine proteases in the surface water and metalloproteases in the deep water. Meanwhile, the Vmax and Km of aminopeptidase exhibited a maximum in the surface water and low values in the deep bathy- and abyssopelagic water, indicating lower rates of hydrolysis and higher substrate affinity in the deeper waters. These results shed new insights into the diversity of the cultivable bacteria and bacterial ECEs and their likely biogeochemical functions in the trench environment.
Collapse
Affiliation(s)
- Qianfeng Liu
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Jiasong Fang
- Hadal Science and Technology Research Center, Shanghai Ocean University, Shanghai, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Department of Natural Sciences, Hawaii Pacific University, Honolulu, HI, United States
| | - Jiangtao Li
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Li Zhang
- State Key Laboratory of Geological Process and Mineral Resources, Faculty of Earth Sciences, China University of Geosciences, Wuhan, China
| | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, China
| | - Yu-Zhong Zhang
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, China
| |
Collapse
|
19
|
Matos MN, Lozada M, Anselmino LE, Musumeci MA, Henrissat B, Jansson JK, Mac Cormack WP, Carroll J, Sjöling S, Lundgren L, Dionisi HM. Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments. Environ Microbiol 2016; 18:4471-4484. [PMID: 27348213 DOI: 10.1111/1462-2920.13433] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 05/23/2016] [Indexed: 12/20/2022]
Abstract
Alginates are abundant polysaccharides in brown algae that constitute an important energy source for marine heterotrophic bacteria. Despite the key role of alginate degradation processes in the marine carbon cycle, little information is available on the bacterial populations involved in these processes. The aim of this work was to gain a better understanding of alginate utilization capabilities in cold coastal environments. Sediment metagenomes from four high-latitude regions of both Hemispheres were interrogated for alginate lyase gene homologue sequences and their genomic context. Sediments contained highly abundant and diverse bacterial assemblages with alginolytic potential, including members of Bacteroidetes and Proteobacteria, as well as several poorly characterized taxa. The microbial communities in Arctic and Antarctic sediments exhibited the most similar alginolytic profiles, whereas brackish sediments showed distinct structures with a higher proportion of novel genes. Examination of the gene neighbourhood of the alginate lyase homologues revealed distinct patterns depending on the potential lineage of the scaffolds, with evidence of evolutionary relationships among alginolytic gene clusters from Bacteroidetes and Proteobacteria. This information is relevant for understanding carbon fluxes in cold coastal environments and provides valuable information for the development of biotechnological applications from brown algae biomass.
Collapse
Affiliation(s)
- Marina N Matos
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Puerto Madryn, U9120ACD, Argentina
| | - Mariana Lozada
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Puerto Madryn, U9120ACD, Argentina
| | - Luciano E Anselmino
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Puerto Madryn, U9120ACD, Argentina
| | - Matías A Musumeci
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Puerto Madryn, U9120ACD, Argentina
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, 13288, France.,INRA, USC 1408 AFMB, Marseille, F-13288, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Walter P Mac Cormack
- Instituto Antártico Argentino, Ciudad Autónoma de Buenos Aires, C1064ABR, Argentina.,Instituto Nanobiotec, CONICET - Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, C1113AAC, Argentina
| | - JoLynn Carroll
- Akvaplan-niva, Fram - High North Research Centre for Climate and the Environment, Tromsø, NO-9296, Norway.,CAGE - Centre for Arctic Gas Hydrate, Environment and Climate, UiT The Arctic University of Norway, Tromsø, N-9037, Norway
| | - Sara Sjöling
- School of Natural Sciences and Environmental Studies, Södertörn University, Huddinge, 141 89, Sweden
| | | | - Hebe M Dionisi
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Puerto Madryn, U9120ACD, Argentina
| |
Collapse
|
20
|
Zoccarato L, Celussi M, Pallavicini A, Fonda Umani S. Aurelia aurita Ephyrae Reshape a Coastal Microbial Community. Front Microbiol 2016; 7:749. [PMID: 27242762 PMCID: PMC4871886 DOI: 10.3389/fmicb.2016.00749] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/03/2016] [Indexed: 11/19/2022] Open
Abstract
Over the last two decades, increasing attention has been paid to the impact of jellyfish blooms on marine communities. Aurelia aurita is one of the most studied of the Scyphozoans, and several studies have been carried out to describe its role as a top-down controller within the classical food web. However, little data are available to define the effects of these jellyfish on microbial communities. The aims of this study were to describe the predation impact of A. aurita ephyrae on a natural microplanktonic assemblage, and to determine any reshaping effects on the prokaryote community composition and functioning. Surface coastal water was used to set up a 24-h grazing experiment in microcosms. Samples were collected to determine the variations in prey biomass, heterotrophic carbon production (HCP), extracellular leucine aminopeptidase activity, and grazing pressure. A next-generation sequencing technique was used to investigate biodiversity shifts within the prokaryote and protist communities through the small subunit rRNA tag approach. This study shows that A. aurita ephyrae were responsible for large decreases in the abundances of the more motile microplankton groups, such as tintinnids, Dinophyceae, and aloricate ciliates. Bacillariophyceae and Mediophyceae showed smaller reductions. No evidence of selective predation emerged in the analysis of the community diversity down to the family level. The heterotrophic prokaryote biomass increased significantly (by up to 45%), in parallel with increases in HCP and leucine aminopeptidase activity (40%). Significant modifications were detected in prokaryotic community composition. Some classes of Gammaproteobacteria and Flavobacteriia showed higher relative abundances when exposed to A. aurita ephyrae, while there was a net decrease for Alphaproteobacteria. Overall, this study provides new insight into the effects of A. aurita on microbial communities, underlining their selective predation toward the more motile groups of microplankton and their impact on prokaryotic assemblages, by favoring blooms of copiotrophic taxa.
Collapse
Affiliation(s)
- Luca Zoccarato
- Marine Ecology Laboratory, Department of Life Science, University of TriesteTrieste, Italy
| | - Mauro Celussi
- Oceanography Division, OGS (Istituto Nazionale di Oceanografia e di Geofisica Sperimentale)Trieste, Italy
| | - Alberto Pallavicini
- Marine Ecology Laboratory, Department of Life Science, University of TriesteTrieste, Italy
| | - Serena Fonda Umani
- Marine Ecology Laboratory, Department of Life Science, University of TriesteTrieste, Italy
| |
Collapse
|
21
|
Torti A, Lever MA, Jørgensen BB. Origin, dynamics, and implications of extracellular DNA pools in marine sediments. Mar Genomics 2015; 24 Pt 3:185-96. [DOI: 10.1016/j.margen.2015.08.007] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 08/29/2015] [Indexed: 12/17/2022]
|