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Zhang P, Zhang H, Li Y, Zhang J, Ma C, Weng N, Gao X, Wu F, Huo S. Strong associations between dissolved organic matter and microbial communities in the sediments of Qinghai-Tibetan Plateau lakes depend on salinity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171857. [PMID: 38521264 DOI: 10.1016/j.scitotenv.2024.171857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/01/2024] [Accepted: 03/19/2024] [Indexed: 03/25/2024]
Abstract
In aquatic ecosystems, dissolved organic matter (DOM) plays a vital role in microbial communities and the biogeochemical cycling of elements. However, little is known about the associations between DOM and microbial communities in lake sediments. This study investigated the composition of water-extractable organic matter and microbial communities in surface sediments of lakes with different salinities on the Qinghai-Tibet Plateau. Ultrahigh-resolution mass spectrometry and high-throughput microbial sequencing techniques were employed to assess the associations between molecular diversity and microbial diversity and the effects of salinity in 19 lakes spanning a salinity range from 0.22 ‰ to 341.87 ‰. Our results show that increasing salinity of lake water led to higher molecular diversity of DOM in surface sediments. High-salinity lakes exhibited distinct DOM characteristics, such as lower aromaticity, smaller molecular weight, and higher oxidation degree, compared to freshwater lakes. The complexity of the microbial network composition of sediments first increased and then decreased with the increase of salinity. Moreover, as salinity increases, the dominant species transitioned from Gammaproteobacteria to Bacteroidia, and this transition was accompanied by a decrease in microbial diversity and an increase in molecular diversity. Microbial factors accounted for 34.68 % of the variation in the molecular composition of DOM. Overall, this study emphasizes the significant effects of salinity on both molecular and microbial diversity in lake sediments. Furthermore, our findings underscore the importance of microbes in controlling the range of organic compounds present in lakes and deepen our knowledge of the biogeochemical cycling of DOM.
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Affiliation(s)
- Peilian Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Hanxiao Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Yi Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Jingtian Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Chunzi Ma
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Nanyan Weng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Xing Gao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Fengchang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Shouliang Huo
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
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Li SA, Wang Q, Ma H, Cao X, Song Y, Cui F, Tanentzap AJ. Photochemical processes transform dissolved organic matter differently depending on its initial composition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171465. [PMID: 38453086 DOI: 10.1016/j.scitotenv.2024.171465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/01/2024] [Accepted: 03/02/2024] [Indexed: 03/09/2024]
Abstract
Dissolved organic matter (DOM) is one of the most important fluxes in the global carbon cycle but its response to light exposure remains unclear at a molecular-level. The chemical response of DOM to light should vary with its molecular composition and environmental conditions while some basic hypotheses are still unclear, such as the balance between photobleaching and photo-humification and the question of oxidative properties. Here we exposed aquatic DOM from diverse freshwaters impacted by different levels of anthropogenic activity and algal exudates to environmentally-realistic light conditions. We found that photobleaching occurred in DOM with relatively high initial humic content producing low H/C molecules, whereas DOM with low initial humic content was humified. DOM pools with relatively high initial saturation and low aromaticity were prone to transform towards more unsaturated molecular formulae and high H/C molecules with a distinct decrease of bioavailability. Photo-transformation was mainly influenced by reactive intermediates, with reactive oxygen species (ROS) playing a dominant role in humification when the initial humus content of DOM was high. In contrast, for algal DOM with high protein content, it was likely that the autoxidation of excited state DOM was more important than indirect oxidation involving ROS. Our results reveal how photo-transformation patterns depend on the initial composition of DOM and provide new insights into the role of photochemical processes in biogeochemical cycling of DOM.
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Affiliation(s)
- Sheng-Ao Li
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Qianru Wang
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Hua Ma
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China.
| | - Xinghong Cao
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Yingyue Song
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Fuyi Cui
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Andrew J Tanentzap
- Ecosystems and Global Change Group, School of the Environment, Trent University, Peterborough, Ontario K9L 0G2, Canada
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Takebe H, Tominaga K, Isozaki T, Watanabe T, Yamamoto K, Kamikawa R, Yoshida T. Taxonomic difference in marine bloom-forming phytoplanktonic species affects the dynamics of both bloom-responding prokaryotes and prokaryotic viruses. mSystems 2024; 9:e0094923. [PMID: 38441030 PMCID: PMC11019789 DOI: 10.1128/msystems.00949-23] [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: 09/05/2023] [Accepted: 02/13/2024] [Indexed: 03/06/2024] Open
Abstract
The production of dissolved organic matter during phytoplankton blooms and consumption by heterotrophic prokaryotes promote marine carbon biogeochemical cycling. Although prokaryotic viruses presumably affect this process, their dynamics during blooms are not fully understood. Here, we investigated the effects of taxonomic difference in bloom-forming phytoplankton on prokaryotes and their viruses. We analyzed the dynamics of coastal prokaryotic communities and viruses under the addition of dissolved intracellular fractions from taxonomically distinct phytoplankton, the diatom Chaetoceros sp. (CIF) and the raphidophycean alga Heterosigma akashiwo (HIF), using microcosm experiments. Ribosomal RNA gene amplicon and viral metagenomic analyses revealed that particular prokaryotes and prokaryotic viruses specifically increased in either CIF or HIF, indicating that taxonomic difference in bloom-forming phytoplankton promotes distinct dynamics of not only the prokaryotic community but also prokaryotic viruses. Furthermore, combining our microcosm experiments with publicly available environmental data mining, we identified both known and novel possible host-virus pairs. In particular, the growth of prokaryotes associating with phytoplanktonic organic matter, such as Bacteroidetes (Polaribacter and NS9 marine group), Vibrio spp., and Rhodobacteriales (Nereida and Planktomarina), was accompanied by an increase in viruses predicted to infect Bacteroidetes, Vibrio, and Rhodobacteriales, respectively. Collectively, our findings suggest that changes in bloom-forming species can be followed by an increase in a specific group of prokaryotes and their viruses and that elucidating these tripartite relationships among specific phytoplankton, prokaryotes, and prokaryotic viruses improves our understanding of coastal biogeochemical cycling in blooms.IMPORTANCEThe primary production during marine phytoplankton bloom and the consumption of the produced organic matter by heterotrophic prokaryotes significantly contribute to coastal biogeochemical cycles. While the activities of those heterotrophic prokaryotes are presumably affected by viral infection, the dynamics of their viruses during blooms are not fully understood. In this study, we experimentally demonstrated that intracellular fractions of taxonomically distinct bloom-forming phytoplankton species, the diatom Chaetoceros sp. and the raphidophycean alga Heterosigma akashiwo, promoted the growth of taxonomically different prokaryotes and prokaryotic viruses. Based on their dynamics and predicted hosts of those viruses, we succeeded in detecting already-known and novel possible host-virus pairs associating with either phytoplankton species. Altogether, we propose that the succession of bloom-forming phytoplankton would change the composition of the abundant prokaryotes, resulting in an increase in their viruses. These changes in viral composition, depending on bloom-forming species, would alter the dynamics and metabolism of prokaryotes, affecting biogeochemical cycling in blooms.
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Affiliation(s)
- Hiroaki Takebe
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kento Tominaga
- Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | | | | | - Keigo Yamamoto
- Research Institute of Environment, Agriculture and Fisheries, Osaka Prefecture, Osaka, Japan
| | - Ryoma Kamikawa
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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Huang H, Zan S, Shao K, Chen H, Fan J. Spatial distribution characteristics and interaction effects of DOM and microbial communities in kelp cultivation areas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 920:170511. [PMID: 38309352 DOI: 10.1016/j.scitotenv.2024.170511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/17/2024] [Accepted: 01/26/2024] [Indexed: 02/05/2024]
Abstract
The influence of macroalgae cultivation on aquaculture carbon sinks is significant, with microbial carbon (C) pumps contributing to a stable inert dissolved carbon pool in this context. Concurrently, dissolved organic matter (DOM) exchange at the marine sediment-water interface profoundly affects global ecosystem element cycling. However, the interactions between DOM and bacterial communities at the sediment-water interface in kelp cultivation areas, especially regarding microbial function prediction, have not been fully explored. This study analyzed the DOM characteristics, environmental factors, and bacterial community structure in the Tahewan kelp--Saccharina japonica cultivated area and compared them with those in non-cultivated areas. The results indicated significantly higher dissolved organic carbon (DOC) concentrations in the kelp culture area, particularly in surface seawater and overlying water. The dominant bacterial phyla in both regions included Pseudomonadota, Actinomycetota, and Bacteroidota in both regions, while Desulfobacterota was more prevalent in the sediment environment of the cultivated region. Parallel factor analysis (EEM-PARAFAC) was used to identify DOM components, among which component C2 (a microbial humic-like substance DOM) was highly resistant to microbial degradation. We infer that C2 has similar properties to recalcitrant dissolved organic matter (RDOM). Analysis of the predicted functional genes based on 16S rRNA gene data showed that methanol oxidation, methylotrophy, and methanotrophy were significant in the bottom seawater of the cultivation area. The carbon (C), nitrogen (N), and sulfur (S) cycle functional genes in the sediment environment of the kelp cultivation area were more active than those in other areas, especially in which sulfate reduction and denitrification were the two main processes. Furthermore, a DOM priming effect was identified in the cultivated sediment environment, where kelp-released labile dissolved organic matter (LDOM) stimulates rapid degradation of the original RDOM, potentially enhancing C sequestration.
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Affiliation(s)
- Huiling Huang
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, China; State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, China
| | - Shuaijun Zan
- Groundwater Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Kuishuang Shao
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, China
| | - Hanjun Chen
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, China; College of Marine Technology and Environment, Dalian Ocean University, Dalian, China
| | - Jingfeng Fan
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, China; State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, China; College of Marine Technology and Environment, Dalian Ocean University, Dalian, China.
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Lv L, Huang H, Lv J, Xu X, Cao D, Rao Z, Geng F, Kang Y. Unique dissolved organic matter molecules and microbial communities in rhizosphere of three typical crop soils and their significant associations based on FT-ICR-MS and high-throughput sequencing analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170904. [PMID: 38354799 DOI: 10.1016/j.scitotenv.2024.170904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/16/2024]
Abstract
Using cucumber, maize, and ryegrass as model plants, the diversity and uniqueness of the molecular compositions of dissolved organic matter (DOM) and the structures of microbial communities in typical crop rhizosphere soils, as well as their associations, were investigated based on high-resolution mass spectrometry combined with high-throughput sequencing. The results showed that the rhizosphere contained 2200 organic molecules that were not identified in the non-rhizosphere soils, as characterized by FT-ICR-MS. The rhizosphere DOM molecules generally contained more N, S, and P heteroatoms, stronger hydrophilicity, and more refractory organic matter, representing high and complex chemical diversity characteristics. 16SrRNA sequencing results demonstrated that Proteobacteria, Actinomycetes and Firmicutes were the dominant flora in the soils. Plant species could significantly change the composition and relative abundance of rhizosphere microbial populations. The microbial community structures of rhizosphere and non-rhizosphere soils showed significant differences at both the phylum and class levels. Multiple interactions between the microorganisms and DOM compositions formed a complex network of relationships. There were strong and remarkable positive or negative couplings between different sizes and categories of DOM molecules and the specific microbial groups (P < 0.05, |R| ≥ 0.9) in the rhizosphere soils as shown by network profiles. The correlations between DOM molecules and microbial groups in rhizosphere soils had plant species specificity. The results above emphasized the relationship between the heterogeneity of DOM and the diversity of microbial communities, and explored the molecular mechanisms of the biochemical associations in typical plant rhizosphere soils, providing a foundation for in-depth understanding of plant-soil-microbe interactions.
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Affiliation(s)
- Lili Lv
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P. O. Box 2871, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China; LMIB and School of Mathematical Sciences, Beihang University, Beijing 100191, China
| | - Honglin Huang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P. O. Box 2871, Beijing 100085, China.
| | - Jitao Lv
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P. O. Box 2871, Beijing 100085, China
| | - Xuehui Xu
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Inner Mongolia Key Laboratory of Soil Quality and Nutrient Resource, Hohhot 010018, China
| | - Dong Cao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P. O. Box 2871, Beijing 100085, China
| | - Ziyu Rao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P. O. Box 2871, Beijing 100085, China
| | - Fanglan Geng
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P. O. Box 2871, Beijing 100085, China
| | - Yuehui Kang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, P. O. Box 2871, Beijing 100085, China
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Wu Q, Yu C, Liu Y, Xing P, Li H, Li B, Wan S, Wu QL. Microcystis blooms caused the decreasing richness of and interactions between free-living microbial functional genes in Lake Taihu, China. FEMS Microbiol Ecol 2024; 100:fiad166. [PMID: 38148131 PMCID: PMC10795575 DOI: 10.1093/femsec/fiad166] [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: 07/07/2023] [Revised: 11/17/2023] [Accepted: 12/23/2023] [Indexed: 12/28/2023] Open
Abstract
Microcystis blooms have a marked effect on microbial taxonomical diversity in eutrophic lakes, but their influence on the composition of microbial functional genes is still unclear. In this study, the free-living microbial functional genes (FMFG) composition was investigated in the period before Microcystis blooms (March) and during Microcystis blooms (July) using a comprehensive functional gene array (GeoChip 5.0). The composition and richness of FMFG in the water column was significantly different between these two periods. The FMFG in March was enriched in the functional categories of nitrogen, sulfur, and phosphorus cycling, whereas the FMFG in July was enriched in carbon cycling, organic remediation, and metal homeostasis. Molecular ecological network analysis further demonstrated fewer functional gene interactions and reduced complexity in July than in March. Module hubs of the March network were mediated by functional genes associated with carbon, nitrogen, sulfur, and phosphorus, whereas those in July by a metal homeostasis functional gene. We also observed stronger deterministic processes in the FMFG assembly in July than in March. Collectively, this study demonstrated that Microcystis blooms induced significant changes in FMFG composition and metabolic potential, and abundance-information, which can support the understanding and management of biogeochemical cycling in eutrophic lake ecosystems.
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Affiliation(s)
- Qiong Wu
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Chunyan Yu
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yanru Liu
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Huabing Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
- The Fuxianhu Station of Deep Lake Research, Chinese Academy of Sciences, Chengjiang 652500, China
| | - Biao Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Shiqiang Wan
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei 071002, China
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
- Center for Evolution and Conservation Biology, Southern Marine Sciences and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Sino Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing 100049, China
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Bouchachi N, Obernosterer I, Carpaneto Bastos C, Li F, Scenna L, Marie B, Crispi O, Catala P, Ortega-Retuerta E. Effects of Phosphorus Limitation on the Bioavailability of DOM Released by Marine Heterotrophic Prokaryotes. MICROBIAL ECOLOGY 2023; 86:1961-1971. [PMID: 36912945 DOI: 10.1007/s00248-023-02201-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Heterotrophic prokaryotes (HP) contribute largely to dissolved organic matter (DOM) processing in the ocean, but they also release diverse organic substances. The bioavailability of DOM released by HP under varying environmental conditions has not been fully elucidated. In this study, we investigated the bioavailability of DOM released by a single bacterial strain (Sphingopyxis alaskensis) and 2 natural HP communities grown under P-replete and P-limited conditions. The released DOM (HP-DOM) was used as a substrate for natural HP communities at a coastal site in the Northwestern Mediterranean Sea. We followed changes in HP growth, enzymatic activity, diversity, and community composition together with the consumption of HP-DOM fluorescence (FDOM). HP-DOM produced under P-replete and P-limited conditions promoted significant growth in all incubations. No clear differences in HP-DOM lability released under P-repletion and P-limitation were evidenced based on the HP growth, and P-limitation was not demonstrated to decrease HP-DOM lability. However, HP-DOM supported the growth of diverse HP communities, and P-driven differences in HP-DOM quality were selected for different indicator taxa in the degrading communities. The humic-like fluorescence, commonly considered recalcitrant, was consumed during the incubations when this peak was initially dominating the FDOM pool, and this consumption coincided with higher alkaline phosphatase activity. Taken together, our findings emphasize that HP-DOM lability is dependent on both DOM quality, which is shaped by P availability, and the composition of the consumer community.
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Affiliation(s)
- Nawal Bouchachi
- CNRS/Sorbonne Université, UMR7621 Laboratoire d'Océanographie Microbienne, Banyuls sur Mer, France.
| | - Ingrid Obernosterer
- CNRS/Sorbonne Université, UMR7621 Laboratoire d'Océanographie Microbienne, Banyuls sur Mer, France
| | - Cécile Carpaneto Bastos
- CNRS/Sorbonne Université, UMR7621 Laboratoire d'Océanographie Microbienne, Banyuls sur Mer, France
| | - Franck Li
- CNRS/Sorbonne Université, UMR7621 Laboratoire d'Océanographie Microbienne, Banyuls sur Mer, France
| | - Lorenzo Scenna
- CNRS/Sorbonne Université, UMR7621 Laboratoire d'Océanographie Microbienne, Banyuls sur Mer, France
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Barbara Marie
- CNRS/Sorbonne Université, UMR7621 Laboratoire d'Océanographie Microbienne, Banyuls sur Mer, France
| | - Olivier Crispi
- CNRS/Sorbonne Université, UMR7621 Laboratoire d'Océanographie Microbienne, Banyuls sur Mer, France
| | - Philippe Catala
- CNRS/Sorbonne Université, UMR7621 Laboratoire d'Océanographie Microbienne, Banyuls sur Mer, France
| | - Eva Ortega-Retuerta
- CNRS/Sorbonne Université, UMR7621 Laboratoire d'Océanographie Microbienne, Banyuls sur Mer, France.
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Eigemann F, Rahav E, Grossart HP, Aharonovich D, Voss M, Sher D. Phytoplankton Producer Species and Transformation of Released Compounds over Time Define Bacterial Communities following Phytoplankton Dissolved Organic Matter Pulses. Appl Environ Microbiol 2023; 89:e0053923. [PMID: 37409944 PMCID: PMC10370336 DOI: 10.1128/aem.00539-23] [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: 03/31/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023] Open
Abstract
Phytoplankton-bacterium interactions are mediated, in part, by phytoplankton-released dissolved organic matter (DOMp). Two factors that shape the bacterial community accompanying phytoplankton are (i) the phytoplankton producer species, defining the initial composition of released DOMp, and (ii) the DOMp transformation over time. We added phytoplankton DOMp from the diatom Skeletonema marinoi and the cyanobacterium Prochlorococcus marinus MIT9312 to natural bacterial communities from the eastern Mediterranean and determined the bacterial responses over a time course of 72 h in terms of cell numbers, bacterial production, alkaline phosphatase activity, and changes in active bacterial community composition based on rRNA amplicon sequencing. Both DOMp types were demonstrated to serve the bacterial community as carbon and, potentially, phosphorus sources. Bacterial communities in diatom-derived DOM treatments maintained higher Shannon diversities throughout the experiment and yielded higher bacterial production and lower alkaline phosphatase activity compared to cyanobacterium-derived DOM after 24 h of incubation (but not after 48 and 72 h), indicating greater bacterial usability of diatom-derived DOM. Bacterial communities significantly differed between DOMp types as well as between different incubation times, pointing to a certain bacterial specificity for the DOMp producer as well as a successive utilization of phytoplankton DOM by different bacterial taxa over time. The highest differences in bacterial community composition with DOMp types occurred shortly after DOMp additions, suggesting a high specificity toward highly bioavailable DOMp compounds. We conclude that phytoplankton-associated bacterial communities are strongly shaped by the phytoplankton producer as well as the transformation of its released DOMp over time. IMPORTANCE Phytoplankton-bacterium interactions influence biogeochemical cycles of global importance. Phytoplankton photosynthetically fix carbon dioxide and subsequently release the synthesized compounds as dissolved organic matter (DOMp), which becomes processed and recycled by heterotrophic bacteria. Yet the importance of phytoplankton producers in combination with the time-dependent transformation of DOMp compounds on the accompanying bacterial community has not been explored in detail. The diatom Skeletonema marinoi and the cyanobacterium Prochlorococcus marinus MIT9312 belong to globally important phytoplankton genera, and our study revealed that DOMp of both species was selectively incorporated by the bacterial community. The producer species had the highest impact shortly after DOMp appropriation, and its effect diminished over time. Our results improve the understanding of the dynamics of organic matter produced by phytoplankton in the oceans as it is utilized and modified by cooccurring bacteria.
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Affiliation(s)
- Falk Eigemann
- Water Quality Engineering, Technical University of Berlin, Berlin, Germany
- Leibniz-Institute for Baltic Sea Research, Warnemuende, Germany
| | - Eyal Rahav
- Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Hans-Peter Grossart
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
- Potsdam University, Potsdam, Germany
| | | | - Maren Voss
- Leibniz-Institute for Baltic Sea Research, Warnemuende, Germany
| | - Daniel Sher
- Leon H. Charney School of Marine Sciences, University Haifa, Israel
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Louati I, Nunan N, Tambosco K, Bernard C, Humbert JF, Leloup J. The phyto-bacterioplankton couple in a shallow freshwater ecosystem: Who leads the dance? HARMFUL ALGAE 2023; 126:102436. [PMID: 37290884 DOI: 10.1016/j.hal.2023.102436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 04/20/2023] [Accepted: 04/20/2023] [Indexed: 06/10/2023]
Abstract
Bloom-forming phytoplankton dynamics are still unpredictable, even though it is known that several abiotic factors, such as nutrient availability and temperature, are key factors for bloom development. We investigated whether biotic factors, i.e. the bacterioplankton composition (via 16SrDNA metabarcoding), were correlated with phytoplankton dynamics, through a weekly monitoring of a shallow lake known to host recurrent cyanobacterial blooms. We detected concomitant changes in both bacterial and phytoplankton community biomass and diversity. During the bloom event, a significant decrease in phytoplankton diversity, was detected, with a first co-dominance of Ceratium, Microcystis and Aphanizomenon, followed by a co-dominance of the two cyanobacterial genera. In the same time, we observed a decrease of the particle-associated (PA) bacterial richness and the emergence of a specific bacterial consortium that was potentially better adapted to the new nutritional niche. Unexpectedly, changes in PA bacterial communities occurred just before the development the emergence of the phytoplanktonic bloom and the associated modification of the phytoplanktonic community composition, suggesting that changes in environmental conditions leading to the bloom, were first sensed by the bacterial PA community. This last was quite stable throughout the bloom event, even though there were changes in the blooming species, suggesting that the association between cyanobacterial species and bacterial communities may not be as tight as previously described for monospecific blooming communities. Finally, the dynamics of the free-living (FL) bacterial communities displayed a different trajectory from those of the PA and phytoplankton communities. This FL communities can be viewed as a reservoir for bacterial recruitment for the PA fraction. Altogether, these data also highlight s that the spatial organization within these different microenvironments in the water column is a relevant factor in the structuring of these communities.
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Affiliation(s)
- Imen Louati
- Sorbonne Université, UMR 7618 CNRS-INRA- RD-Paris Cité-UPEC, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), 4 place Jussieu, Paris cedex 05 75252, France
| | - Naoise Nunan
- Sorbonne Université, UMR 7618 CNRS-INRA- RD-Paris Cité-UPEC, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), 4 place Jussieu, Paris cedex 05 75252, France; Department of Soil and Environment, Swedish University of Agricultural Sciences, P.O. Box 7014, Uppsala 75007, Sweden
| | - Kevin Tambosco
- Sorbonne Université, UMR 7618 CNRS-INRA- RD-Paris Cité-UPEC, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), 4 place Jussieu, Paris cedex 05 75252, France
| | - Cécile Bernard
- Muséum National d'Histoire Naturelle, UMR 7245 CNRS-MNHN, Molécules de Communication et Adaptation des Microorganismes, Paris, France
| | - Jean-François Humbert
- Sorbonne Université, UMR 7618 CNRS-INRA- RD-Paris Cité-UPEC, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), 4 place Jussieu, Paris cedex 05 75252, France
| | - Julie Leloup
- Sorbonne Université, UMR 7618 CNRS-INRA- RD-Paris Cité-UPEC, Institut d'Ecologie et des Sciences de l'Environnement de Paris (iEES-Paris), 4 place Jussieu, Paris cedex 05 75252, France.
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10
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Cheng Y, Jiao L, Cheng Q, He J, Zhang Y, Ding S. The evolution of a typical plateau lake from macrophyte to algae leads to the imbalance of nutrient retention. WATER RESEARCH 2023; 236:119937. [PMID: 37054612 DOI: 10.1016/j.watres.2023.119937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/31/2023] [Accepted: 04/02/2023] [Indexed: 06/19/2023]
Abstract
Long-term anthropogenic nitrogen (N) and phosphorus (P) inputs have led to lake eutrophication and decreased environmental quality. However, the imbalance in nutrient cycling caused by ecosystem transformation during lake eutrophication is still unclear. The N, P, organic matter (OM) and their extractable forms in the sediment core of Dianchi Lake were investigated. Combining ecological data and geochronological techniques, a coupling relationship between the evolution of lake ecosystems and nutrient retention was established. The results show that the evolution of lake ecosystems promotes the accumulation and mobilization of N and P in sediments, leading to an imbalance in nutrient cycling in the lake system. From the "macrophyte-dominated" period to the "algae-dominated" period, the accumulation rates of potential mobile N and P (PMN, PMP) in sediments have significantly increased, and the retention efficiency of total N and P (TN, TP) has decreased. The increased TN/TP ratio (5.38 ± 1.52 ‒ 10.19 ± 2.94) and PMN/PMP ratio (4.34 ± 0.41 ‒ 8.85 ± 4.16), as well as the reduced humic-like/protein-like ratio (H/P, 11.18 ± 4.43 ‒ 5.97 ± 3.67), indicated an imbalance in nutrient retention during sedimentary diagenesis. Our results show that eutrophication has resulted in the potential mobilization of N in sediments exceeding P, providing new insights for further understanding the nutrient cycle in the lake system and strengthening lake management.
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Affiliation(s)
- Yunxuan Cheng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Institute of Water Environment Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Lixin Jiao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Institute of Water Environment Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Qinglin Cheng
- School of Chemical and Environmental Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Jia He
- Kunming Institute of Eco-Environmental Sciences, Kunming, Yunnan 650032, China
| | - Yue Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Institute of Water Environment Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Shuai Ding
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Institute of Water Environment Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
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11
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Behera S, Tanuku NRS, Moturi SRK, Loganathan J, Modali S, Tadi SR, Rachuri V. Huge anthropogenic microbial load during southwest monsoon season in coastal waters of Kakinada, Bay of Bengal. MARINE POLLUTION BULLETIN 2023; 192:114977. [PMID: 37167663 DOI: 10.1016/j.marpolbul.2023.114977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 04/16/2023] [Accepted: 04/19/2023] [Indexed: 05/13/2023]
Abstract
To examine the influence of anthropogenic activities on the marine ecosystem near the coastal waters of the port city, Kakinada, a study was conducted to investigate the abundance of heterotrophic, indicator and pathogenic bacteria during the spring inter monsoon (SIM) and southwest monsoon (SWM) seasons. A drastic change in the marine bacteria due to the input of allochthonous bacteria during SWM was noticed. An order of magnitude higher abundance of indicators (Escherichia coli and Enterococcus faecalis) and bacterial pathogens (Proteus mirabilis and Pseudomonas aeruginosa) was observed during SWM. In contrast, Chlorophyll-a, heterotrophic bacterial abundance, Aeromonas hydrophila and Klebsiella pneumoniae were higher during SIM. A significant increase in some of the indicator and pathogenic bacterial abundance due to moderate rainfall suggests that the improper drainage system in the city could spread these bacteria, posing a considerable threat to both environment and human health.
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Affiliation(s)
- Swarnaprava Behera
- CSIR-National Institute of Oceanography, Regional Centre, 176, Lawson's Bay Colony, Visakhapatnam 530017, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Naga Radha Srinivas Tanuku
- CSIR-National Institute of Oceanography, Regional Centre, 176, Lawson's Bay Colony, Visakhapatnam 530017, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| | - Sri Rama Krishna Moturi
- CSIR-National Institute of Oceanography, Regional Centre, 176, Lawson's Bay Colony, Visakhapatnam 530017, India
| | - Jagadeesan Loganathan
- CSIR-National Institute of Oceanography, Regional Centre, 176, Lawson's Bay Colony, Visakhapatnam 530017, India
| | - Sravani Modali
- CSIR-National Institute of Oceanography, Regional Centre, 176, Lawson's Bay Colony, Visakhapatnam 530017, India
| | - Satyanarayana Reddy Tadi
- CSIR-National Institute of Oceanography, Regional Centre, 176, Lawson's Bay Colony, Visakhapatnam 530017, India
| | - Vivek Rachuri
- CSIR-National Institute of Oceanography, Regional Centre, 176, Lawson's Bay Colony, Visakhapatnam 530017, India
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12
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Dithugoe CD, Bezuidt OKI, Cavan EL, Froneman WP, Thomalla SJ, Makhalanyane TP. Bacteria and Archaea Regulate Particulate Organic Matter Export in Suspended and Sinking Marine Particle Fractions. mSphere 2023:e0042022. [PMID: 37093039 DOI: 10.1128/msphere.00420-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
The biological carbon pump (BCP) in the Southern Ocean is driven by phytoplankton productivity and is a significant organic matter sink. However, the role of particle-attached (PA) and free-living (FL) prokaryotes (bacteria and archaea) and their diversity in influencing the efficiency of the BCP is still unclear. To investigate this, we analyzed the metagenomes linked to suspended and sinking marine particles from the Sub-Antarctic Southern Ocean Time Series (SOTS) by deploying a Marine Snow Catcher (MSC), obtaining suspended and sinking particulate material, determining organic carbon and nitrogen flux, and constructing metagenome-assembled genomes (MAGs). The suspended and sinking particle-pools were dominated by bacteria with the potential to degrade organic carbon. Bacterial communities associated with the sinking fraction had more genes related to the degradation of complex organic carbon than those in the suspended fraction. Archaea had the potential to drive nitrogen metabolism via nitrite and ammonia oxidation, altering organic nitrogen concentration. The data revealed several pathways for chemoautotrophy and the secretion of recalcitrant dissolved organic carbon (RDOC) from CO2, with bacteria and archaea potentially sequestering particulate organic matter (POM) via the production of RDOC. These findings provide insights into the diversity and function of prokaryotes in suspended and sinking particles and their role in organic carbon/nitrogen export in the Southern Ocean. IMPORTANCE The biological carbon pump is crucial for the export of particulate organic matter in the ocean. Recent studies on marine microbes have shown the profound influence of bacteria and archaea as regulators of particulate organic matter export. Yet, despite the importance of the Southern Ocean as a carbon sink, we lack comparable insights regarding microbial contributions. This study provides the first insights regarding prokaryotic contributions to particulate organic matter export in the Southern Ocean. We reveal evidence that prokaryotic communities in suspended and sinking particle fractions harbor widespread genomic potential for mediating particulate organic matter export. The results substantially enhance our understanding of the role played by microorganisms in regulating particulate organic matter export in suspended and sinking marine fractions in the Southern Ocean.
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Affiliation(s)
- Choaro D Dithugoe
- Southern Ocean Carbon-Climate Observatory (SOCCO), Council of Scientific & Industrial Research (CSIR), Rosebank, Cape Town, South Africa
- SARChI Chair: Marine Ecosystems and Resources, Department of Entomology & Zoology, Rhodes University (RU), Makhanda, Eastern Cape, South Africa
- SARChI Chair: Marine Microbiomics, microbiome@UP, Department of Biochemistry, Genetics and Microbiology, University of Pretoria (UP), Hatfield, Pretoria, South Africa
| | - Oliver K I Bezuidt
- SARChI Chair: Marine Microbiomics, microbiome@UP, Department of Biochemistry, Genetics and Microbiology, University of Pretoria (UP), Hatfield, Pretoria, South Africa
| | - Emma L Cavan
- Imperial College London, Berks, Silwood Park, Berkshire, United Kingdom
| | - William P Froneman
- SARChI Chair: Marine Ecosystems and Resources, Department of Entomology & Zoology, Rhodes University (RU), Makhanda, Eastern Cape, South Africa
| | - Sandy J Thomalla
- Southern Ocean Carbon-Climate Observatory (SOCCO), Council of Scientific & Industrial Research (CSIR), Rosebank, Cape Town, South Africa
| | - Thulani P Makhalanyane
- SARChI Chair: Marine Microbiomics, microbiome@UP, Department of Biochemistry, Genetics and Microbiology, University of Pretoria (UP), Hatfield, Pretoria, South Africa
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13
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Pushpakumara BLDU, Tandon K, Willis A, Verbruggen H. Unravelling microalgal-bacterial interactions in aquatic ecosystems through 16S rRNA gene-based co-occurrence networks. Sci Rep 2023; 13:2743. [PMID: 36797257 PMCID: PMC9935533 DOI: 10.1038/s41598-023-27816-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/09/2023] [Indexed: 02/18/2023] Open
Abstract
Interactions between microalgae and bacteria can directly influence the global biogeochemical cycles but the majority of such interactions remain unknown. 16S rRNA gene-based co-occurrence networks have potential to help identify microalgal-bacterial interactions. Here, we used data from 10 Earth microbiome projects to identify potential microalgal-bacterial associations in aquatic ecosystems. A high degree of clustering was observed in microalgal-bacterial modules, indicating densely connected neighbourhoods. Proteobacteria and Bacteroidetes predominantly co-occurred with microalgae and represented hubs of most modules. Our results also indicated that species-specificity may be a global characteristic of microalgal associated microbiomes. Several previously known associations were recovered from our network modules, validating that biologically meaningful results can be inferred using this approach. A range of previously unknown associations were recognised such as co-occurrences of Bacillariophyta with uncultured Planctomycetes OM190 and Deltaproteobacteria order NB1-j. Planctomycetes and Verrucomicrobia were identified as key associates of microalgae due to their frequent co-occurrences with several microalgal taxa. Despite no clear taxonomic pattern, bacterial associates appeared functionally similar across different environments. To summarise, we demonstrated the potential of 16S rRNA gene-based co-occurrence networks as a hypothesis-generating framework to guide more focused research on microalgal-bacterial associations.
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Affiliation(s)
| | - Kshitij Tandon
- School of Biosciences, University of Melbourne, Melbourne, VIC, Australia
| | - Anusuya Willis
- Australian National Algae Culture Collection, CSIRO, Hobart, TAS, 7000, Australia
| | - Heroen Verbruggen
- School of Biosciences, University of Melbourne, Melbourne, VIC, Australia.
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14
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Jia Y, Lahm M, Chen Q, Powers L, Gonsior M, Chen F. The Predominance of Ammonia-Oxidizing Archaea in an Oceanic Microbial Community Amended with Cyanobacterial Lysate. Microbiol Spectr 2023; 11:e0240522. [PMID: 36622233 PMCID: PMC9927567 DOI: 10.1128/spectrum.02405-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
When the oligotrophic microbial community was amended with Synechococcus-derived dissolved organic matter (SDOM) and incubated under the dark condition, archaea relative abundance was initially very low but made up more than 60% of the prokaryotic community on day 60, and remained dominant for at least 9 months. The archaeal sequences were dominated by Candidatus Nitrosopumilus, the Group I.1a Thaumarchaeota. The increase of Thaumarchaeota in the dark incubation corresponded to the period of delayed ammonium oxidation upon an initially steady increase in ammonia, supporting the remarkable competency of Thaumarchaeota in energy utilization and fixation of inorganic carbon in the ocean. IMPORTANCE Thaumarchaeota, which are ammonia-oxidizing archaea (AOA), are mainly chemolithoautotrophs that can fix inorganic carbon to produce organic matter in the dark. Their distinctive physiological traits and high abundance in the water column indicate the significant ecological roles they play in the open ocean. In our study, we found predominant Thaumarchaeota in the microbial community amended with cyanobacteria-derived lysate under the dark condition. Furthermore, Thaumarchaeota remained dominant in the microbial community even after 1 year of incubation. Through the ammonification process, dissolved organic matter (DOM) from cyanobacterial lysate was converted to ammonium which was used as an energy source for Thaumarchaeota to fix inorganic carbon into biomass. Our study further advocates the important roles of Thaumarchaeota in the ocean's biogeochemical cycle.
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Affiliation(s)
- Yufeng Jia
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
| | - Madeline Lahm
- Chesapeake Biological Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
| | - Qi Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Leanne Powers
- Chesapeake Biological Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
- State University of New York College of Environmental Science and Forestry, Department of Chemistry, Syracuse, New York, USA
| | - Michael Gonsior
- Chesapeake Biological Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
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15
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Liu C, Liao K, Wang J, Wu B, Hu H, Ren H. Microbial Transformation of Dissolved Organic Sulfur during the Oxic Process in 47 Full-Scale Municipal Wastewater Treatment Plants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:2118-2128. [PMID: 36608328 DOI: 10.1021/acs.est.2c06776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Dissolved organic sulfur (DOS) is a significant part of effluent organic matter of wastewater treatment plants (WWTPs) and poses a potential ecological risk for receiving waters. However, the oxic process is a critical unit of biological wastewater treatment for microorganisms performing organic matter removal, wherein DOS transformation and its mechanism are poorly understood. This study investigated the transformation of DOS during the oxic process in 47 full-scale municipal WWTPs across China from molecular and microbial aspects. Surprisingly, evident differences in DOS variations (ΔDOS) separated sampled WWTPs into two groups: 28 WWTPs with decreased DOS concentrations in effluents (ΔDOS < 0) and 19 WWTPs with increased DOS (ΔDOS > 0). These two groups also presented differences in DOS molecular characteristics: higher nitrogen/carbon (N/C) ratios (0.030) and more peptide-like DOS (8.2%) occurred in WWTPs with ΔDOS > 0, implying that peptide-like DOS generated from microbes contributed to increased DOS in effluents. Specific microbe-DOS correlations (Spearman correlation, p < 0.05) indicated that increased effluent DOS might be explained by peptide-like DOS preferentially being produced during copiotrophic bacterial growth and accumulating due to less active cofactor metabolisms. Considering the potential environmental issues accompanying DOS discharge from WWTPs with ΔDOS > 0, our study highlights the importance of focusing on the transformation and control of DOS in the oxic process.
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Affiliation(s)
- Caifeng Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Kewei Liao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Jinfeng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Bing Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Haidong Hu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
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16
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Xia F, Liu Z, Zhao M, Li Q, Li D, Cao W, Zeng C, Hu Y, Chen B, Bao Q, Zhang Y, He Q, Lai C, He X, Ma Z, Han Y, He H. High stability of autochthonous dissolved organic matter in karst aquatic ecosystems: Evidence from fluorescence. WATER RESEARCH 2022; 220:118723. [PMID: 35696806 DOI: 10.1016/j.watres.2022.118723] [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: 03/01/2022] [Revised: 05/20/2022] [Accepted: 06/06/2022] [Indexed: 05/26/2023]
Abstract
Biological carbon pump (BCP) in karst areas has received intensive attention for years due to their significant contribution to the global missing carbon sink. The stability of autochthonous dissolved organic matter (Auto-DOM) produced by BCP in karst aquatic ecosystems may play a critical role in the missing carbon sink. However, the source of dissolved organic matter (DOM) in inland waters and its consumption by planktonic bacteria have not been thoroughly examined. Recalcitrant dissolved organic matter (RDOM) may exist in karst aquatic ecosystem as in the ocean. Through the study of the chromophoric dissolved organic matter (CDOM) and the interaction between CDOM and the planktonic bacterial community under different land uses at the Shawan Karst Water-carbon Cycle Test Site, SW China, we found that C2, as the fluorescence component of Auto-DOM mineralised by planktonic bacteria, may have some of the characteristics of RDOM and is an important DOM source in karst aquatic ecosystems. The stability ratio (Fmax(C2/(C1+C2))) of Auto-DOM reached 89.6 ± 6.71% in winter and 64.1 ± 7.19% in spring. Moreover, correlation-based network analysis determined that the planktonic bacterial communities were controlled by different fluorescence types of CDOM, of which C1 (fresh Auto-DOM), C3 (conventional allochthonous DOM (Allo-DOM)) and C4 (the Allo-DOM mineralised by bacteria) were clustered in one module together with prevalent organic-degrading planktonic bacteria; C2 was clustered in another tightly combined module, suggesting specific microbial utilization strategies for the C2 component. In addition, some important planktonic bacterium and functional genes (including chemotrophic heterotrophs and photosynthetic bacteria) were found to be affected by high Ca2+ and dissolved inorganic carbon (DIC) concentrations in karst aquatic ecosystems. Our research showed that Auto-DOM may be as an important carbon sink as the Allo-DOM in karst ecosystems, the former generally being neglected based on a posit that it is easily and first mineralized by planktonic bacteria.
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Affiliation(s)
- Fan Xia
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China; Puding Karst Ecosystem Research Station, CAS, Chinese Ecosystem Research Network, Puding 562100, China
| | - Zaihua Liu
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; Puding Karst Ecosystem Research Station, CAS, Chinese Ecosystem Research Network, Puding 562100, China; CAS Center for Excellence in Quaternary Science and Global Change, Xi'an 710061, China.
| | - Min Zhao
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; Puding Karst Ecosystem Research Station, CAS, Chinese Ecosystem Research Network, Puding 562100, China
| | - Qiang Li
- Key Laboratory of Karst Dynamics, Ministry of Nature Resources/Guangxi, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin 541004, China
| | - Dong Li
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenfang Cao
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China
| | - Cheng Zeng
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; Puding Karst Ecosystem Research Station, CAS, Chinese Ecosystem Research Network, Puding 562100, China
| | - Yundi Hu
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; Puding Karst Ecosystem Research Station, CAS, Chinese Ecosystem Research Network, Puding 562100, China
| | - Bo Chen
- Guizhou University of Finance and Economics, Guiyang 550025, China
| | - Qian Bao
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; Key Laboratory of Land Resources Evaluation and Monitoring in Southwest China of Ministry of Education, Sichuan Normal University, Chengdu 610066, China
| | - Yi Zhang
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China; Resources and Environmental Engineering, Guizhou Institute of Technology, Guiyang 550008, China
| | - Qiufang He
- Chongqing Key Laboratory of Karst Environment, School of Geographical Sciences, Southwest University, Chongqing 400700, China; Key Laboratory of Karst Dynamics, Ministry of Nature Resources/Guangxi, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin 541004, China
| | - Chaowei Lai
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China
| | - Xuejun He
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China; Puding Karst Ecosystem Research Station, CAS, Chinese Ecosystem Research Network, Puding 562100, China
| | - Zhen Ma
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China
| | - Yongqiang Han
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China; Puding Karst Ecosystem Research Station, CAS, Chinese Ecosystem Research Network, Puding 562100, China
| | - Haibo He
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China
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17
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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.
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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
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18
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Chen L, Wang M, Li Y, Shang W, Tang J, Zhang Z, Liu F. Effects of Magnetic Minerals Exposure and Microbial Responses in Surface Sediment across the Bohai Sea. Microorganisms 2021; 10:microorganisms10010006. [PMID: 35056455 PMCID: PMC8778929 DOI: 10.3390/microorganisms10010006] [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: 11/17/2021] [Revised: 12/13/2021] [Accepted: 12/20/2021] [Indexed: 11/24/2022] Open
Abstract
Extensive production and application of magnetic minerals introduces significant amounts of magnetic wastes into the environment. Exposure to magnetic minerals could affect microbial community composition and geographic distribution. Here, we report that magnetic susceptibility is involved in determining bacterial α-diversity and community composition in surface sediment across the Bohai Sea by high-throughput sequencing analysis of the 16S rRNA gene. The results showed that environmental factors (explained 9.80%) played a larger role than spatial variables (explained 6.72%) in conditioning the bacterial community composition. Exposure to a magnetite center may shape the geographical distribution of five dissimilatory iron reducing bacteria. The microbial iron reduction ability and electroactive activity in sediment close to a magnetite center are stronger than those far away. Our study provides a novel understanding for the response of DIRB and electroactive bacteria to magnetic minerals exposure.
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Affiliation(s)
- Lei Chen
- School of Life Science, Qufu Normal University, Qufu 273165, China;
- Key Laboratory of Coastal Biology and Biological Resources Conversation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; (W.S.); (J.T.)
| | - Mingpeng Wang
- School of Life Science, Qufu Normal University, Qufu 273165, China;
- Correspondence: (M.W.); (F.L.)
| | - Yuntao Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China;
| | - Weitao Shang
- Key Laboratory of Coastal Biology and Biological Resources Conversation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; (W.S.); (J.T.)
| | - Jianhui Tang
- Key Laboratory of Coastal Biology and Biological Resources Conversation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; (W.S.); (J.T.)
| | - Zhaojie Zhang
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA;
| | - Fanghua Liu
- Key Laboratory of Coastal Biology and Biological Resources Conversation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; (W.S.); (J.T.)
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Correspondence: (M.W.); (F.L.)
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19
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Albert S, Hedberg P, Motwani NH, Sjöling S, Winder M, Nascimento FJA. Phytoplankton settling quality has a subtle but significant effect on sediment microeukaryotic and bacterial communities. Sci Rep 2021; 11:24033. [PMID: 34911983 PMCID: PMC8674317 DOI: 10.1038/s41598-021-03303-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/30/2021] [Indexed: 11/10/2022] Open
Abstract
In coastal aphotic sediments, organic matter (OM) input from phytoplankton is the primary food resource for benthic organisms. Current observations from temperate ecosystems like the Baltic Sea report a decline in spring bloom diatoms, while summer cyanobacteria blooms are becoming more frequent and intense. These climate-driven changes in phytoplankton communities may in turn have important consequences for benthic biodiversity and ecosystem functions, but such questions are not yet sufficiently explored experimentally. Here, in a 4-week experiment, we investigated the response of microeukaryotic and bacterial communities to different types of OM inputs comprising five ratios of two common phytoplankton species in the Baltic Sea, the diatom Skeletonema marinoi and filamentous cyanobacterium Nodularia spumigena. Metabarcoding analyses on 16S and 18S ribosomal RNA (rRNA) at the experiment termination revealed subtle but significant changes in diversity and community composition of microeukaryotes in response to settling OM quality. Sediment bacteria were less affected, although we observed a clear effect on denitrification gene expression (nirS and nosZ), which was positively correlated with increasing proportions of cyanobacteria. Altogether, these results suggest that future changes in OM input to the seafloor may have important effects on both the composition and function of microbenthic communities.
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Affiliation(s)
- Séréna Albert
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius 20A, 106 91, Stockholm, Sweden.
| | - Per Hedberg
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius 20A, 106 91, Stockholm, Sweden
| | - Nisha H Motwani
- Department of Environmental Science, School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Huddinge, Sweden
| | - Sara Sjöling
- Department of Environmental Science, School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Huddinge, Sweden
| | - Monika Winder
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius 20A, 106 91, Stockholm, Sweden
| | - Francisco J A Nascimento
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius 20A, 106 91, Stockholm, Sweden.,Baltic Sea Centre, Stockholm University, Stockholm, Sweden
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20
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Kieft B, Li Z, Bryson S, Hettich RL, Pan C, Mayali X, Mueller RS. Phytoplankton exudates and lysates support distinct microbial consortia with specialized metabolic and ecophysiological traits. Proc Natl Acad Sci U S A 2021; 118:e2101178118. [PMID: 34620710 PMCID: PMC8521717 DOI: 10.1073/pnas.2101178118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2021] [Indexed: 11/18/2022] Open
Abstract
Blooms of marine phytoplankton fix complex pools of dissolved organic matter (DOM) that are thought to be partitioned among hundreds of heterotrophic microbes at the base of the food web. While the relationship between microbial consumers and phytoplankton DOM is a key component of marine carbon cycling, microbial loop metabolism is largely understood from model organisms and substrates. Here, we took an untargeted approach to measure and analyze partitioning of four distinct phytoplankton-derived DOM pools among heterotrophic populations in a natural microbial community using a combination of ecogenomics, stable isotope probing (SIP), and proteomics. Each 13C-labeled exudate or lysate from a diatom or a picocyanobacterium was preferentially assimilated by different heterotrophic taxa with specialized metabolic and physiological adaptations. Bacteroidetes populations, with their unique high-molecular-weight transporters, were superior competitors for DOM derived from diatom cell lysis, rapidly increasing growth rates and ribosomal protein expression to produce new relatively high C:N biomass. Proteobacteria responses varied, with relatively low levels of assimilation by Gammaproteobacteria populations, while copiotrophic Alphaproteobacteria such as the Roseobacter clade, with their diverse array of ABC- and TRAP-type transporters to scavenge monomers and nitrogen-rich metabolites, accounted for nearly all cyanobacteria exudate assimilation and produced new relatively low C:N biomass. Carbon assimilation rates calculated from SIP data show that exudate and lysate from two common marine phytoplankton are being used by taxonomically distinct sets of heterotrophic populations with unique metabolic adaptations, providing a deeper mechanistic understanding of consumer succession and carbon use during marine bloom events.
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Affiliation(s)
- Brandon Kieft
- Department of Microbiology, Oregon State University, Corvallis, OR 97331;
| | - Zhou Li
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996
| | - Samuel Bryson
- Department of Microbiology, Oregon State University, Corvallis, OR 97331
- Department of Civil & Environmental Engineering, The University of Washington, Seattle, WA 98195
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830
| | - Chongle Pan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996
- Department of Microbiology and Plant Microbiology, University of Oklahoma, Norman, OK 73019
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Ryan S Mueller
- Department of Microbiology, Oregon State University, Corvallis, OR 97331;
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21
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Liang J, Liu J, Zhan Y, Zhou S, Xue CX, Sun C, Lin Y, Luo C, Wang X, Zhang XH. Succession of marine bacteria in response to Ulva prolifera-derived dissolved organic matter. ENVIRONMENT INTERNATIONAL 2021; 155:106687. [PMID: 34144477 DOI: 10.1016/j.envint.2021.106687] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 05/21/2021] [Accepted: 05/30/2021] [Indexed: 06/12/2023]
Abstract
Increasing macroalgal blooms as a consequence of climate warming and coastal eutrophication have profound effects on the marine environment. The outbreaks of Ulva prolifera in the Yellow Sea of China occurring every summer since 2007 to present have formed the world's largest green tide. The green tide releases huge amounts of dissolved organic matter (DOM) to the seawater, causing an organic overload. However, how marine bacteria respond to this issue and the potential impact on the marine environment are still unclear. Here, we monitored the highly temporally resolved dynamics of marine bacterial community that occur in response to Ulva prolifera-derived DOM by performing a 168-h microcosm incubation experiment. DOM inputs significantly increased bacterial abundances within 6 h, decreased bacterial diversity and triggered clear community successions during the whole period of incubation. Vibrio of Gammaproteobacteria robustly and rapidly grew over short timescales (6-24 h), with its relative abundance accounting for up to 52.5% of active bacteria. From 24 to 48 h, some genera of Flavobacteriia grew rapidly, which was more conspicuous at a higher DOM concentration than at a lower concentration. The genus Donghicola of Alphaproteobacteria was predominant at later time points (>48 h). This bacterial community succession was accompanied by significant variations in the activity of 12 different extracellular enzymes, resulting in a rapid reduction of dissolved organic carbon by 74.5% within the first 36 h. In summary, our study demonstrates rapid successions of bacterial community and extracellular enzyme activity after DOM inputs, suggesting that the bacterial response to Ulva prolifera-derived organic matter may contribute to environmental restoration and may pose a health threat due to the bloom of potential pathogenic Vibrio.
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Affiliation(s)
- Jinchang Liang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
| | - Jiwen Liu
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, 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; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yuanchao Zhan
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, 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; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Shun Zhou
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
| | - Chun-Xu Xue
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
| | - Chuang Sun
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
| | - Yu Lin
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
| | - Chunle Luo
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Qingdao 266100, China
| | - Xuchen Wang
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Qingdao 266100, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, 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; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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22
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Chen Q, Chen F, Gonsior M, Li Y, Wang Y, He C, Cai R, Xu J, Wang Y, Xu D, Sun J, Zhang T, Shi Q, Jiao N, Zheng Q. Correspondence between DOM molecules and microbial community in a subtropical coastal estuary on a spatiotemporal scale. ENVIRONMENT INTERNATIONAL 2021; 154:106558. [PMID: 33878614 DOI: 10.1016/j.envint.2021.106558] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 03/09/2021] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
Dissolved organic matter (DOM) changes in quantity and quality over time and space, especially in highly dynamic coastal estuaries. Bacterioplankton usually display seasonal and spatial variations in abundance and composition in the coastal regions, and influence the DOM pool via assimilation, transformation and release of organic molecules. The change in DOM can also affect the composition of bacterial community. However, little is known on the correspondence between DOM molecules and bacterial composition, particularly through a systematic field survey. In this study, the spatiotemporal signatures of microbial communities and DOM composition in the subtropical coastal estuary of Xiamen are investigated over one and half years. The co-occurrence analysis between bacteria and DOM suggested microorganisms likely transformed the DOM from a relatively high (>400 Da) to a low (<400 Da) molecular weight, corresponding to an apparent increase in overall aromaticity. This might be the reason why microbial transformation renders "dark" organic matter visible in mass spectrometry due to more efficient ionization of microbial metabolites, as well as photodegradation processes. K- and r-strategists exhibited different correlations with two-size categories of DOM molecules owing to their different lifestyles and responses to environmental nutrient conditions. A comparison of the environmental variables and DOM composition with the microbial communities showed that the environmental/DOM variations played a more important role in shaping the microbial communities than vice versa. This study sheds light on the interactions between microbial populations and DOM molecules at the spatiotemporal scale, improving our understanding of microbial roles in marine biogeochemical cycles.
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Affiliation(s)
- Qi Chen
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, 701 East Pratt Street, Baltimore, MD 21202, United States
| | - Michael Gonsior
- Chesapeake Biological Laboratory, University of Maryland Center for Environmental Science, 146 Williams Street, Solomons, MD 20688, United States
| | - Yunyun Li
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, 18 Fuxue Road, Changping District, Beijing 102249, China
| | - Yu Wang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, 18 Fuxue Road, Changping District, Beijing 102249, China
| | - Ruanhong Cai
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China
| | - Jinxin Xu
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China
| | - Yimeng Wang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China
| | - Dapeng Xu
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China
| | - Jia Sun
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China
| | - Ting Zhang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, 18 Fuxue Road, Changping District, Beijing 102249, China
| | - Nianzhi Jiao
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China
| | - Qiang Zheng
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiang'an Campus, Xiang'an South Road, Xiamen 361102, China.
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23
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Zhou L, Zhou Y, Tang X, Zhang Y, Jeppesen E. Biodegradable dissolved organic carbon shapes bacterial community structures and co-occurrence patterns in large eutrophic Lake Taihu. J Environ Sci (China) 2021; 107:205-217. [PMID: 34412783 DOI: 10.1016/j.jes.2021.02.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 02/07/2021] [Accepted: 02/07/2021] [Indexed: 06/13/2023]
Abstract
Interactions between dissolved organic matter (DOM) and bacteria are central in the biogeochemical cycles of aquatic ecosystems; however, the relative importance of biodegradable dissolved organic carbon (BDOC) compared with other environmental variables in structuring the bacterial communities needs further investigation. Here, we investigated bacterial communities, chromophoric DOM (CDOM) characteristics and physico-chemical parameters as well as examined BDOC via bioassay incubations in large eutrophic Lake Taihu, China, to explore the importance of BDOC for shaping bacterial community structures and co-occurrence patterns. We found that the proportion of BDOC (%BDOC) correlated significantly and positively with the DOC concentration and the index of the contribution of recent produced autochthonous CDOM (BIX). %BDOC, further correlated positively with the relative abundance of the tryptophan-like component and negatively with CDOM aromaticity, indicating that autochthonous production of protein-like CDOM was an important source of BDOC. The richness of the bacterial communities correlated negatively with %BDOC, indicating an enhanced number of species in the refractory DOC environments. %BDOC was identified as a significant stronger factor than DOC in shaping bacterial community composition and the co-occurrence network, suggesting that substrate biodegradability is more significant than DOC quantity determining the bacterial communities in a eutrophic lake. Environmental factors explained a larger proportion of the variation in the conditionally rare and abundant subcommunity than for the abundant and the rare bacterial subcommunities. Our findings emphasize the importance of considering bacteria with different abundance patterns and DOC biodegradability when studying the interactions between DOM and bacteria in eutrophic lakes.
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Affiliation(s)
- Lei Zhou
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongqiang Zhou
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangming Tang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunlin Zhang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Erik Jeppesen
- Department of Bioscience, Aarhus University, Silkeborg 8600, Denmark; Sino-Danish Centre for Education and Research, Beijing 100049, China; Limnology Laboratory, Department of Biological Sciences and Centre for Ecosystem Research and Implementation, Middle East Technical University, Ankara 06800, Turkey; Institute of Marine Sciences, Middle East Technical University, Mersin, Turkey
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24
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Bacterial community structure and functional profiling of high Arctic fjord sediments. World J Microbiol Biotechnol 2021; 37:133. [PMID: 34255189 DOI: 10.1007/s11274-021-03098-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/23/2021] [Indexed: 10/20/2022]
Abstract
Kongsfjorden, an Arctic fjord is significantly affected by the glacier melt and Atlantification, both the processes driven by accelerated warming in the Arctic. This has lead to changes in primary production, carbon pool and microbial communities, especially that in the sediment. In this study, we have examined the bacterial community structure of surface (0-2 cm) and subsurface (3-9 cm) sediments of Kongsfjorden using the high throughput sequencing analysis. Results revealed that bacterial community structure of Kongsfjorden sediments were dominated by phylum Proteobacteria followed by Bacteroidetes and Epsilonbacteraeota. While α- and γ-Proteobacterial class were dominant in surface sediments; δ-Proteobacteria were found to be predominant in subsurface sediments. The bacterial community structure in the surface and subsurface sediments showed significant variations (p ≤ 0.05). Total organic carbon could be one of the major parameters controlling the bacterial diversity in the surface and subsurface sediments. Functional prediction analysis indicated that the bacterial community could be involved in the degradation of complex organic compounds such as glycans, glycosaminoglycans, polycyclic aromatic hydrocarbons and also in the biosynthesis of secondary metabolites.
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25
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Izabel-Shen D, Albert S, Winder M, Farnelid H, Nascimento FJA. Quality of phytoplankton deposition structures bacterial communities at the water-sediment interface. Mol Ecol 2021; 30:3515-3529. [PMID: 33993575 DOI: 10.1111/mec.15984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 02/16/2021] [Accepted: 05/11/2021] [Indexed: 11/28/2022]
Abstract
Phytoplankton comprises a large fraction of the vertical carbon flux to deep water via the sinking of particulate organic matter (POM). However, despite the importance of phytoplankton in the coupling of benthic-pelagic productivity, the extent to which its deposition in the sediment affects bacterial dynamics at the water-sediment interface is poorly understood. Here, we conducted a microcosm experiment in which varying mixtures of diatom and cyanobacteria, representing phytoplankton-derived POM of differing quality, served as inputs to sediment cores. Characterization of 16S rRNA gene of the bacterial communities at the water-sediment interface showed that bacterial α-diversity was not affected by POM addition, while bacterial β-diversity changed significantly along the POM quality gradient, with the variation driven by changes in relative abundance rather than in taxon replacement. Analysing individual taxa abundances across the POM gradient revealed two distinct bacterial responses, in which taxa within either diatom- or cyanobacteria-favoured groups were more phylogenetically closely related to one another than other taxa found in the water. Moreover, there was little overlap in taxon identity between sediment and water communities, suggesting the minor role played by sediment bacteria in influencing the observed changes in bacterial communities in the overlying water. Together, these results showed that variability in phytoplankton-originated POM can impact bacterial dynamics at the water-sediment interface. Our findings highlight the importance of considering the potential interactions between phytoplankton and bacteria in benthic-pelagic coupling in efforts to understand the structure and function of bacterial communities under a changing climate.
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Affiliation(s)
- Dandan Izabel-Shen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Séréna Albert
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Monika Winder
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Hanna Farnelid
- Center for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
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26
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Figueroa D, Capo E, Lindh MV, Rowe OF, Paczkowska J, Pinhassi J, Andersson A. Terrestrial dissolved organic matter inflow drives temporal dynamics of the bacterial community of a subarctic estuary (northern Baltic Sea). Environ Microbiol 2021; 23:4200-4213. [PMID: 33998121 DOI: 10.1111/1462-2920.15597] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/29/2021] [Accepted: 04/15/2021] [Indexed: 11/29/2022]
Abstract
Climate change is projected to cause increased inflow of terrestrial dissolved organic matter to coastal areas in northerly regions. Estuarine bacterial community will thereby receive larger loads of organic matter and inorganic nutrients available for microbial metabolism. The composition of the bacterial community and its ecological functions may thus be affected. We studied the responses of bacterial community to inflow of terrestrial dissolved organic matter in a subarctic estuary in the northern Baltic Sea, using a 16S rRNA gene metabarcoding approach. Betaproteobacteria dominated during the spring river flush, constituting ~ 60% of the bacterial community. Bacterial diversity increased as the runoff decreased during summer, when Verrucomicrobia, Betaproteobacteria, Bacteroidetes, Gammaproteobacteria and Planctomycetes dominated the community. Network analysis revealed that a larger number of associations between bacterial populations occurred during the summer than in spring. Betaproteobacteria and Bacteroidetes populations appeared to display similar correlations to environmental factors. In spring, freshly discharged organic matter favoured specialists, while in summer a mix of autochthonous and terrestrial organic matter promoted the development of generalists. Our study indicates that increased inflows of terrestrial organic matter-loaded freshwater to coastal areas would promote specialist bacteria, which in turn might enhance the transformation of terrestrial organic matter in estuarine environments.
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Affiliation(s)
- Daniela Figueroa
- Department of Ecology and Environmental Science, Umeå University, Umeå, SE-901 87, Sweden.,Umeå Marine Sciences Centre, Hörnefors, SE-905 71, Sweden
| | - Eric Capo
- Department of Ecology and Environmental Science, Umeå University, Umeå, SE-901 87, Sweden
| | - Markus V Lindh
- Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus University, Kalmar, SE-391 82, Sweden
| | - Owen F Rowe
- Baltic Marine Environment Protection Commission HELCOM, Helsinki, FI-00160, Finland
| | - Joanna Paczkowska
- Department of Ecology and Environmental Science, Umeå University, Umeå, SE-901 87, Sweden.,Umeå Marine Sciences Centre, Hörnefors, SE-905 71, Sweden
| | - Jarone Pinhassi
- Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus University, Kalmar, SE-391 82, Sweden
| | - Agneta Andersson
- Department of Ecology and Environmental Science, Umeå University, Umeå, SE-901 87, Sweden.,Umeå Marine Sciences Centre, Hörnefors, SE-905 71, Sweden
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27
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Han Y, Jiao N, Zhang Y, Zhang F, He C, Liang X, Cai R, Shi Q, Tang K. Opportunistic bacteria with reduced genomes are effective competitors for organic nitrogen compounds in coastal dinoflagellate blooms. MICROBIOME 2021; 9:71. [PMID: 33762013 PMCID: PMC7992965 DOI: 10.1186/s40168-021-01022-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/02/2021] [Indexed: 05/29/2023]
Abstract
BACKGROUND Phytoplankton blooms are frequent events in coastal areas and increase the production of organic matter that initially shapes the growth of opportunistic heterotrophic bacteria. However, it is unclear how these opportunists are involved in the transformation of dissolved organic matter (DOM) when blooms occur and the subsequent impacts on biogeochemical cycles. RESULTS We used a combination of genomic, proteomic, and metabolomic approaches to study bacterial diversity, genome traits, and metabolic responses to assess the source and lability of DOM in a spring coastal bloom of Akashiwo sanguinea. We identified molecules that significantly increased during bloom development, predominantly belonging to amino acids, dipeptides, lipids, nucleotides, and nucleosides. The opportunistic members of the bacterial genera Polaribacter, Lentibacter, and Litoricola represented a significant proportion of the free-living and particle-associated bacterial assemblages during the stationary phase of the bloom. Polaribacter marinivivus, Lentibacter algarum, and Litoricola marina were isolated and their genomes exhibited streamlining characterized by small genome size and low GC content and non-coding densities, as well as a smaller number of transporters and peptidases compared to closely related species. However, the core proteomes identified house-keeping functions, such as various substrate transporters, peptidases, motility, chemotaxis, and antioxidants, in response to bloom-derived DOM. We observed a unique metabolic signature for the three species in the utilization of multiple dissolved organic nitrogen compounds. The metabolomic data showed that amino acids and dipeptides (such as isoleucine and proline) were preferentially taken up by P. marinivivus and L. algarum, whereas nucleotides and nucleosides (such as adenosine and purine) were preferentially selected by L. marina. CONCLUSIONS The results suggest that the enriched DOM in stationary phase of phytoplankton bloom is a result of ammonium depletion. This environment drives genomic streamlining of opportunistic bacteria to exploit their preferred nitrogen-containing compounds and maintain nutrient cycling. Video abstract.
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Affiliation(s)
- Yu Han
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Fan Zhang
- Department of Molecular Virology & Microbiology, Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (Beijing), Beijing, 102249, People's Republic of China
| | - Xuejiao Liang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Ruanhong Cai
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum (Beijing), Beijing, 102249, People's Republic of China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, People's Republic of China.
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Zhou L, Zhou Y, Tang X, Zhang Y, Jang KS, Székely AJ, Jeppesen E. Resource aromaticity affects bacterial community successions in response to different sources of dissolved organic matter. WATER RESEARCH 2021; 190:116776. [PMID: 33387955 DOI: 10.1016/j.watres.2020.116776] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/17/2020] [Accepted: 12/20/2020] [Indexed: 05/18/2023]
Abstract
Microbe-mediated transformation of dissolved organic matter (DOM) contributes substantially to the carbon dynamics and energy flow of aquatic ecosystems; yet, the temporal dynamics of bacterial communities in response to diverse DOM sources are scarcely known. Here, we supplied four distinct sources of DOM (algae-derived, macrophyte-derived, sewage-derived, and soil-derived) to the same bacterial community to track the effects of these DOM sources on the carbon processing and successional dynamics of bacterial communities. Although by the end of the incubation the proportion of bio-degraded DOM was significantly lower in the soil-derived DOM treatment than for the other sources, rapid initial metabolism of protein-like and aliphatic compounds and increasing aromaticity and humification degree of DOM during the incubation period were observed for all sources. The role of stochastic processes in governing the community assembly decreased substantially from 61.4% on the first day to 16.7% at the end of the incubation. Moreover, stronger deterministic selection and lower temporal turnover rate were observed for the soil-derived than the other DOM sources, indicating stronger environmental filtering by the more aromatic DOM. Significant correlations were also observed between the humification index (HIX) of DOM and bacterial community diversities, co-occurrence patterns, habitat niche breadths, and the contribution of deterministic ecological processes. In addition, we demonstrated that taxa with different abundance patterns all play crucial but different roles in the response to DOM variation. Our results indicate the importance of DOM aromaticity as a predictor of the outcome of different DOM sources on bacterial community dynamics.
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Affiliation(s)
- Lei Zhou
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongqiang Zhou
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangming Tang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunlin Zhang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Kyoung-Soon Jang
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju 28119, South Korea
| | - Anna J Székely
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala 75236, Sweden
| | - Erik Jeppesen
- Department of Bioscience, Aarhus University, Silkeborg 8600, Denmark; Sino-Danish Centre for Education and Research, Beijing 100049, China; Limnology Laboratory, Department of Biological Sciences and Centre for Ecosystem Research and Implementation, Middle East Technical University, Ankara 06800, Turkey; Institute of Marine Sciences, Middle East Technical University, Mersin, Turkey
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29
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Ruiz-González C, Rodellas V, Garcia-Orellana J. The microbial dimension of submarine groundwater discharge: current challenges and future directions. FEMS Microbiol Rev 2021; 45:6128669. [PMID: 33538813 PMCID: PMC8498565 DOI: 10.1093/femsre/fuab010] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 01/28/2021] [Indexed: 12/22/2022] Open
Abstract
Despite the relevance of submarine groundwater discharge (SGD) for ocean biogeochemistry, the microbial dimension of SGD remains poorly understood. SGD can influence marine microbial communities through supplying chemical compounds and microorganisms, and in turn, microbes at the land–ocean transition zone determine the chemistry of the groundwater reaching the ocean. However, compared with inland groundwater, little is known about microbial communities in coastal aquifers. Here, we review the state of the art of the microbial dimension of SGD, with emphasis on prokaryotes, and identify current challenges and future directions. Main challenges include improving the diversity description of groundwater microbiota, characterized by ultrasmall, inactive and novel taxa, and by high ratios of sediment-attached versus free-living cells. Studies should explore microbial dynamics and their role in chemical cycles in coastal aquifers, the bidirectional dispersal of groundwater and seawater microorganisms, and marine bacterioplankton responses to SGD. This will require not only combining sequencing methods, visualization and linking taxonomy to activity but also considering the entire groundwater–marine continuum. Interactions between traditionally independent disciplines (e.g. hydrogeology, microbial ecology) are needed to frame the study of terrestrial and aquatic microorganisms beyond the limits of their presumed habitats, and to foster our understanding of SGD processes and their influence in coastal biogeochemical cycles.
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Affiliation(s)
- Clara Ruiz-González
- Institut de Ciències del Mar (ICM-CSIC). Passeig Marítim de la Barceloneta 37-49, E08003 Barcelona, Spain
| | - Valentí Rodellas
- Institut de Ciència i Tecnologia Ambientals (ICTA-UAB), Universitat Autònoma de Barcelona, E08193 Bellaterra, Spain
| | - Jordi Garcia-Orellana
- Institut de Ciència i Tecnologia Ambientals (ICTA-UAB), Universitat Autònoma de Barcelona, E08193 Bellaterra, Spain.,Departament de Física, Universitat Autònoma de Barcelona, E08193 Bellaterra, Spain
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30
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Using metacommunity ecology to understand environmental metabolomes. Nat Commun 2020; 11:6369. [PMID: 33311510 PMCID: PMC7732844 DOI: 10.1038/s41467-020-19989-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 10/29/2020] [Indexed: 12/26/2022] Open
Abstract
Environmental metabolomes are fundamentally coupled to microbially-linked biogeochemical processes within ecosystems. However, significant gaps exist in our understanding of their spatiotemporal organization, limiting our ability to uncover transferrable principles and predict ecosystem function. We propose that a theoretical paradigm, which integrates concepts from metacommunity ecology, is necessary to reveal underlying mechanisms governing metabolomes. We call this synthesis between ecology and metabolomics ‘meta-metabolome ecology’ and demonstrate its utility using a mass spectrometry dataset. We developed three relational metabolite dendrograms using molecular properties and putative biochemical transformations and performed ecological null modeling. Based upon null modeling results, we show that stochastic processes drove molecular properties while biochemical transformations were structured deterministically. We further suggest that potentially biochemically active metabolites were more deterministically assembled than less active metabolites. Understanding variation in the influences of stochasticity and determinism provides a way to focus attention on which meta-metabolomes and which parts of meta-metabolomes are most likely to be important to consider in mechanistic models. We propose that this paradigm will allow researchers to study the connections between ecological systems and their molecular processes in previously inaccessible detail. Despite growing interest in environmental metabolomics, we lack conceptual frameworks for considering how metabolites vary across space and time in ecological systems. Here, the authors apply (species) community assembly concepts to metabolomics data, offering a way forward in understanding the assembly of metabolite assemblages.
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31
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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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Tisserand L, Dadaglio L, Intertaglia L, Catala P, Panagiotopoulos C, Obernosterer I, Joux F. Use of organic exudates from two polar diatoms by bacterial isolates from the Arctic Ocean. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2020; 378:20190356. [PMID: 32862822 PMCID: PMC7481660 DOI: 10.1098/rsta.2019.0356] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Global warming affects primary producers in the Arctic, with potential consequences for the bacterial community composition through the consumption of microalgae-derived dissolved organic matter (DOM). To determine the degree of specificity in the use of an exudate by bacterial taxa, we used simple microalgae-bacteria model systems. We isolated 92 bacterial strains from the sea ice bottom and the water column in spring-summer in the Baffin Bay (Arctic Ocean). The isolates were grouped into 42 species belonging to Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes. Forty strains were tested for their capacity to grow on the exudate from two Arctic diatoms. Most of the strains tested (78%) were able to grow on the exudate from the pelagic diatom Chaetoceros neogracilis, and 33% were able to use the exudate from the sea ice diatom Fragilariopsis cylindrus. 17.5% of the strains were not able to grow with any exudate, while 27.5% of the strains were able to use both types of exudates. All strains belonging to Flavobacteriia (n = 10) were able to use the DOM provided by C. neogracilis, and this exudate sustained a growth capacity of up to 100 times higher than diluted Marine Broth medium, of two Pseudomonas sp. strains and one Sulfitobacter strain. The variable bioavailability of exudates to bacterial strains highlights the potential role of microalgae in shaping the bacterial community composition. This article is part of the theme issue 'The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystem functioning'.
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Affiliation(s)
- Lucas Tisserand
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, 66650 Banyuls/mer, France
| | - Laëtitia Dadaglio
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, 66650 Banyuls/mer, France
| | - Laurent Intertaglia
- Sorbonne Université, CNRS, FR3724, Observatoire Océanologique, 66650 Banyuls/Mer, France
| | - Philippe Catala
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, 66650 Banyuls/mer, France
| | | | - Ingrid Obernosterer
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, 66650 Banyuls/mer, France
| | - Fabien Joux
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique de Banyuls, 66650 Banyuls/mer, France
- e-mail:
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33
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Hach PF, Marchant HK, Krupke A, Riedel T, Meier DV, Lavik G, Holtappels M, Dittmar T, Kuypers MMM. Rapid microbial diversification of dissolved organic matter in oceanic surface waters leads to carbon sequestration. Sci Rep 2020; 10:13025. [PMID: 32747679 PMCID: PMC7400608 DOI: 10.1038/s41598-020-69930-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/14/2020] [Indexed: 11/09/2022] Open
Abstract
The pool of dissolved organic matter (DOM) in the deep ocean represents one of the largest carbon sinks on the planet. In recent years, studies have shown that most of this pool is recalcitrant, because individual compounds are present at low concentrations and because certain compounds seem resistant to microbial degradation. The formation of the diverse and recalcitrant deep ocean DOM pool has been attributed to repeated and successive processing of DOM by microorganisms over time scales of weeks to years. Little is known however, about the transformation and cycling that labile DOM undergoes in the first hours upon its release from phytoplankton. Here we provide direct experimental evidence showing that within hours of labile DOM release, its breakdown and recombination with ambient DOM leads to the formation of a diverse array of new molecules in oligotrophic North Atlantic surface waters. Furthermore, our results reveal a preferential breakdown of N and P containing molecules versus those containing only carbon. Hence, we show the preferential breakdown and molecular diversification are the crucial first steps in the eventual formation of carbon rich DOM that is resistant to microbial remineralization.
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Affiliation(s)
- Philipp F Hach
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Hannah K Marchant
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Andreas Krupke
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Thomas Riedel
- IWW Water Centre, Moritzstr. 26, 45476, Mülheim an der Ruhr, Germany
| | - Dimitri V Meier
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14 UZA I, 1090, Vienna, Austria
| | - Gaute Lavik
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Moritz Holtappels
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - Thorsten Dittmar
- Research Group for Marine Geochemistry (ICBM-MPI Bridging Group), at the Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), University of Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129, Oldenburg, Germany
| | - Marcel M M Kuypers
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.
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Takebe H, Tominaga K, Fujiwara K, Yamamoto K, Yoshida T. Differential Responses of a Coastal Prokaryotic Community to Phytoplanktonic Organic Matter Derived from Cellular Components and Exudates. Microbes Environ 2020; 35. [PMID: 32554942 PMCID: PMC7511794 DOI: 10.1264/jsme2.me20033] [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] [Indexed: 11/21/2022] Open
Abstract
The phytoplanktonic production and prokaryotic consumption of organic matter significantly contribute to marine carbon cycling. Organic matter released from phytoplankton via three processes (exudation of living cells, cell disruption through grazing, and viral lysis) shows distinct chemical properties. We herein investigated the effects of phytoplanktonic whole-cell fractions (WF) (representing cell disruption by grazing) and extracellular fractions (EF) (representing exudates) prepared from Heterosigma akashiwo, a bloom-forming Raphidophyceae, on prokaryotic communities using culture-based experiments. We analyzed prokaryotic community changes for two weeks. The shift in cell abundance by both treatments showed similar dynamics, reaching the first peak (~4.1×106 cells mL–1) on day 3 and second peak (~1.1×106 cells mL–1) on day 13. We classified the sequences obtained into operational taxonomic units (OTUs). A Bray-Curtis dissimilarity analysis revealed that the OTU-level community structure changed distinctively with the two treatments. Ten and 13 OTUs were specifically abundant in the WF and EF treatments, respectively. These OTUs were assigned as heterotrophic bacteria mainly belonging to the Alteromonadales (Gammaproteobacteria) and Bacteroidetes clades and showed successive dynamics following the addition of organic matter. We also analyzed the dynamics of these OTUs in the ocean using publicly available metagenomic data from a natural coastal bloom in Monterey Bay, USA. At least two WF treatment OTUs showed co-occurrence with H. akashiwo, indicating that the blooms of H. akashiwo also affect these OTUs in the ocean. The present results strongly suggest that the thriving and dead cells of uninfected phytoplankton differentially influence the marine prokaryotic community.
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Affiliation(s)
| | | | | | - Keigo Yamamoto
- Research Institute of Environment, Agriculture and Fisheries, Osaka Prefecture
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35
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Li Y, Xu C, Zhang W, Lin L, Wang L, Niu L, Zhang H, Wang P, Wang C. Response of bacterial community in composition and function to the various DOM at river confluences in the urban area. WATER RESEARCH 2020; 169:115293. [PMID: 31734394 DOI: 10.1016/j.watres.2019.115293] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/20/2019] [Accepted: 11/06/2019] [Indexed: 06/10/2023]
Abstract
River confluences result in mixture and transformation of dissolved organic matter (DOM), influencing the phylogeny of microbial community, furthermore, the integrity and function of river systems. The relationship between the microbial community and DOM is complex, especially in the confluence zone. Previous reports focused on shifts in the different bacterial community in response to exposure to the same terrestrial DOM. However, the transformation of bacterial community induced by convergent DOM remains unknown. This study showed the shifts of DOM components at the junction via excitation-emission matrices parallel factor analysis. Metabolic differences were also determined via phylogenetic investigation of communities by reconstruction of unobserved states. The results demonstrated a direct link between the microbial metabolism and DOM biodegradation during the heterotrophic process. In response to diverse DOM conditions, the taxonomic composition and metabolic function of the microbial community presented significant differences. Different taxa may be involved in metabolizing various DOM components. As indicative bacteria that are closely associated with DOM components, Proteobacteria (Sphingomonas) are significant for microbial utilization and were important during the DOM-degrading process. Compared with other conditions, the abundance of carbon metabolism was higher in convergences where urban rivers joined with estuary or source water. Furthermore, humic-like DOM, converging in the confluence zone, induced a more active lipid metabolism. This study applied techniques that capture the diversity and complexity of bacterial communities and DOM, and provides new insight on the basis of the interaction between bacterial communities and DOM in confluence processes of biogeochemical significance.
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Affiliation(s)
- Yi Li
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
| | - Chen Xu
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China.
| | - Li Lin
- Basin Water Environmental Research Department, Changjiang River Scientific Research Institute, Wuhan, 430010, PR China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, 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, Xikang Road #1, Nanjing, 210098, PR China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210098, PR China
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Distinct capabilities of different Gammaproteobacterial strains on utilizing small peptides in seawater. Sci Rep 2020; 10:464. [PMID: 31949195 PMCID: PMC6965191 DOI: 10.1038/s41598-019-57189-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/21/2019] [Indexed: 11/23/2022] Open
Abstract
Proteins and peptides account for 20–75% of marine biota biomass, of which a major fraction is metabolized by bacteria, thus deciphering interactions between bacteria and peptides is important in understanding marine carbon and nitrogen cycling. To better understand capabilities of different bacterial strains on peptide decomposition, four Gammaproteobacteria (Pseudoalteromonas atlantica, Alteromonas sp., Marinobacterium jannaschii, Amphritea japonica) were incubated in autoclaved seawater amended with tetrapeptide alanine-valine-phenylalanine-alanine (AVFA), a fragment of RuBisCO. While AVFA was decomposed greatly by Pseudoalteromonas atlantica and Alteromonas sp, it remained nearly intact in the Marinobacterium jannaschii and Amphritea japonica incubations. Pseudoalteromonas and Alteromonas decomposed AVFA mainly through extracellular hydrolysis pathway, releasing 71–85% of the AVFA as hydrolysis products to the surrounding seawater. Overall, this study showed that Gammaproteobacterial strains differ greatly in their capabilities of metabolizing peptides physiologically, providing insights into interactions of bacteria and labile organic matter in marine environments.
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Roebuck JA, Seidel M, Dittmar T, Jaffé R. Controls of Land Use and the River Continuum Concept on Dissolved Organic Matter Composition in an Anthropogenically Disturbed Subtropical Watershed. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:195-206. [PMID: 31742395 DOI: 10.1021/acs.est.9b04605] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
About 250 Tg of dissolved organic carbon are annually transported from inland waters to coastal systems making rivers a critical link between terrestrial and ocean carbon pools. During transport through fluvial systems, various biogeochemical processes selectively remove or transform labile material, effectively altering the composition of dissolved organic matter (DOM) exported to the ocean. The river continuum concept (RCC) has been historically used as a model to predict the fate and quality of organic matter along a river continuum. However, the conversion of natural landscapes for urban and agricultural practices can also alter the sources and quality of DOM exported from fluvial systems, and the RCC may be significantly limited in predicting DOM quality in anthropogenically impacted watersheds. Here, we studied DOM dynamics in the Altamaha River watershed in Georgia, USA, a fluvial system where headwater streams are highly impacted by anthropogenic activities. The primary goal of this study was to quantitatively assess the importance of both the RCC and land use as environmental drivers controlling DOM composition. Land use was a stronger predictor of spatial variation (∼50%) in DOM composition defined by both excitation-emission matrix-parallel factor analysis (EEM-PARAFAC) and ultrahigh-resolution mass spectrometry. This is compared to an 8% explained variability that can be attributed to the RCC. This study highlights the importance of incorporating land use among other controls into the RCC to better predict the fate and quality of DOM exported from terrestrial to coastal systems.
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Affiliation(s)
- Jesse Alan Roebuck
- Southeast Environmental Research Center and Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Michael Seidel
- Research Group for Marine Geochemistry, Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, D-26129 Oldenburg, Germany
| | - Thorsten Dittmar
- Research Group for Marine Geochemistry, Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, D-26129 Oldenburg, Germany
- Helmholtz Institute for Functional Marine Diversity, University of Oldenburg (HIFMB), D-26129 Oldenburg, Germany
| | - Rudolf Jaffé
- Southeast Environmental Research Center and Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
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Microbial transformation of virus-induced dissolved organic matter from picocyanobacteria: coupling of bacterial diversity and DOM chemodiversity. ISME JOURNAL 2019; 13:2551-2565. [PMID: 31227815 DOI: 10.1038/s41396-019-0449-1] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 03/27/2019] [Accepted: 05/03/2019] [Indexed: 02/01/2023]
Abstract
Picocyanobacteria make up half of the ocean's primary production, and they are subjected to frequent viral infection. Viral lysis of picocyanobacteria is a major driving force converting biologically fixed carbon into dissolved organic carbon (DOC). Viral-induced dissolved organic matter (vDOM) released from picocyanobacteria provides complex organic matter to bacterioplankton in the marine ecosystem. In order to understand how picocyanobacterial vDOM are transformed by bacteria and the impact of this process on bacterial community structure, viral lysate of picocyanobacteria was incubated with coastal seawater for 90 days. The transformation of vDOM was analyzed by ultrahigh-resolution mass spectrometry and the shift of bacterial populations analyzed using high-throughput sequencing technology. Addition of picocyanobacterial vDOM introduced abundant nitrogen components into the coastal water, which were largely degraded during the 90 days' incubation period. However, some DOM signatures were accumulated and the total assigned formulae number increased over time. In contrast to the control (no addition of vDOM), bacterial community enriched with vDOM changed markedly with increased biodiversity indices. The network analysis showed that key bacterial species formed complex relationship with vDOM components, suggesting the potential correspondence between bacterial populations and DOM molecules. We demonstrate that coastal bacterioplankton are able to quickly utilize and transform lysis products of picocyanobacteria, meanwhile, bacterial community varies with changing chemodiverisity of DOM. vDOM released from picocyanobacteria generated a complex labile DOM pool, which was converted to a rather stable DOM pool after microbial processing in the time frame of days to weeks.
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Li P, Tao J, Lin J, He C, Shi Q, Li X, Zhang C. Stratification of dissolved organic matter in the upper 2000 m water column at the Mariana Trench. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 668:1222-1231. [PMID: 31018462 DOI: 10.1016/j.scitotenv.2019.03.094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/07/2019] [Accepted: 03/07/2019] [Indexed: 06/09/2023]
Abstract
Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and absorbance spectroscopy were utilized to investigate the molecular composition of marine dissolved organic matter (DOM) from the upper 2000 m water column at the Mariana Trench. Molecular indices, calculated based on the relative abundance of 4699 formulas assigned from FT-ICR MS data, showed depth stratification. The degradation index (IDEG) varied from 0.610 to 0.663 (0.645 ± 0.014) in the surface layer to 0.668-0.754 (0.722 ± 0.021) in the deep ocean (below 500 m), indicating that the DOM in the deep layer was more refractory than that of the surface layer. This was confirmed by an increase of modified aromaticity index (AImod) from 0.196 to 0.207 (0.200 ± 0.003) in the surface layer to 0.213-0.225 (0.220 ± 0.003) at depth. Multivariate analysis based on both bulk molecular parameters and relative abundance of individual formulas showed that the molecular composition of DOM was highly stratified and could be well separated into three groups: the upper layer (5-75 m), the middle layer (200 m) and the deep layer (500-2000 m). In addition, surface-enriched and deep-enriched formulas were identified based on Spearman correlation between relative abundance of individual formulas and depth. The surface-enriched formulas were characterized by higher H/C and lower AImod, while deep-enriched formulas showed lower H/C and higher AImod. Variations in AImod and H/C for these formulas indicated that extracellular release (mainly from primary production) and photochemical processes strongly affected the DOM composition in euphotic zone, while microbial processes likely exerted a tremendous influence on the DOM composition at all depths. Moreover, strong correlations between spectroscopic indices (a325, S275-295 and S280-400) and FT- ICR MS derived proxies indicated these two approaches can be integrated to provide valuable information on the molecular characterization of open ocean DOM.
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Affiliation(s)
- Penghui Li
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
| | - Jianchang Tao
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jian Lin
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA; Key Laboratory of Ocean and Marginal Sea Geology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 102249, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 102249, China
| | - Xinxin Li
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266061, China
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Noriega-Ortega BE, Wienhausen G, Mentges A, Dittmar T, Simon M, Niggemann J. Does the Chemodiversity of Bacterial Exometabolomes Sustain the Chemodiversity of Marine Dissolved Organic Matter? Front Microbiol 2019; 10:215. [PMID: 30837961 PMCID: PMC6382689 DOI: 10.3389/fmicb.2019.00215] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 01/25/2019] [Indexed: 11/13/2022] Open
Abstract
Marine dissolved organic matter (DOM) is a complex mixture of chemical compounds. At 750 Pg C, it is one of the biggest pools of reduced carbon on Earth. It has been proposed that the diversity of DOM is responsible for its recalcitrance. We hypothesize that the chemodiversity of marine DOM is a reflection of the chemodiversity of bacterial exometabolomes. To test this, we incubated two model strains of the Roseobacter group; Phaeobacter inhibens and Dinoroseobacter shibae in pure culture using three different simple organic compounds as sole carbon sources (glutamate, glucose, and acetate and succinate for P. inhibens and D. shibae, respectively). The exometabolome of the model organisms was characterized using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS) and ecological diversity measures. We detected thousands of molecular masses in the exometabolomes of P. inhibens and D. shibae (21,105 and 9,386, respectively), reflecting the capability of single bacterial strains to diversify simple organic compounds. The chemical composition of the exometabolomes changed with growth phase and also differed according to the strain incubated and the utilized substrate. We mimicked a higher diversity of substrates, bacterial species and heterogeneous growth (different growth phases) to approach the complexity of natural environments, by computationally creating combinations of detected exometabolomes. We compared the chemodiversity of these combinations, indicative for chemodiversity of freshly produced microbial DOM to that of refractory DOM from one of the oldest oceanic water masses (North Equatorial Pacific Intermediate Water). Some combinations of exometabolomes showed higher richness than the deep ocean refractory DOM, and all the combinations showed higher functional diversity. About 15% of the 13,509 molecular formulae detected in exometabolomes and refractory oceanic DOM were shared, i.e., occurred in Roseobacter exometabolomes and in deep water samples. This overlap provides further support for our hypothesis that marine bacteria from the Roseobacter group contribute to the sustainability of marine DOM chemodiversity and stability.
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Affiliation(s)
- Beatriz E Noriega-Ortega
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.,Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Gerrit Wienhausen
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Andrea Mentges
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Thorsten Dittmar
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.,Helmhotz Institute for Functional Marine Biodiversity (HIMFB), University of Oldenburg, Oldenburg, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.,Helmhotz Institute for Functional Marine Biodiversity (HIMFB), University of Oldenburg, Oldenburg, Germany
| | - Jutta Niggemann
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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Chen J, Robb CS, Unfried F, Kappelmann L, Markert S, Song T, Harder J, Avcı B, Becher D, Xie P, Amann RI, Hehemann JH, Schweder T, Teeling H. Alpha- and beta-mannan utilization by marine Bacteroidetes. Environ Microbiol 2018; 20:4127-4140. [PMID: 30246424 DOI: 10.1111/1462-2920.14414] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 09/12/2018] [Indexed: 11/28/2022]
Abstract
Marine microscopic algae carry out about half of the global carbon dioxide fixation into organic matter. They provide organic substrates for marine microbes such as members of the Bacteroidetes that degrade algal polysaccharides using carbohydrate-active enzymes (CAZymes). In Bacteroidetes genomes CAZyme encoding genes are mostly grouped in distinct regions termed polysaccharide utilization loci (PULs). While some studies have shown involvement of PULs in the degradation of algal polysaccharides, the specific substrates are for the most part still unknown. We investigated four marine Bacteroidetes isolated from the southern North Sea that harbour putative mannan-specific PULs. These PULs are similarly organized as PULs in human gut Bacteroides that digest α- and β-mannans from yeasts and plants respectively. Using proteomics and defined growth experiments with polysaccharides as sole carbon sources we could show that the investigated marine Bacteroidetes express the predicted functional proteins required for α- and β-mannan degradation. Our data suggest that algal mannans play an as yet unknown important role in the marine carbon cycle, and that biochemical principles established for gut or terrestrial microbes also apply to marine bacteria, even though their PULs are evolutionarily distant.
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Affiliation(s)
- Jing Chen
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China.,College of Ocean, Hebei Agricultural University, Qinhuangdao, China
| | - Craig S Robb
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Frank Unfried
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
| | | | - Stephanie Markert
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
| | - Tao Song
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Jens Harder
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Burak Avcı
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Dörte Becher
- Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Ping Xie
- Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology of China, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology, Greifswald, Germany
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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42
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Mühlenbruch M, Grossart HP, Eigemann F, Voss M. Mini-review: Phytoplankton-derived polysaccharides in the marine environment and their interactions with heterotrophic bacteria. Environ Microbiol 2018; 20:2671-2685. [PMID: 30028074 DOI: 10.1111/1462-2920.14302] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/25/2018] [Accepted: 05/28/2018] [Indexed: 01/20/2023]
Abstract
Within the wealth of molecules constituting marine dissolved organic matter, carbohydrates make up the largest coherent and quantifiable fraction. Their main sources are from primary producers, which release large amounts of photosynthetic products - mainly polysaccharides - directly into the surrounding water via passive and active exudation. The organic carbon and other nutrients derived from these photosynthates enrich the 'phycosphere' and attract heterotrophic bacteria. The rapid uptake and remineralization of dissolved free monosaccharides by heterotrophic bacteria account for the barely detectable levels of these compounds. By contrast, dissolved combined polysaccharides can reach high concentrations, especially during phytoplankton blooms. Polysaccharides are too large to be taken up directly by heterotrophic bacteria, instead requiring hydrolytic cleavage to smaller oligo- or monomers by bacteria with a suitable set of exoenzymes. The release of diverse polysaccharides by various phytoplankton taxa is generally interpreted as the deposition of excess organic material. However, these molecules likely also fulfil distinct, yet not fully understood functions, as inferred from their active modulation in terms of quality and quantity when phytoplankton becomes nutrient limited or is exposed to heterotrophic bacteria. This minireview summarizes current knowledge regarding the exudation and composition of phytoplankton-derived exopolysaccharides and acquisition of these compounds by heterotrophic bacteria.
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Affiliation(s)
- Marco Mühlenbruch
- Leibniz-Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Hans-Peter Grossart
- Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany.,Potsdam University, Institute of Biochemistry and Biology, Potsdam, Germany
| | - Falk Eigemann
- Leibniz-Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Maren Voss
- Leibniz-Institute for Baltic Sea Research Warnemünde, Rostock, Germany
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43
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Ruiz-González C, Archambault E, Laforest-Lapointe I, del Giorgio PA, Kembel SW, Messier C, Nock CA, Beisner BE. Soils associated to different tree communities do not elicit predictable responses in lake bacterial community structure and function. FEMS Microbiol Ecol 2018; 94:5037915. [DOI: 10.1093/femsec/fiy115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 06/14/2018] [Indexed: 01/09/2023] Open
Affiliation(s)
- Clara Ruiz-González
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
- Department of Biological Sciences, University of Québec at Montréal, Montréal, Canada
| | - Esther Archambault
- Department of Biological Sciences, University of Québec at Montréal, Montréal, Canada
| | | | - Paul A del Giorgio
- Department of Biological Sciences, University of Québec at Montréal, Montréal, Canada
| | - Steven W Kembel
- Department of Biological Sciences, University of Québec at Montréal, Montréal, Canada
| | - Christian Messier
- Department of Biological Sciences, University of Québec at Montréal, Montréal, Canada
| | - Charles A Nock
- Geobotany, Faculty of Biology, University of Freiburg, Germany
| | - Beatrix E Beisner
- Department of Biological Sciences, University of Québec at Montréal, Montréal, Canada
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44
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Osterholz H, Kirchman DL, Niggemann J, Dittmar T. Diversity of bacterial communities and dissolved organic matter in a temperate estuary. FEMS Microbiol Ecol 2018; 94:5037919. [DOI: 10.1093/femsec/fiy119] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 06/10/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Helena Osterholz
- ICBM-MPI Bridging Group for Marine Geochemistry, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
| | - David L Kirchman
- School of Marine Science and Policy, University of Delaware, Lewes, DE 19958, USA
| | - Jutta Niggemann
- ICBM-MPI Bridging Group for Marine Geochemistry, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
| | - Thorsten Dittmar
- ICBM-MPI Bridging Group for Marine Geochemistry, Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity, Carl von Ossietzky University, Oldenburg, Germany
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45
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Landa M, Blain S, Harmand J, Monchy S, Rapaport A, Obernosterer I. Major changes in the composition of a Southern Ocean bacterial community in response to diatom-derived dissolved organic matter. FEMS Microbiol Ecol 2018; 94:4935155. [DOI: 10.1093/femsec/fiy034] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 03/13/2018] [Indexed: 02/05/2023] Open
Affiliation(s)
- Marine Landa
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique, F-66650, Banyuls/mer, France
| | - Stéphane Blain
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique, F-66650, Banyuls/mer, France
| | | | - Sébastien Monchy
- Univ. Littoral Côte d'Opale, CNRS, Univ. Lille, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, F 59 000 Lille, France
| | - Alain Rapaport
- MISTEA, Univ. Montpellier, INRA, Montpellier SupAgro, 2, pl. Viala 34060 Montpellier, France
| | - Ingrid Obernosterer
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique, F-66650, Banyuls/mer, France
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Yu X, Cai G, Wang H, Hu Z, Zheng W, Lei X, Zhu X, Chen Y, Chen Q, Din H, Xu H, Tian Y, Fu L, Zheng T. Fast-growing algicidal Streptomyces sp. U3 and its potential in harmful algal bloom controls. JOURNAL OF HAZARDOUS MATERIALS 2018; 341:138-149. [PMID: 28777959 DOI: 10.1016/j.jhazmat.2017.06.046] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 06/18/2017] [Accepted: 06/20/2017] [Indexed: 06/07/2023]
Abstract
To find the potential algicidal microorganisms and apply them to prevent and terminate harmful algal blooms (HABs), we isolated an actinomycete U3 from Mangrove, which had a potent algicidal effect on the harmful alga Heterosigma akashiwo. It could completely lyse the algal cells by producing active compounds, which were highly sensitive to high temperature and strong alkaline, but resistant to acid. One μg/mL of crude extract of the fermentation supernatant could kill 70% of H. akashiwo cells in 3 d. Unlike most of the other known algicidal Streptomyces, U3 showed strong ability of proliferation with the algal inclusion as the nutrient source. The washed mycelial pellets also gradually exhibited significant algicidal effect during the visible growth in the algal culture. It suggests that U3 could efficiently absorb nutrients from algal culture to support its growth and produce algicidal compounds that might cause the autophagy of algal cells. Therefore, applying U3, as a long-term and environmentally friendly bio-agent to control the harmful blooms of H. akashiwo, would be effective and promising. And the decrease of bioavailable DOM and increase of bio-refractory DOM during the algicidal process of U3 provided new insights into the ecological influence of algicial microorganisms on marine ecosystem.
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Affiliation(s)
- Xiaoqi Yu
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Guanjing Cai
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Hui Wang
- Biology Department, College of Life Science, Shantou University, Shantou 515063, China
| | - Zhong Hu
- Biology Department, College of Life Science, Shantou University, Shantou 515063, China
| | - Wei Zheng
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Xueqian Lei
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Xiaoying Zhu
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yao Chen
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Qiuliang Chen
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Hongyan Din
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Hong Xu
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yun Tian
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Lijun Fu
- Fujian Provincial Key Laboratory of Ecology-Toxicological Effects & Control for Emerging Contaminants, Putian University, Putian 351100, China.
| | - Tianling Zheng
- State Key Laboratory of Marine Environmental Science and Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China.
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47
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Toyama T, Kasuya M, Hanaoka T, Kobayashi N, Tanaka Y, Inoue D, Sei K, Morikawa M, Mori K. Growth promotion of three microalgae, Chlamydomonas reinhardtii, Chlorella vulgaris and Euglena gracilis, by in situ indigenous bacteria in wastewater effluent. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:176. [PMID: 29983739 PMCID: PMC6016138 DOI: 10.1186/s13068-018-1174-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 06/15/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND Microalgae are a promising biomass feedstock for biofuels production. The use of wastewater effluent as a nutrient medium would improve the economics of microalgal biofuels production. Bacterial communities in aquatic environments may either stimulate or inhibit microalgal growth. Microalgal productivity could be enhanced if the positive effects of indigenous bacteria could be exploited. However, much is unknown about the effects of indigenous bacteria on microalgal growth and the characteristics of bacterial communities associated with microalgae in microalgae-effluent culture. To assess the effects of the indigenous bacteria in wastewater effluent on microalgal growth, three microalgae, Chlamydomonas reinhardtii, Chlorella vulgaris, and Euglena gracilis, were cultured in two municipal wastewater effluents and one swine wastewater effluent with and without indigenous bacteria for 7 days. RESULTS All microalgae grew better in all effluents with indigenous bacteria than without bacteria. Biomass production of C. reinhardtii, C. vulgaris, and E. gracilis increased > 1.5, 1.8-2.8, and > 2.1-fold, respectively, compared to the axenic cultures of each microalga. The in situ indigenous bacterial communities in the effluents therefore promoted the growth of the three microalgae during 7-day cultures. Furthermore, the total numbers of bacterial 16S rRNA genes in the 7-day microalgae-effluent cultures were 109‒793 times the initial numbers. These results suggest that the three microalgae produced and supplied organic carbon that supported bacterial growth in the effluent. At the phylum and class levels, Proteobacteria (Alphaproteobacteria and Betaproteobacteria) and Bacteroidetes (Sphingobacteriia and Saprospirae) were selectively enriched in all microalgae-effluent cultures. The enriched core bacterial families and genera were functions of the microalgal species and effluents. These results suggest that certain members of the bacterial community promote the growth of their "host" microalgal species. CONCLUSION To enhance their own growth, microalgae may be able to selectively stimulate specific bacterial groups from among the in situ indigenous bacterial community found in wastewater effluent (i.e., microalgae growth-promoting bacteria: MGPB). The MGPB from effluent cultures could be used as "probiotics" to enhance microalgal growth in effluent culture. Wastewater effluent may therefore be a valuable resource, not only of nutrients, but also of MGPB to enable more efficient microalgal biomass production.
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Affiliation(s)
- Tadashi Toyama
- Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511 Japan
| | - Mari Kasuya
- Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511 Japan
| | - Tsubasa Hanaoka
- Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511 Japan
| | - Naoto Kobayashi
- Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511 Japan
| | - Yasuhiro Tanaka
- Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511 Japan
| | - Daisuke Inoue
- Division of Sustainable Energy and Environmental Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Kazunari Sei
- Department of Health Science, Kitasato University, 1-15-1 Kitasato, Sagamihara-Minami, Kanagawa 252-0373 Japan
| | - Masaaki Morikawa
- Division of Biosphere Science, Graduate School of Environmental Science, Hokkaido University, Kita-10 Nishi-5, Kita-ku, Sapporo, 060-0810 Japan
| | - Kazuhiro Mori
- Graduate Faculty of Interdisciplinary Research, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511 Japan
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Maske H, Cajal-Medrano R, Villegas-Mendoza J. Substrate-Limited and -Unlimited Coastal Microbial Communities Show Different Metabolic Responses with Regard to Temperature. Front Microbiol 2017; 8:2270. [PMID: 29218033 PMCID: PMC5703737 DOI: 10.3389/fmicb.2017.02270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 11/03/2017] [Indexed: 11/29/2022] Open
Abstract
Bacteria are the principal consumers of dissolved organic carbon (DOC) in the ocean and predation of bacteria makes organic carbon available to higher trophic levels. The efficiency with which bacteria convert the consumed carbon (C) into biomass (i.e., carbon growth efficiency, Y) determines their ecological as well as biogeochemical role in marine ecosystems. Yet, it is still unclear how changes in temperature will affect Y and, hence, the transfer of consumed C to higher trophic levels. Here, we experimentally investigated the effect of temperature on metabolic functions of coastal microbial communities inoculated in both nutrient-limited chemostats and nutrient–unlimited turbidostats. We inoculated chemostats and turbidostats with coastal microbial communities into seawater culture medium augmented with 20 and 100 μmol L−1 of glucose respectively and measured CO2 production, carbon biomass and cell abundance. Chemostats were cultured between 14 and 26°C and specific growth rates (μ) between 0.05 and 6.0 day−1, turbidostats were cultured between 10 and 26°C with specific growth rates ranging from 28 to 62 day−1. In chemostats under substrate limitation, which is common in the ocean, the specific respiration rate (r, day−1) showed no trend with temperature and was roughly proportional to μ, implying that carbon growth efficiency (Y) displayed no tendency with temperature. The response was very different in turbidostats under temperature-limited, nutrient-repleted growth, here μ increased with temperature but r decreased resulting in an increase of Y with temperature (Q10: 2.6). Comparison of our results with data from the literature on the respiration rate and cell weight of monospecific bacteria indicates that in general the literature data behaved similar to chemostat data, showing no trend in specific respiration with temperature. We conclude that respiration rates of nutrient-limited bacteria measured at a certain temperature cannot be adjusted to different temperatures with a temperature response function similar to Q10 or Arrhenius. However, the cellular respiration rate and carbon demand rate (both: mol C cell−1 day−1) show statistically significant relations with cellular carbon content (mol C cell−1) in chemostats, turbidostats, and the literature data.
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Affiliation(s)
- Helmut Maske
- Departamento de Oceanografía Biológica, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Mexico
| | - Ramón Cajal-Medrano
- Departamento de Oceanografía Biológica, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Mexico.,Facultad de Ciencias Marinas, Universidad Autónoma de Baja California (UABC), Ensenada, Mexico
| | - Josué Villegas-Mendoza
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California (UABC), Ensenada, Mexico
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49
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Ricão Canelhas M, Andersson M, Eiler A, Lindström ES, Bertilsson S. Influence of pulsed and continuous substrate inputs on freshwater bacterial community composition and functioning in bioreactors. Environ Microbiol 2017; 19:5078-5087. [PMID: 29124844 DOI: 10.1111/1462-2920.13979] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 10/17/2017] [Accepted: 10/30/2017] [Indexed: 11/26/2022]
Abstract
Aquatic environments are typically not homogenous, but characterized by changing substrate concentration gradients and nutrient patches. This heterogeneity in substrate availability creates a multitude of niches allowing bacteria with different substrate utilization strategies to hypothetically coexist even when competing for the same substrate. To study the impact of heterogeneous distribution of organic substrates on bacterioplankton, bioreactors with freshwater bacterial communities were fed artificial freshwater medium with acetate supplied either continuously or in pulses. After a month-long incubation, bacterial biomass and community-level substrate uptake rates were twice as high in the pulsed treatment compared to the continuously fed reactors even if the same total amount of acetate was supplied to both treatments. The composition of the bacterial communities emerging in the two treatments differed significantly with specific taxa overrepresented in the respective treatments. The higher estimated growth yield in cultures that received pulsed substrate inputs, imply that such conditions enable bacteria to use resources more efficiently for biomass production. This finding agrees with established concepts of basal maintenance energy requirements and high energetic costs to assimilate substrates at low concentration. Our results further imply that degradation of organic matter is influenced by temporal and spatial heterogeneity in substrate availability.
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Affiliation(s)
- Monica Ricão Canelhas
- Department of Ecology and Genetics/Limnology, Uppsala University, Norbyvägen 18D, Uppsala, 752 36, Sweden
| | - Martin Andersson
- Department of Ecology and Genetics/Limnology, Uppsala University, Norbyvägen 18D, Uppsala, 752 36, Sweden
| | - Alexander Eiler
- Department of Ecology and Genetics/Limnology, Uppsala University, Norbyvägen 18D, Uppsala, 752 36, Sweden
| | - Eva S Lindström
- Department of Ecology and Genetics/Limnology, Uppsala University, Norbyvägen 18D, Uppsala, 752 36, Sweden
| | - Stefan Bertilsson
- Department of Ecology and Genetics/Limnology, Uppsala University, Norbyvägen 18D, Uppsala, 752 36, Sweden
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50
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Luria CM, Amaral-Zettler LA, Ducklow HW, Repeta DJ, Rhyne AL, Rich JJ. Seasonal Shifts in Bacterial Community Responses to Phytoplankton-Derived Dissolved Organic Matter in the Western Antarctic Peninsula. Front Microbiol 2017; 8:2117. [PMID: 29163409 PMCID: PMC5675858 DOI: 10.3389/fmicb.2017.02117] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 10/17/2017] [Indexed: 11/13/2022] Open
Abstract
Bacterial consumption of dissolved organic matter (DOM) drives much of the movement of carbon through the oceanic food web and the global carbon cycle. Understanding complex interactions between bacteria and marine DOM remains an important challenge. We tested the hypothesis that bacterial growth and community succession would respond differently to DOM additions due to seasonal changes in phytoplankton abundance in the environment. Four mesocosm experiments were conducted that spanned the spring transitional period (August-December 2013) in surface waters of the Western Antarctic Peninsula (WAP). Each mesocosm consisted of nearshore surface seawater (50 L) incubated in the laboratory for 10 days. The addition of DOM, in the form of cell-free exudates extracted from Thalassiosira weissflogii diatom cultures led to changes in bacterial abundance, production, and community composition. The timing of each mesocosm experiment (i.e., late winter vs. late spring) influenced the magnitude and direction of bacterial changes. For example, the same DOM treatment applied at different times during the season resulted in different levels of bacterial production and different bacterial community composition. There was a mid-season shift from Collwelliaceae to Polaribacter having the greatest relative abundance after incubation. This shift corresponded to a modest but significant increase in the initial relative abundance of Polaribacter in the nearshore seawater used to set up experiments. This finding supports a new hypothesis that starting community composition, through priority effects, influenced the trajectory of community succession in response to DOM addition. As strong inter-annual variability and long-term climate change may shift the timing of WAP phytoplankton blooms, and the corresponding production of DOM exudates, this study suggests a mechanism by which different seasonal successional patterns in bacterial communities could occur.
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Affiliation(s)
- Catherine M. Luria
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, United States
| | - Linda A. Amaral-Zettler
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, MA, United States
- Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, RI, United States
- NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, Netherlands
| | - Hugh W. Ducklow
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States
| | - Daniel J. Repeta
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Andrew L. Rhyne
- Department of Biology, Marine Biology, and Environmental Science, Roger Williams University, Bristol, RI, United States
| | - Jeremy J. Rich
- School of Marine Sciences, Darling Marine Center, University of Maine, Walpole, ME, United States
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