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Vipindas PV, Jabir T, Venkatachalam S, Yang EJ, Jain A, Krishnan KP. Vertical segregation and phylogenetic characterization of archaea and archaeal ammonia monooxygenase gene in the water column of the western Arctic Ocean. Extremophiles 2023; 27:24. [PMID: 37668803 DOI: 10.1007/s00792-023-01310-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/21/2023] [Indexed: 09/06/2023]
Abstract
Archaea constitute a substantial fraction of marine microbial biomass and play critical roles in the biogeochemistry of oceans. However, studies on their distribution and ecology in the Arctic Ocean are relatively scarce. Here, we studied the distributions of archaea and archaeal ammonia monooxygenase (amoA) gene in the western Arctic Ocean, using the amplicon sequencing approach from the sea surface to deep waters up to 3040 m depth. A total of five archaeal phyla, Nitrososphaerota, "Euryarchaeota", "Halobacteriota," "Nanoarchaeota", and Candidatus Thermoplasmatota, were detected. We observed a clear, depth-dependent vertical segregation among archaeal communities. Ca. Thermoplasmatota (66.8%) was the most dominant phylum in the surface waters. At the same time, Nitrososphaerota (55.9%) was dominant in the deep waters. Most of the amoA gene OTUs (99%) belonged to the Nitrosopumilales and were further clustered into five subclades ("NP-Alpha", "NP-Delta", "NP-Epsilon", "NP-Gamma", and "NP-Theta"). "NP-Epsilon" was the most dominant clade throughout the water column and "NP_Alpha" showed higher abundance only in the deeper water. Salinity and inorganic nutrient concentrations were the major factors that determined the vertical segregation of archaea. We anticipate that the observed differences in the vertical distribution of archaea might contribute to the compartmentalization of dark carbon fixation and nitrification in deeper water and organic matter degradation in surface waters of the Arctic Ocean.
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Affiliation(s)
- Puthiya Veettil Vipindas
- Arctic Ecology and Biogeochemistry Division, Ministry of Earth Sciences, National Centre for Polar and Ocean Research, Vasco-da-Gama, Goa, 403 804, India.
| | - Thajudeen Jabir
- Arctic Ecology and Biogeochemistry Division, Ministry of Earth Sciences, National Centre for Polar and Ocean Research, Vasco-da-Gama, Goa, 403 804, India
| | - Siddarthan Venkatachalam
- Arctic Ecology and Biogeochemistry Division, Ministry of Earth Sciences, National Centre for Polar and Ocean Research, Vasco-da-Gama, Goa, 403 804, India
| | - Eun Jin Yang
- Division of Ocean Sciences, Korea Polar Research Institute, 26 Songdo-dong, Yeonsu-gu, Incheon, 21990, Republic of Korea
| | - Anand Jain
- Arctic Ecology and Biogeochemistry Division, Ministry of Earth Sciences, National Centre for Polar and Ocean Research, Vasco-da-Gama, Goa, 403 804, India
| | - Kottekkatu Padinchati Krishnan
- Arctic Ecology and Biogeochemistry Division, Ministry of Earth Sciences, National Centre for Polar and Ocean Research, Vasco-da-Gama, Goa, 403 804, India
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2
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Amano C, Reinthaler T, Sintes E, Varela MM, Stefanschitz J, Kaneko S, Nakano Y, Borchert W, Herndl GJ, Utsumi M. A device for assessing microbial activity under ambient hydrostatic pressure: The in situ microbial incubator (ISMI). LIMNOLOGY AND OCEANOGRAPHY, METHODS 2023; 21:69-81. [PMID: 38505832 PMCID: PMC10946486 DOI: 10.1002/lom3.10528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/22/2022] [Accepted: 11/22/2022] [Indexed: 03/21/2024]
Abstract
Microbes in the dark ocean are exposed to hydrostatic pressure increasing with depth. Activity rate measurements and biomass production of dark ocean microbes are, however, almost exclusively performed under atmospheric pressure conditions due to technical constraints of sampling equipment maintaining in situ pressure conditions. To evaluate the microbial activity under in situ hydrostatic pressure, we designed and thoroughly tested an in situ microbial incubator (ISMI). The ISMI allows autonomously collecting and incubating seawater at depth, injection of substrate and fixation of the samples after a preprogramed incubation time. The performance of the ISMI was tested in a high-pressure tank and in several field campaigns under ambient hydrostatic pressure by measuring prokaryotic bulk 3H-leucine incorporation rates. Overall, prokaryotic leucine incorporation rates were lower at in situ pressure conditions than under to depressurized conditions reaching only about 50% of the heterotrophic microbial activity measured under depressurized conditions in bathypelagic waters in the North Atlantic Ocean off the northwestern Iberian Peninsula. Our results show that the ISMI is a valuable tool to reliably determine the metabolic activity of deep-sea microbes at in situ hydrostatic pressure conditions. Hence, we advocate that deep-sea biogeochemical and microbial rate measurements should be performed under in situ pressure conditions to obtain a more realistic view on deep-sea biotic processes.
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Affiliation(s)
- Chie Amano
- Department of Functional and Evolutionary Ecology, Bio‐Oceanography UnitUniversity of ViennaViennaAustria
| | - Thomas Reinthaler
- Department of Functional and Evolutionary Ecology, Bio‐Oceanography UnitUniversity of ViennaViennaAustria
| | - Eva Sintes
- Instituto Español de Oceanografía‐CSIC, Centro Oceanográfico de BalearesPalma de MallorcaSpain
| | - Marta M. Varela
- Instituto Español de Oceanografia‐CSIC, Centro Oceanografico de A CoruñaA CoruñaSpain
| | - Julia Stefanschitz
- Department of Functional and Evolutionary Ecology, Bio‐Oceanography UnitUniversity of ViennaViennaAustria
- Present address:
Marine Evolutionary Ecology, Deep‐Sea Biology Group, GEOMAR Helmholtz Centre for Ocean Research KielKielGermany
| | | | - Yoshiyuki Nakano
- Japan Agency for Marine‐Earth Science and Technology (JAMSTEC)YokosukaJapan
| | | | - Gerhard J. Herndl
- Department of Functional and Evolutionary Ecology, Bio‐Oceanography UnitUniversity of ViennaViennaAustria
- NIOZ, Department of Marine Microbiology and BiogeochemistryRoyal Netherlands Institute for Sea Research, Utrecht UniversityTexelThe Netherlands
| | - Motoo Utsumi
- Faculty of Life and Environmental SciencesUniversity of TsukubaIbarakiJapan
- Microbiology Research Center for SustainabilityUniversity of TsukubaIbarakiJapan
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3
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Wang J, Guo X, Li Y, Song G, Zhao L. Understanding the Variation of Bacteria in Response to Summertime Oxygen Depletion in Water Column of Bohai Sea. Front Microbiol 2022; 13:890973. [PMID: 35756048 PMCID: PMC9221365 DOI: 10.3389/fmicb.2022.890973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/05/2022] [Indexed: 11/14/2022] Open
Abstract
Aiming to reveal the variation in bacteria community under oxygen depletion formed every summer in water column of central Bohai Sea, a time-scenario sampling from June to August in 2018 at a 20-day interval along one inshore-offshore transect was settled. Water samples were collected at the surface, middle, and bottom layer and then analyzed by high-throughput sequencing targeting both 16S rRNA and nosZ genes. Compared to the surface and middle water, oxygen depletion occurred at bottom layer in August. In top two layers, Cyanobacteria dominated the bacterial community, whereas heterotrophic bacteria became dominant in bottom water of Bohai Sea. Based on the time scenario, distinct community separation was observed before (June and July) and after (August) oxygen depletion (p = 0.003). Vertically, strict stratification of nosZ gene was stably formed along 3 sampling layers. As a response to oxygen depletion, the diversity indices of both total bacteria (16S rRNA) and nosZ gene-encoded denitrification bacteria all increased, which indicated the intense potential of nitrogen lose when oxygen depleted. Dissolved oxygen (DO) was the key impacting factor on the community composition of total bacteria in June, whereas nutrients together with DO play the important roles in August for both total and denitrifying bacteria. The biotic impact was revealed further by strong correlations which showed between Cyanobacteria and heterotrophic bacteria in June from co-occurrence network analysis, which became weak in August when DO was depleted. This study discovered the variation in bacteria community in oxygen-depleted water with further effort to understand the potential role of denitrifying bacteria under oxygen depletion in Bohai Sea for the first time, which provided insights into the microbial response to the world-wide expanding oxygen depletion and their contributions in the ocean nitrogen cycling.
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Affiliation(s)
- Jing Wang
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China
| | - Xiaoxiao Guo
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China
| | - Yanying Li
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China
| | - Guisheng Song
- School of Marine Science and Technology, Tianjin University, Tianjin, China
| | - Liang Zhao
- College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin, China
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Zhu X, Wang Z, Luo Y, Ma Y, Xu Z, Wang L, Peng F, Pang Q, Li Y, He F, Xu B. Overlying water fluoride concentrations influence dissolved organic matter composition and migration from pore water in sediment via bacterial mechanisms. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2022; 10:100163. [PMID: 36159732 PMCID: PMC9488004 DOI: 10.1016/j.ese.2022.100163] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 02/23/2022] [Accepted: 02/23/2022] [Indexed: 06/16/2023]
Abstract
Fluoride (F-) is widespread in aquatic environments; however, it is not clear whether the fluctuation of F- concentrations in overlying lake water affects the composition and migration of dissolved organic matter (DOM) from sediment. A case study was presented in Sand Lake, China, and an experiment was conducted to analyze the influence of different F- concentrations in overlying water on DOM characteristics. Diffusion resulted in similarities in DOM components between overlying and pore waters, and bacterial activities and enzyme variation resulted in differences between them. Higher F- concentrations in overlying water resulted in a higher pH of pore water, which favored the enrichment of protein-like substances. Higher F- concentrations caused lower DOM concentrations and lower maximum fluorescence intensities (Fmax) of protein-like components in pore water. The F- concentrations had significantly negative correlations with Shannon indexes (P < 0.05). Thiobacillus influenced the migration of tyrosine-like substances by decreasing the pH of pore water. Trichococcus and Fusibacter altered the Fmax of protein-like, humic-like, and fulvic-like substances. The F- concentrations affected the DOM composition and migration due to the response of functional bacterial communities, which were positively correlated with the relative abundance of Thiobacillus and negatively correlated with the relative abundances of Trichococcus and Fusibacter. The high F- concentrations influenced the biosynthesis and degradation of protein-like substances by shifting the abundances of the relevant enzymes. The results of this study may provide ideas for investigating DOM cycling under the influence of F-, especially in lakes with fluctuations in F- concentrations.
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Affiliation(s)
- Xiang Zhu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, PR China
| | - Zibo Wang
- China National Environmental Monitoring Centre, No8-2 Anwai Dayangfang, Chaoyang District, Beijing, 100012, PR China
| | - Yidan Luo
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, PR China
- College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Yushen Ma
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, PR China
- College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Zhipeng Xu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, PR China
- College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Longmian Wang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, PR China
| | - Fuquan Peng
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, PR China
| | - Qingqing Pang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, PR China
| | - Yiping Li
- College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Fei He
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, PR China
| | - Bin Xu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210042, PR China
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5
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Shao Q, Sun D, Fang C, Feng Y, Wang C. Biodiversity and Biogeography of Abundant and Rare Microbial Assemblages in the Western Subtropical Pacific Ocean. Front Microbiol 2022; 13:839562. [PMID: 35432250 PMCID: PMC9006148 DOI: 10.3389/fmicb.2022.839562] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
The levels of chlorophyll a and nutrient concentrations in the surface waters of the western subtropical Pacific Ocean are among the lowest globally. In addition, our knowledge of basin-scale diversity and biogeography of microbial communities in this vast extremely oligotrophic environment is still rather limited. Here, high-throughput sequencing was used to examine the biodiversity and biogeography of abundant and rare microbial assemblages throughout the water column from the surface to a depth of 3,000 m across a horizontal distance of 1,100 km in the western Pacific Ocean. Microbial alpha diversity in the 200-m layer was higher than at other depths, with Gammaproteobacteria, Alphaproteobacteria, and Clostridia as the dominant classes in all samples. Distinctly vertical distributions within the microbial communities were revealed, with no difference horizontally. Some microbes exhibited depth stratification. For example, the relative abundances of Cyanobacteria and Alphaproteobacteria decreased with depth, while Nitrososphaeria, Actinobacteria, and Gammaproteobacteria increased with depth in the aphotic layers. Furthermore, we found that environmental (selective process) and spatial (neutral process) factors had different effects on abundant and rare taxa. Geographical distance showed little effect on the dispersal of all and abundant taxa, while statistically significant distance-decay relationships were observed among the rare taxa. Temperature and chlorophyll a were strongly associated with all, abundant, and rare taxa in the photic layers, while total inorganic nitrogen was recognized as the crucial factor in the aphotic layers. Variance partitioning analysis indicated that environmental selection played a relatively important role in shaping all and abundant taxa, while the variation in rare taxa explained by environmental and spatial processes was relatively low, as more than 70% of the variation remained unexplained. This study provides novel knowledge related to microbial community diversity in the western subtropical Pacific Ocean, and the analyzes biogeographical patterns among abundant and rare taxa.
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Affiliation(s)
- Qianwen Shao
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- Ningbo Institute of Oceanography, Ningbo, China
| | - Dong Sun
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Chen Fang
- College of Oceanography, Hohai University, Nanjing, China
| | - Yunzhi Feng
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Chunsheng Wang
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
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6
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Vijayan J, Ammini P, Nathan VK. Diversity pattern of marine culturable heterotrophic bacteria in a region with coexisting upwelling and mud banks in the southeastern Arabian Sea. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:3967-3982. [PMID: 34398377 DOI: 10.1007/s11356-021-15772-8] [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: 04/26/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
Mud banks and upwelling are two important oceanographic features occurring along the southwest coast of India during the southwest monsoon period. The study region, Alappuzha lying on the southwest coast of India, is unique due to the co-existence of upwelling and mud banks during the monsoon (MON) season. Water samples were collected from three stations, M1, M2, and M3, from April to September 2014, at weekly/biweekly intervals to determine the total bacterial abundance, viable prokaryotic counts, and total plate counts, along with measurements on physico-chemical parameters. For determining the heterotrophic culturable bacterial diversity, water samples were collected during two seasons, monsoon and pre-monsoon (PRM), from three stations. Water samples were inoculated into two non-selective broths for enrichment, DNA was extracted, and next-generation sequencing analysis was performed using Illumina Miseq sequencing. The sequence analysis revealed that dominant communities were Proteobacteria, followed by Firmicutes and Fusobacteria. Proportions of Fusobacteria increased during monsoon and proportions of Firmicutes were high in premonsoon season. Among Proteobacteria, Gammaproteobacteri is presented more than 99% of all the classes, irrespective of seasons. Vibrio was the most dominant genus during both seasons. The presence of anaerobic genera such as Propionigenium and Cetobacterium at all the stations during MON indicated the presence of upwelled waters. The genus Stenotrophomonas was observed in the M2 station alone. This study provides an overview of the culturable heterotrophic bacterial communities in a region in the southeastern Arabian Sea with coexisting mud banks and upwelling. The results of this study were compared with a published report on culture-independent bacterial diversity (from environmental DNA) from the same region. The study demonstrates that the use of culture media underrepresented the phylogenetic diversity and selectively enriched the class Gammaproteobacteria alone.
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Affiliation(s)
- Jasna Vijayan
- National Institute of Oceanography-CSIR, Regional Center, Dr. Salim Ali Road, Kochi, Kerala, 682018, India
| | - Parvathi Ammini
- National Institute of Oceanography-CSIR, Regional Center, Dr. Salim Ali Road, Kochi, Kerala, 682018, India.
- Department of Biotechnology, Cochin University of Science and Technology, Kochi, Kerala, 682022, India.
| | - Vinod Kumar Nathan
- National Institute of Oceanography-CSIR, Regional Center, Dr. Salim Ali Road, Kochi, Kerala, 682018, India
- School of Chemical and Biotechnology, Sastra Deemed University Tirumalaisamudram, Thanjavur, Tamilnadu, 613401, India
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7
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Orta-Ponce CP, Rodríguez-Ramos T, Nieto-Cid M, Teira E, Guerrero-Feijóo E, Bode A, Varela MM. Empirical leucine-to-carbon conversion factors in north-eastern Atlantic waters (50-2000 m) shaped by bacterial community composition and optical signature of DOM. Sci Rep 2021; 11:24370. [PMID: 34934099 PMCID: PMC8692456 DOI: 10.1038/s41598-021-03790-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/09/2021] [Indexed: 11/09/2022] Open
Abstract
Microbial heterotrophic activity is a major process regulating the flux of dissolved organic matter (DOM) in the ocean, while the characteristics of this DOM strongly influence its microbial utilization and fate in the ocean. In order to broaden the vertical resolution of leucine-to-carbon conversion factors (CFs), needed for converting substrate incorporation into biomass production by heterotrophic bacteria, 20 dilution experiments were performed in the North Atlantic Ocean. We found a depth-stratification in empirical CFs values from epipelagic to bathypelagic waters (4.00 ± 1.09 to 0.10 ± 0.00 kg C mol Leu−1). Our results demonstrated that the customarily used theoretical CF of 1.55 kg C mol Leu−1 in oceanic samples can lead to an underestimation of prokaryotic heterotrophic production in epi- and mesopelagic waters, while it can overestimate it in the bathypelagic ocean. Pearson correlations showed that CFs were related not only to hydrographic variables such as temperature, but also to specific phylogenetic groups and DOM quality and quantity indices. Furthermore, a multiple linear regression model predicting CFs from relatively simple hydrographic and optical spectroscopic measurements was attempted. Taken together, our results suggest that differences in CFs throughout the water column are significantly connected to DOM, and also reflect differences linked to specific prokaryotic groups.
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Affiliation(s)
- C Pamela Orta-Ponce
- Instituto Español de Oceanografía (IEO-CSIC), Centro Oceanográfico de A Coruña, 15080, A Coruña, Spain. .,Facultade de Ciencias, Zapateira, Universidade da Coruña, 15071, A Coruña, Spain.
| | - Tamara Rodríguez-Ramos
- Instituto Español de Oceanografía (IEO-CSIC), Centro Oceanográfico de A Coruña, 15080, A Coruña, Spain
| | - Mar Nieto-Cid
- Instituto Español de Oceanografía (IEO-CSIC), Centro Oceanográfico de A Coruña, 15080, A Coruña, Spain.,Laboratorio de Geoquímica Orgánica, Instituto de Investigaciones Marinas (CSIC), 36208, Vigo, Spain
| | - Eva Teira
- Departamento de Ecología y Biología Animal, Universidade de Vigo, Centro de Investigación Mariña da Universidade de Vigo (CIM-UVigo), 36310, Vigo, Spain
| | - Elisa Guerrero-Feijóo
- Instituto Español de Oceanografía (IEO-CSIC), Centro Oceanográfico de A Coruña, 15080, A Coruña, Spain
| | - Antonio Bode
- Instituto Español de Oceanografía (IEO-CSIC), Centro Oceanográfico de A Coruña, 15080, A Coruña, Spain
| | - Marta M Varela
- Instituto Español de Oceanografía (IEO-CSIC), Centro Oceanográfico de A Coruña, 15080, A Coruña, Spain
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Varela MM, Rodríguez-Ramos T, Guerrero-Feijóo E, Nieto-Cid M. Changes in Activity and Community Composition Shape Bacterial Responses to Size-Fractionated Marine DOM. Front Microbiol 2020; 11:586148. [PMID: 33329457 PMCID: PMC7714726 DOI: 10.3389/fmicb.2020.586148] [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: 07/22/2020] [Accepted: 09/30/2020] [Indexed: 12/21/2022] Open
Abstract
To study the response of bacteria to different size-fractions of naturally occurring dissolved organic matter (DOM), a natural prokaryotic community from North Atlantic mesopelagic waters (1000 m depth) was isolated and grown in (i) 0.1-μm filtered seawater (CONTROL), (ii) the low-molecular-weight (<1 kDa) DOM fraction (L-DOM), and (iii) the recombination of high- (>1 kDa) and low-molecular-weight DOM fractions (H + L-DOM), to test the potential effect of ultrafiltration on breaking the DOM size continuum. Prokaryotic abundance and leucine incorporation were consistently higher in the H + L-DOM niche than in the L-DOM and CONTROL treatments, suggesting a different interaction with each DOM fraction and the disruption of the structural DOM continuum by ultrafiltration, respectively. Rhodobacterales (Alphaproteobacteria) and Flavobacteriales (Bacteroidetes) were particularly enriched in L-DOM and closely related to the colored DOM (CDOM) fraction, indicating the tight link between these groups and changes in DOM aromaticity. Conversely, some other taxa that were rare or undetectable in the original bacterial community were enriched in the H + L-DOM treatment (e.g., Alteromonadales belonging to Gammaproteobacteria), highlighting the role of the rare biosphere as a seed bank of diversity against ecosystem disturbance. The relationship between the fluorescence of protein-like CDOM and community composition of populations in the H + L-DOM treatment suggested their preference for labile DOM. Conversely, the communities growing on the L-DOM niche were coupled to humic-like CDOM, which may indicate their ability to degrade more reworked DOM and/or the generation of refractory substrates (as by-products of the respiration processes). Most importantly, L- and/or H + L-DOM treatments stimulated the growth of unique bacterial amplicon sequence variants (ASVs), suggesting the potential of environmental selection (i.e., changes in DOM composition and availability), particularly in the light of climate change scenarios. Taken together, our results suggest that different size-fractions of DOM induced niche-specialization and differentiation of mesopelagic bacterial communities.
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Affiliation(s)
- Marta M. Varela
- Centro Oceanográfico de A Coruña, Instituto Español de Oceanografía (IEO), A Coruña, Spain
| | - Tamara Rodríguez-Ramos
- Centro Oceanográfico de A Coruña, Instituto Español de Oceanografía (IEO), A Coruña, Spain
| | - Elisa Guerrero-Feijóo
- Centro Oceanográfico de A Coruña, Instituto Español de Oceanografía (IEO), A Coruña, Spain
| | - Mar Nieto-Cid
- Centro Oceanográfico de A Coruña, Instituto Español de Oceanografía (IEO), A Coruña, Spain
- Laboratorio de Geoquímica Orgánica, Instituto de Investigaciones Marinas (CSIC), Vigo, Spain
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9
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Liu S, Baetge N, Comstock J, Opalk K, Parsons R, Halewood E, English CJ, Giovannoni S, Bolaños LM, Nelson CE, Vergin K, Carlson CA. Stable Isotope Probing Identifies Bacterioplankton Lineages Capable of Utilizing Dissolved Organic Matter Across a Range of Bioavailability. Front Microbiol 2020; 11:580397. [PMID: 33117322 PMCID: PMC7575717 DOI: 10.3389/fmicb.2020.580397] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/03/2020] [Indexed: 01/04/2023] Open
Abstract
Bacterioplankton consume about half of the dissolved organic matter (DOM) produced by phytoplankton. DOM released from phytoplankton consists of a myriad of compounds that span a range of biological reactivity from labile to recalcitrant. Linking specific bacterioplankton lineages to the incorporation of DOM compounds into biomass is important to understand microbial niche partitioning. We conducted a series of DNA-stable isotope probing (SIP) experiments using 13C-labeled substrates of varying lability including amino acids, cyanobacteria lysate, and DOM from diatom and cyanobacteria isolates concentrated on solid phase extraction PPL columns (SPE-DOM). Amendments of substrates into Sargasso Sea bacterioplankton communities were conducted to explore microbial response and DNA-SIP was used to determine which lineages of Bacteria and Archaea were responsible for uptake and incorporation. Greater increases in bacterioplankton abundance and DOC removal were observed in incubations amended with cyanobacteria-derived lysate and amino acids compared to the SPE-DOM, suggesting that the latter retained proportionally more recalcitrant DOM compounds. DOM across a range of bioavailability was utilized by diverse prokaryotic taxa with copiotrophs becoming the most abundant 13C-incorporating taxa in the amino acid treatment and oligotrophs becoming the most abundant 13C-incorporating taxa in SPE-DOM treatments. The lineages that responded to SPE-DOM amendments were also prevalent in the mesopelagic of the Sargasso Sea, suggesting that PPL extraction of phytoplankton-derived DOM isolates compounds of ecological relevance to oligotrophic heterotrophic bacterioplankton. Our study indicates that DOM quality is an important factor controlling the diversity of the microbial community response, providing insights into the roles of different bacterioplankton in resource exploitation and efficiency of marine carbon cycling.
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Affiliation(s)
- Shuting Liu
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Nicholas Baetge
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Jacqueline Comstock
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Keri Opalk
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Rachel Parsons
- Bermuda Institute of Ocean Sciences, Saint George, Bermuda
| | - Elisa Halewood
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Chance J English
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Stephen Giovannoni
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Luis M Bolaños
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Craig E Nelson
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, Department of Oceanography and Hawai'i Sea Grant, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, United States
| | - Kevin Vergin
- Microbial DNA Analytics, Phoenix, OR, United States
| | - Craig A Carlson
- Department of Ecology, Evolution, and Marine Biology, Marine Science Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
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10
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Wang M, Ma Y, Feng C, Cai L, Li W. Diversity of Pelagic and Benthic Bacterial Assemblages in the Western Pacific Ocean. Front Microbiol 2020; 11:1730. [PMID: 33071990 PMCID: PMC7533643 DOI: 10.3389/fmicb.2020.01730] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 07/02/2020] [Indexed: 12/28/2022] Open
Abstract
Despite numerous studies on marine prokaryotes, the vertical distribution patterns of bacterial community, either on the taxonomic composition or the functional structure, remains relatively unexplored. Using HiSeq-derived 16S rRNA data, the depth-related distribution patterns of taxonomic diversity and functional structure predicted from diversity data in the water column and sediments of the Western Pacific Ocean were explored. The OTU richness declined along the water column after peaking between 100 to 200 m deep. Relative abundance of Cyanobacteria and SAR11 decreased significantly with depth, while Actinobacteria and Gammaproteobacteria increased. This clearly mirrors the vertical distribution pattern of the predicted functional composition with the shift between phototrophic to chemoheterotrophic groups from the surface to the deeper layers. In terms of community composition and functional structure, the epipelagic zone differed from other deeper ones (i.e., meso-, bathy-, and abyssopelagic zones) where no obvious differences were detected. For the epipelagic zone, temperature, dissolved oxygen, and salinity were recognized as the crucial factors shaping both community composition and the functional structure of bacteria. Compared with water samples, benthic sediment samples harbored unexpectedly higher read abundance of Proteobacteria, presenting distinguishable taxonomic and functional compositions. This study provides novel knowledge on the vertical distribution of bacterial taxonomic and functional compositions in the western Pacific.
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Affiliation(s)
- Mengmeng Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yiyuan Ma
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Chunhui Feng
- Beihai Ocean Engineering Survey Research Institute, State Oceanic Administration, Qingdao, China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
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11
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Bagnaro A, Baltar F, Brownstein G, Lee WG, Morales SE, Pritchard DW, Hepburn CD. Reducing the arbitrary: fuzzy detection of microbial ecotones and ecosystems - focus on the pelagic environment. ENVIRONMENTAL MICROBIOME 2020; 15:16. [PMID: 33902717 PMCID: PMC8066478 DOI: 10.1186/s40793-020-00363-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 07/18/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND One of the central objectives of microbial ecology is to study the distribution of microbial communities and their association with their environments. Biogeographical studies have partitioned the oceans into provinces and regions, but the identification of their boundaries remains challenging, hindering our ability to study transition zones (i.e. ecotones) and microbial ecosystem heterogeneity. Fuzzy clustering is a promising method to do so, as it creates overlapping sets of clusters. The outputs of these analyses thus appear both structured (into clusters) and gradual (due to the overlaps), which aligns with the inherent continuity of the pelagic environment, and solves the issue of defining ecosystem boundaries. RESULTS We show the suitability of applying fuzzy clustering to address the patchiness of microbial ecosystems, integrating environmental (Sea Surface Temperature, Salinity) and bacterioplankton data (Operational Taxonomic Units (OTUs) based on 16S rRNA gene) collected during six cruises over 1.5 years from the subtropical frontal zone off New Zealand. The technique was able to precisely identify ecological heterogeneity, distinguishing both the patches and the transitions between them. In particular we show that the subtropical front is a distinct, albeit transient, microbial ecosystem. Each water mass harboured a specific microbial community, and the characteristics of their ecotones matched the characteristics of the environmental transitions, highlighting that environmental mixing lead to community mixing. Further explorations into the OTU community compositions revealed that, although only a small proportion of the OTUs explained community variance, their associations with given water mass were consistent through time. CONCLUSION We demonstrate recurrent associations between microbial communities and dynamic oceanic features. Fuzzy clusters can be applied to any ecosystem (terrestrial, human, marine, etc) to solve uncertainties regarding the position of microbial ecological boundaries and to refine the relation between the distribution of microorganisms and their environment.
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Affiliation(s)
- Antoine Bagnaro
- Department of Marine Sciences, University of Otago, Dunedin, New Zealand.
| | - Federico Baltar
- Department of Marine Sciences, University of Otago, Dunedin, New Zealand
- NIWA, University of Otago, Dunedin, New Zealand
- Department of Functional & Evolutionary Ecology, Center of Functional Ecology, University of Vienna, Vienna, Austria
| | | | - William G Lee
- Manaaki Whenua, Landcare Research, Dunedin, New Zealand
| | - Sergio E Morales
- Department of Microbiology & Immunology, University of Otago, Dunedin, New Zealand
| | - Daniel W Pritchard
- Department of Marine Sciences, University of Otago, Dunedin, New Zealand
- Te Ao Tūroa, Te Rūnanga o Ngāi Tahu, Dunedin, New Zealand
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12
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Yan M, Zeng X, Wang J, Meharg AA, Meharg C, Tang X, Zhang L, Bai L, Zhang J, Su S. Dissolved organic matter differentially influences arsenic methylation and volatilization in paddy soils. JOURNAL OF HAZARDOUS MATERIALS 2020; 388:121795. [PMID: 31818673 DOI: 10.1016/j.jhazmat.2019.121795] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/15/2019] [Accepted: 11/29/2019] [Indexed: 06/10/2023]
Abstract
The effect of dissolved organic matter (DOM), derived from composted pig manure or rice straw, on arsenic methylation and subsequent biovolatilization in paddy soils was investigated. Arsine production following pig manure DOM application was 2.7- and 9.6-fold higher than that of soils treated with rice straw DOM and the control, respectively. Trimethylarsine was the dominant arsine at 54 %, followed by dimethylarsine at 22 %, arsine at 21 %, and monomethylarsine at 3 %. The copy numbers of the total and As-methylating bacteria were significantly enhanced in paddy soils treated with DOM. Pig manure DOM altered soil bacterial profile by increasing the OTU number of As methylation-inducing bacteria, such as Proteobacteria, Bacteroidetes, Geobacter, Sphingomonas, Streptomyces, and Rhodopseudomonas, thereby promoting As volatilization and methylation in paddy soils. The higher relative content of alkyl-C, N-alkyl C, and carboxyl-C in pig manure DOM was responsible for the increase in total and arsM-carrying bacteria in paddy soils, leading to enhanced As methylation. These observations will promote a better understanding of the role of DOM in mediating As methylation and volatilization, along with how organic fertilization affects straighthead disorder of rice, a condition caused by methylated arsenic species.
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Affiliation(s)
- Mengmeng Yan
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Ministry of Agriculture, Beijing, 100081, PR China; School of Geography & Environmental Science, Guizhou Normal University, Guiyang, 550001, Guizhou Province, PR China
| | - Xibai Zeng
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Ministry of Agriculture, Beijing, 100081, PR China
| | - Ji Wang
- School of Geography & Environmental Science, Guizhou Normal University, Guiyang, 550001, Guizhou Province, PR China
| | - Andy A Meharg
- Institute for Global Food Security, Queen's University Belfast, Biological Sciences, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
| | - Caroline Meharg
- Institute for Global Food Security, Queen's University Belfast, Biological Sciences, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
| | - Xianjing Tang
- Institute of Soil and Water Resources and Environmental Science, Zhejiang University, Hangzhou, 310058, PR China
| | - Lili Zhang
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, PR China
| | - Lingyu Bai
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Ministry of Agriculture, Beijing, 100081, PR China
| | - Junzheng Zhang
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, Harbin, 150080, PR China
| | - Shiming Su
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-Environment, Ministry of Agriculture, Beijing, 100081, PR China.
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13
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Sun L, Shi P, He N, Zhang Q, Duan X. Antibiotic resistance genes removal and membrane fouling in secondary effluents by combined processes of PAC/BPAC-UF. JOURNAL OF WATER AND HEALTH 2019; 17:910-920. [PMID: 31850898 DOI: 10.2166/wh.2019.160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Antibiotic resistance genes (ARGs), as emerging environmental contaminants, are becoming a threat to human health. In this study, the combined processes of powdered activated carbon (PAC)/biological PAC (BPAC)-ultrafiltration (UF) were adopted to reduce the levels of ARGs in secondary effluents from a wastewater treatment plant. The removal of dissolved organic carbon (DOC) and the change of normalized flux in the UF process were investigated. In addition, the structural characteristics of the microorganisms of the BPAC were analyzed. The results showed that the appropriate dosage of PAC and BPAC was 40 mg/L. At this dosage, PAC/BPAC-UF combined processes could effectively remove the ARGs in secondary effluents by 1.26-2.69-log and 1.55-2.97-log, respectively; and the removal rates of DOC would be 60.7% and 54.1%, respectively. Relative to the direct UF, the membrane fluxes of the two combined processes were increased by 15.6% and 25.1%, respectively. Significant removal correlations were found between ARGs, intI1, DOC and 16SrDNA. These results revealed that the PAC/BPAC-UF combined process might play a promising role in ARG reduction in secondary effluents from wastewater treatment plants.
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Affiliation(s)
- Lihua Sun
- Key Laboratory of Urban Stormwater System and Water Environment, Ministry of Education, Beijing University of Civil Engineering and Architecture, Beijing 100044, China E-mail:
| | - Pengfei Shi
- School Environment and Energy Engineering, Beijing University of Civil Engineering and Architecture, Beijing 100044, China
| | - Ning He
- Sunac China Holdings Limited, Beijing 100032, China
| | - Qiwei Zhang
- Beijing General Municipal Engineering Design & Research Institute Co., Ltd., Beijing 100082, China
| | - Xi Duan
- Beijing Waterworks Group Co., Ltd., Beijing 100000, China
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14
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Li W, Wang M, Burgaud G, Yu H, Cai L. Fungal Community Composition and Potential Depth-Related Driving Factors Impacting Distribution Pattern and Trophic Modes from Epi- to Abyssopelagic Zones of the Western Pacific Ocean. MICROBIAL ECOLOGY 2019; 78:820-831. [PMID: 30993370 DOI: 10.1007/s00248-019-01374-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/22/2019] [Indexed: 06/09/2023]
Abstract
Fungi play an important role in cycling organic matter and nutrients in marine ecosystems. However, the distribution of fungal communities in the ocean, especially the vertical distribution along depth in the water column, remained poorly understood. Here, we assess the depth-related distribution pattern of fungal communities along the water column from epi- to abyssopelagic zones of the Western Pacific Ocean using internal transcribed spacer 2 (ITS2) metabarcoding. Majority of the assigned OTUs were affiliated to Ascomycota, followed by three other minor phyla (Basidiomycota, Chytridiomycota, and Mucoromycota). The epipelagic zone harbored a higher OTU richness with distinct fungal communities as compared with meso-, bathy-, and abyssopelagic zones. Across the whole water column, depth appears as a key parameter for both fungal α- and β-diversity. However, when the dataset was split into the upper (5-500 m) and deeper (below 500 m) layers, no significant correlation was observed between depth and community compositions. In the upper layer, temperature and dissolved oxygen were recognized as the primary environmental factors shaping fungal α- and β- diversity. By parsing fungal OTUs into ecological categories, multi-trophic mode of nutrition was found to be more prevalent with increasing depth, suggesting a potential adaptation to the extreme conditions of the deep sea. This study provides new and meaningful information on the depth-stratified fungal diversity, community structure, and putative ecological roles in the open sea.
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Affiliation(s)
- Wei Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Mengmeng Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Gaëtan Burgaud
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise, 29280, Plouzané, France
| | - Huaming Yu
- College of Oceanic and Atmospheric Sciences, Ocean University of China, Qingdao, China
- Key Laboratory of Physical Oceanography, MOE, Qingdao, China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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15
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Clifford EL, Varela MM, De Corte D, Bode A, Ortiz V, Herndl GJ, Sintes E. Taurine Is a Major Carbon and Energy Source for Marine Prokaryotes in the North Atlantic Ocean off the Iberian Peninsula. MICROBIAL ECOLOGY 2019; 78:299-312. [PMID: 30666368 PMCID: PMC6647121 DOI: 10.1007/s00248-019-01320-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 01/03/2019] [Indexed: 05/31/2023]
Abstract
Taurine, an amino acid-like compound, acts as an osmostress protectant in many marine metazoans and algae and is released via various processes into the oceanic dissolved organic matter pool. Taurine transporters are widespread among members of the marine prokaryotic community, tentatively indicating that taurine might be an important substrate for prokaryotes in the ocean. In this study, we determined prokaryotic taurine assimilation and respiration throughout the water column along two transects in the North Atlantic off the Iberian Peninsula. Taurine assimilation efficiency decreased from the epipelagic waters from 55 ± 14% to 27 ± 20% in the bathypelagic layers (means of both transects). Members of the ubiquitous alphaproteobacterial SAR11 clade accounted for a large fraction of cells taking up taurine, especially in surface waters. Archaea (Thaumarchaeota + Euryarchaeota) were also able to take up taurine in the upper water column, but to a lower extent than Bacteria. The contribution of taurine assimilation to the heterotrophic prokaryotic carbon biomass production ranged from 21% in the epipelagic layer to 16% in the bathypelagic layer. Hence, we conclude that dissolved free taurine is a significant carbon and energy source for prokaryotes throughout the oceanic water column being utilized with similar efficiencies as dissolved free amino acids.
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Affiliation(s)
- Elisabeth L Clifford
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Marta M Varela
- Instituto Español de Oceanografía (IEO), Centro Oceanográfico de A Coruña, Apdo 130, 15080, A Coruña, Spain
| | - Daniele De Corte
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natushima 2-15, Yokosuka, Kanagawa, 237-0061, Japan
| | - Antonio Bode
- Instituto Español de Oceanografía (IEO), Centro Oceanográfico de A Coruña, Apdo 130, 15080, A Coruña, Spain
| | - Victor Ortiz
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Gerhard J Herndl
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
- Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Microbiology and Biogeochemistry, Utrecht University, PO Box 59, 1790 AB, Den Burg, The Netherlands
| | - Eva Sintes
- Department of Limnology and Bio-Oceanography, Center of Functional Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
- Instituto Español de Oceanografía (IEO), Centro Oceanográfico de Baleares, Moll de Ponent s/n, 07015, Palma de Mallorca, Spain.
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16
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Ávila MP, Brandão LPM, Brighenti LS, Tonetta D, Reis MP, Stæhr PA, Asmala E, Amado AM, Barbosa FAR, Bezerra-Neto JF, Nascimento AMA. Linking shifts in bacterial community with changes in dissolved organic matter pool in a tropical lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 672:990-1003. [PMID: 30981171 DOI: 10.1016/j.scitotenv.2019.04.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/15/2019] [Accepted: 04/02/2019] [Indexed: 06/09/2023]
Abstract
Bacterioplankton communities have a pivotal role in the global carbon cycle. Still the interaction between microbial community and dissolved organic matter (DOM) in freshwater ecosystems remains poorly understood. Here, we report results from a 12-day mesocosm study performed in the epilimnion of a tropical lake, in which inorganic nutrients and allochthonous DOM were supplemented under full light and shading. Although the production of autochthonous DOM triggered by nutrient addition was the dominant driver of changes in bacterial community structure, temporal covariations between DOM optical proxies and bacterial community structure revealed a strong influence of community shifts on DOM fate. Community shifts were coupled to a successional stepwise alteration of the DOM pool, with different fractions being selectively consumed by specific taxa. Typical freshwater clades as Limnohabitans and Sporichthyaceae were associated with consumption of low molecular weight carbon, whereas Gammaproteobacteria and Flavobacteria utilized higher molecular weight carbon, indicating differences in DOM preference among clades. Importantly, Verrucomicrobiaceae were important in the turnover of freshly produced autochthonous DOM, ultimately affecting light availability and dissolved organic carbon concentrations. Our findings suggest that taxonomically defined bacterial assemblages play definite roles when influencing DOM fate, either by changing specific fractions of the DOM pool or by regulating light availability and DOC levels.
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Affiliation(s)
- Marcelo P Ávila
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Luciana P M Brandão
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Ludmila S Brighenti
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Denise Tonetta
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Mariana P Reis
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil.
| | - Peter A Stæhr
- Department of Bioscience, Aarhus University, Frederiksborgvej 399, Box 358, 4000 Roskilde, Denmark
| | - Eero Asmala
- Department of Bioscience, Aarhus University, Frederiksborgvej 399, Box 358, 4000 Roskilde, Denmark; Tvärminne Zoological Station, University of Helsinki, J.A. Palménin tie 260, 10900 Hanko, Finland
| | - André M Amado
- Limnology Laboratory, Department of Oceanography and Limnology, Universidade Federal do Rio Grande do Norte, Rio Grande do Norte, Brazil
| | - Francisco A R Barbosa
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - José F Bezerra-Neto
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Andréa M A Nascimento
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil.
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17
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Hernando-Morales V, Varela MM, Needham DM, Cram J, Fuhrman JA, Teira E. Vertical and Seasonal Patterns Control Bacterioplankton Communities at Two Horizontally Coherent Coastal Upwelling Sites off Galicia (NW Spain). MICROBIAL ECOLOGY 2018; 76:866-884. [PMID: 29675703 DOI: 10.1007/s00248-018-1179-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 03/14/2018] [Indexed: 06/08/2023]
Abstract
Analysis of seasonal patterns of marine bacterial community structure along horizontal and vertical spatial scales can help to predict long-term responses to climate change. Several recent studies have shown predictable seasonal reoccurrence of bacterial assemblages. However, only a few have assessed temporal variability over both horizontal and vertical spatial scales. Here, we simultaneously studied the bacterial community structure at two different locations and depths in shelf waters of a coastal upwelling system during an annual cycle. The most noticeable biogeographic patterns observed were seasonality, horizontal homogeneity, and spatial synchrony in bacterial diversity and community structure related with regional upwelling-downwelling dynamics. Water column mixing eventually disrupted bacterial community structure vertical heterogeneity. Our results are consistent with previous temporal studies of marine bacterioplankton in other temperate regions and also suggest a marked influence of regional factors on the bacterial communities inhabiting this coastal upwelling system. Bacterial-mediated carbon fluxes in this productive region appear to be mainly controlled by community structure dynamics in surface waters, and local environmental factors at the base of the euphotic zone.
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Affiliation(s)
- Víctor Hernando-Morales
- Grupo de Oceanografía Biolóxica, Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, 36310, Vigo, Spain.
- Estación de Ciencias Mariñas de Toralla (ECIMAT), Universidade de Vigo, Illa de Toralla, 36331, Vigo, Spain.
| | - Marta M Varela
- IEO, Instituto Español de Oceanografía, Centro Oceanográfico de A Coruña, Apdo 130, 15080, A Coruña, Spain
| | - David M Needham
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-0371, USA
| | - Jacob Cram
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-0371, USA
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-0371, USA
| | - Eva Teira
- Grupo de Oceanografía Biolóxica, Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, 36310, Vigo, Spain
- Estación de Ciencias Mariñas de Toralla (ECIMAT), Universidade de Vigo, Illa de Toralla, 36331, Vigo, Spain
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18
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Le Moine Bauer S, Stensland A, Daae FL, Sandaa RA, Thorseth IH, Steen IH, Dahle H. Water Masses and Depth Structure Prokaryotic and T4-Like Viral Communities Around Hydrothermal Systems of the Nordic Seas. Front Microbiol 2018; 9:1002. [PMID: 29904373 PMCID: PMC5990851 DOI: 10.3389/fmicb.2018.01002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 04/30/2018] [Indexed: 12/04/2022] Open
Abstract
The oceanographic features of the Nordic Seas, situated between Iceland and Svalbard, have been extensively studied over the last decades. As well, the Nordic Seas hydrothermal systems situated on the Arctic Mid-Ocean Ridge System have received an increasing interest. However, there is very little knowledge on the microbial communities inhabiting the water column of the Nordic Seas, and nothing is known about the influence of the different water masses and hydrothermal plumes on the microbial community structures. In this study, we aimed at characterizing the impact of hydrothermal plumes on prokaryotic and T4-like viral communities around the island of Jan Mayen. To this end, we used 16S rRNA-gene and g23-gene profiling as well as flow cytometry counts to examine prokaryotic and viral communities in 27 samples obtained from different water masses in this area. While Thaumarchaeota and Marine group II Archaea dominated the waters deeper than 500 m, members of Flavobacteria generally dominated the shallower waters. Furthermore, extensive chemical and physical characteristics of all samples were obtained, including temperature measurements and concentrations of major ions and gases. The effect of these physiochemical variables on the communities was measured by using constrained and unconstrained multivariate analyzes, Mantel tests, network analyzes, phylogenetic analyzes, taxonomic analyzes and temperature-salinity (Θ-S) plots. Our results suggest that hydrothermal activity has little effect on pelagic microbial communities in hydrothermal plumes of the Nordic Seas. However, we provide evidences that observed differences in prokaryotic community structure can largely be attributed to which water mass each sample was taken from. In contrast, depth was the major factor structuring the T4-like viral communities. Our results also show that it is crucial to include water masses when studying the influence of hydrothermal plumes on microbial communities, as it could prevent to falsely associate a change in community structure with the presence of a plume.
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Affiliation(s)
- Sven Le Moine Bauer
- Department of Biological Sciences and K.G. Jebsen Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Anne Stensland
- Department of Earth Science and K.G. Jebsen Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Frida L Daae
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Ruth-Anne Sandaa
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Ingunn H Thorseth
- Department of Earth Science and K.G. Jebsen Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Ida H Steen
- Department of Biological Sciences and K.G. Jebsen Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Håkon Dahle
- Department of Biological Sciences and K.G. Jebsen Center for Deep Sea Research, University of Bergen, Bergen, Norway
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19
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Guerrero-Feijóo E, Sintes E, Herndl GJ, Varela MM. High dark inorganic carbon fixation rates by specific microbial groups in the Atlantic off the Galician coast (NW Iberian margin). Environ Microbiol 2017; 20:602-611. [DOI: 10.1111/1462-2920.13984] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 10/30/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Elisa Guerrero-Feijóo
- IEO, Instituto Español de Oceanografía, Centro Oceanográfico de A Coruña, Apdo 130; 15080 A Coruña Spain
| | - Eva Sintes
- Department of Limnology and Bio-Oceanography; University of Vienna, Center of Ecology; Austria
| | - Gerhard J. Herndl
- Department of Limnology and Bio-Oceanography; University of Vienna, Center of Ecology; Austria
- Department of Marine Microbiology and Biogeochemistry; NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, PO Box 59, 1790 AB Den Burg; The Netherlands
| | - Marta M. Varela
- IEO, Instituto Español de Oceanografía, Centro Oceanográfico de A Coruña, Apdo 130; 15080 A Coruña Spain
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