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Zhou H, Timalsina H, Tang S, Circenis S, Kandume J, Cooke R, Si B, Bhattarai R, Zheng W. Simultaneous removal of nutrients and pharmaceuticals and personal care products using two-stage woodchip bioreactor-biochar treatment systems. JOURNAL OF HAZARDOUS MATERIALS 2024; 480:135882. [PMID: 39298967 DOI: 10.1016/j.jhazmat.2024.135882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 09/08/2024] [Accepted: 09/16/2024] [Indexed: 09/22/2024]
Abstract
The co-occurrence of nutrients and pharmaceuticals and personal care products (PPCPs) in sewage effluent can degrade water quality of the receiving watersheds. This study investigated the simultaneous removal of excess nutrients and PPCP contaminants by developing a novel woodchip bioreactor and biochar (B2) treatment system. The result revealed that woodchip bioreactors could effectively remove nitrate via a denitrification process and adsorb some PPCPs. Biochar as a secondary treatment system significantly reduced the concentrations of PPCPs and dissolved reactive phosphorus (DRP) (p < 0.05), compared to the woodchip bioreactor. The removal efficiencies of all targeted contaminants by the B2 system were evaluated using various hydraulic retention times (HRTs) and biochar types (pelletized versus granular biochar). Longer HRTs and smaller biochar particles (granular biochar) could enhance the removal efficiencies of targeted contaminants. Average contaminant removals were 77.25 % for nitrate-N, 99.03 % for DRP, 69.51 % for ibuprofen, 73.65 % for naproxen, 91.09 % for sitagliptin, and 96.96 % for estrone, with woodchip bioreactor HRTs of 12 ± 1.4 h and granular biochar HRTs of 2.1 ± 0.1 h. Notably, the second-stage biochar systems effectively mitigated by-products leaching from woodchip bioreactors. The presence of PPCPs in the woodchip bioreactors enriched certain species, such as Methylophilus (69.6 %), while inhibiting other microorganisms and reducing microbial community diversity. Furthermore, a scaled-up B2 system was analyzed and assessed, indicating that the proposed engineering treatment system could provide decades of service in real-world applications. Overall, this study suggests that the B2 system has promising applications for addressing emerging and conventional contaminants.
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Affiliation(s)
- Hongxu Zhou
- Illinois Sustainable Technology Center, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA; Department of Agricultural and Biological Engineering, University of Illinois at Urbana, Champaign, Urbana, IL 61801, USA
| | - Haribansha Timalsina
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana, Champaign, Urbana, IL 61801, USA
| | - Shuai Tang
- Key Laboratory of Agricultural Engineering in Structure and Environment, Ministry of Agriculture and Rural Affairs, College of Water Resources and Civil Engineering, China Agricultural University, Beijing 100083, China
| | - Sophie Circenis
- Illinois Sustainable Technology Center, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA
| | - Jason Kandume
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana, Champaign, Urbana, IL 61801, USA
| | - Richard Cooke
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana, Champaign, Urbana, IL 61801, USA
| | - Buchun Si
- Key Laboratory of Agricultural Engineering in Structure and Environment, Ministry of Agriculture and Rural Affairs, College of Water Resources and Civil Engineering, China Agricultural University, Beijing 100083, China
| | - Rabin Bhattarai
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana, Champaign, Urbana, IL 61801, USA.
| | - Wei Zheng
- Illinois Sustainable Technology Center, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA.
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2
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Bicaldo IEC, Padilla KSAR, Tu TH, Chen WT, Mendoza-Pascual MU, Vicera CVB, de Leon JR, Poblete KN, Austria ES, Lopez MLD, Kobayashi Y, Shiah FK, Papa RDS, Okuda N, Wang PL, Lin LH. The methane-oxidizing microbial communities of three maar lakes in tropical monsoon Asia. Front Microbiol 2024; 15:1410666. [PMID: 39044952 PMCID: PMC11263035 DOI: 10.3389/fmicb.2024.1410666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/21/2024] [Indexed: 07/25/2024] Open
Abstract
Methane-oxidizing bacteria (MOB) is a group of planktonic microorganisms that use methane as their primary source of cellular energy. For tropical lakes in monsoon Asia, there is currently a knowledge gap on MOB community diversity and the factors influencing their abundance. Herewith, we present a preliminary assessment of the MOB communities in three maar lakes in tropical monsoon Asia using Catalyzed Reporter Deposition, Fluorescence In-Situ Hybridization (CARD-FISH), 16S rRNA amplicon sequencing, and pmoA gene sequencing. Correlation analysis between MOB abundances and lakes' physicochemical parameters following seasonal monsoon events were performed to explain observed spatial and temporal patterns in MOB diversity. The CARD-FISH analyses detected the three MOB types (I, II, and NC10) which aligned with the results from 16S rRNA amplicons and pmoA gene sequencing. Among community members based on 16S rRNA genes, Proteobacterial Type I MOB (e.g., Methylococcaceae and Methylomonadaceae), Proteobacterial Type II (Methylocystaceae), Verrucomicrobial (Methylacidiphilaceae), Methylomirabilota/NC10 (Methylomirabilaceae), and archaeal ANME-1a were found to be the dominant methane-oxidizers in three maar lakes. Analysis of microbial diversity and distribution revealed that the community compositions in Lake Yambo vary with the seasons and are more distinct during the stratified period. Temperature, DO, and pH were significantly and inversely linked with type I MOB and Methylomirabilota during stratification. Only MOB type I was influenced by monsoon changes. This research sought to establish a baseline for the diversity and ecology of planktonic MOB in tropical monsoon Asia to better comprehend their contribution to the CH4 cycle in tropical freshwater ecosystems.
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Affiliation(s)
- Iona Eunice C. Bicaldo
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| | - Karol Sophia Agape R. Padilla
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Philippine Genome Center, University of the Philippines, Quezon City, Philippines
- Department of Science and Technology, Science Education Institute, Taguig, Philippines
| | - Tzu-Hsuan Tu
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Wan Ting Chen
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
| | - Milette U. Mendoza-Pascual
- Department of Environmental Science, School of Science and Engineering, Ateneo Research Institute for Science and Engineering, Ateneo de Manila University, Quezon City, Philippines
| | | | - Justine R. de Leon
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- Department of Biological Sciences, University of Santo Tomas, Manila, Philippines
| | | | | | - Mark Louie D. Lopez
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Yuki Kobayashi
- Center for Ecological Research, Kyoto University, Shiga, Japan
| | - Fuh-Kwo Shiah
- Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan
| | - Rey Donne S. Papa
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- Department of Biological Sciences, University of Santo Tomas, Manila, Philippines
| | - Noboru Okuda
- Center for Ecological Research, Kyoto University, Shiga, Japan
- Research Center for Inland Seas, Kobe University, Kobe, Japan
- Research Institute for Humanity and Nature, Kamigamo Motoyama, Kita Ward, Kyoto, Japan
| | - Pei-Ling Wang
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
- Research Center for Future Earth, National Taiwan University, Taipei, Taiwan
| | - Li-Hung Lin
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
- Research Center for Future Earth, National Taiwan University, Taipei, Taiwan
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3
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Blais MA, Matveev A, Lovejoy C, Vincent WF. Size-Fractionated Microbiome Structure in Subarctic Rivers and a Coastal Plume Across DOC and Salinity Gradients. Front Microbiol 2022; 12:760282. [PMID: 35046910 PMCID: PMC8762315 DOI: 10.3389/fmicb.2021.760282] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/01/2021] [Indexed: 11/16/2022] Open
Abstract
Little is known about the microbial diversity of rivers that flow across the changing subarctic landscape. Using amplicon sequencing (rRNA and rRNA genes) combined with HPLC pigment analysis and physicochemical measurements, we investigated the diversity of two size fractions of planktonic Bacteria, Archaea and microbial eukaryotes along environmental gradients in the Great Whale River (GWR), Canada. This large subarctic river drains an extensive watershed that includes areas of thawing permafrost, and discharges into southeastern Hudson Bay as an extensive plume that gradually mixes with the coastal marine waters. The microbial communities differed by size-fraction (separated with a 3-μm filter), and clustered into three distinct environmental groups: (1) the GWR sites throughout a 150-km sampling transect; (2) the GWR plume in Hudson Bay; and (3) small rivers that flow through degraded permafrost landscapes. There was a downstream increase in taxonomic richness along the GWR, suggesting that sub-catchment inputs influence microbial community structure in the absence of sharp environmental gradients. Microbial community structure shifted across the salinity gradient within the plume, with changes in taxonomic composition and diversity. Rivers flowing through degraded permafrost had distinct physicochemical and microbiome characteristics, with allochthonous dissolved organic carbon explaining part of the variation in community structure. Finally, our analyses of the core microbiome indicated that while a substantial part of all communities consisted of generalists, most taxa had a more limited environmental range and may therefore be sensitive to ongoing change.
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Affiliation(s)
- Marie-Amélie Blais
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Takuvik Joint International Laboratory, Université Laval, Quebec City, QC, Canada.,Centre for Northern Studies (CEN), Université Laval, Quebec City, QC, Canada
| | - Alex Matveev
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Takuvik Joint International Laboratory, Université Laval, Quebec City, QC, Canada.,Centre for Northern Studies (CEN), Université Laval, Quebec City, QC, Canada
| | - Connie Lovejoy
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Takuvik Joint International Laboratory, Université Laval, Quebec City, QC, Canada.,Québec-Océan, Université Laval, Quebec City, QC, Canada
| | - Warwick F Vincent
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Takuvik Joint International Laboratory, Université Laval, Quebec City, QC, Canada.,Centre for Northern Studies (CEN), Université Laval, Quebec City, QC, Canada
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4
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Vincent K, Holland-Moritz H, Solon AJ, Gendron EMS, Schmidt SK. Crossing Treeline: Bacterioplankton Communities of Alpine and Subalpine Rocky Mountain Lakes. Front Microbiol 2022; 12:533121. [PMID: 35046907 PMCID: PMC8762171 DOI: 10.3389/fmicb.2021.533121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 09/23/2021] [Indexed: 01/04/2023] Open
Abstract
From the aboveground vegetation to the belowground microbes, terrestrial communities differ between the highly divergent alpine (above treeline) and subalpine (below treeline) ecosystems. Yet, much less is known about the partitioning of microbial communities between alpine and subalpine lakes. Our goal was to determine whether the composition of bacterioplankton communities of high-elevation mountain lakes differed across treeline, identify key players in driving the community composition, and identify potential environmental factors that may be driving differences. To do so, we compared bacterial community composition (using 16S rDNA sequencing) of alpine and subalpine lakes in the Southern Rocky Mountain ecoregion at two time points: once in the early summer and once in the late summer. In the early summer (July), shortly after peak runoff, bacterial communities of alpine lakes were distinct from subalpine lakes. Interestingly, by the end of the summer (approximately 5 weeks after the first visit in August), bacterial communities of alpine and subalpine lakes were no longer distinct. Several bacterial amplicon sequence variants (ASVs) were also identified as key players by significantly contributing to the community dissimilarity. The community divergence across treeline found in the early summer was correlated with several environmental factors, including dissolved organic carbon (DOC), pH, chlorophyll-a (chl-a), and total dissolved nitrogen (TDN). In this paper, we offer several potential scenarios driven by both biotic and abiotic factors that could lead to the observed patterns. While the mechanisms for these patterns are yet to be determined, the community dissimilarity in the early summer correlates with the timing of increased hydrologic connections with the terrestrial environment. Springtime snowmelt brings the flushing of mountain watersheds that connects terrestrial and aquatic ecosystems. This connectivity declines precipitously throughout the summer after snowmelt is complete. Regional climate change is predicted to bring alterations to precipitation and snowpack, which can modify the flushing of solutes, nutrients, and terrestrial microbes into lakes. Future preservation of the unique alpine lake ecosystem is dependent on a better understanding of ecosystem partitioning across treeline and careful consideration of terrestrial-aquatic connections in mountain watersheds.
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Affiliation(s)
- Kim Vincent
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, United States
| | - Hannah Holland-Moritz
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, United States
| | - Adam J Solon
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, United States
| | - Eli M S Gendron
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, United States
| | - Steven K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, United States
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5
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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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6
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Ping T, Zeshun X, Penghui M, Yongchao Z. Laboratory investigation on Bacillus subtilis addition to alleviate bio-clogging for constructed wetlands. ENVIRONMENTAL RESEARCH 2021; 194:110642. [PMID: 33352184 DOI: 10.1016/j.envres.2020.110642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 06/03/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
Bio-clogging is a major problem in the operation of constructed wetlands (CWs) and is caused by accumulation of biofilm and extracellular polymeric substances (EPS) in the substrate. B. subtilis can successfully produce α-amylase and endoglucanase, which can degrade polysaccharides and, consequently, disperse the EPS. Therefore, the addition of B. subtilis was used to decrease the bio-clogging of lab-scale vertical-flow constructed wetlands (VFCW) in this study, and the feasibility and performance of VFCWs were assessed. The results indicate that the addition of B. subtilis can degrade the polysaccharides in the clogging matter and thereby increase the porosity of the substrate. The hydraulic conductivity of Column 1 (with addition) increased by six times, which was 57 times that of control (Column 2). Meanwhile, the chemical oxygen demand (COD) removal rate also increased after the addition of B. subtilis. The microbial communities show that the richness and diversity within the substrate increased after addition. The relative abundance of functional groups of chemoheterotrophy, aerobic chemoheterotrophy, as well as that connected to N cycles also increased, which implied the improvement of the pollution removal efficiency. Meanwhile, the copy number of α-amylase and endoglucanase increased significantly in Column 1 with the addition of B. subtilis, which offers further support for a hydrolase-induced reduction of polysaccharides and the efficiency of B. subtilis on bio-clogging alleviation. The results showed that B. subtilis addition is an effective and safe solution to control the bio-clogging for CWs. However, further research about long-term effect assessment and dosing strategy optimization should be conducted.
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Affiliation(s)
- Tang Ping
- The College of Material and Environment Engineering, Hangzhou Dianzi University, Hangzhou, Zhejiang, China
| | - Xiang Zeshun
- The College of Material and Environment Engineering, Hangzhou Dianzi University, Hangzhou, Zhejiang, China
| | - Ma Penghui
- The College of Material and Environment Engineering, Hangzhou Dianzi University, Hangzhou, Zhejiang, China
| | - Zhou Yongchao
- The Institute of Municipal Engineering, The College of Civil Engineering and Architecture, Zhejiang University, Hangzhou, Zhejiang, China.
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Santos-Júnior CD, Sarmento H, de Miranda FP, Henrique-Silva F, Logares R. Uncovering the genomic potential of the Amazon River microbiome to degrade rainforest organic matter. MICROBIOME 2020; 8:151. [PMID: 33126925 PMCID: PMC7597016 DOI: 10.1186/s40168-020-00930-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The Amazon River is one of the largest in the world and receives huge amounts of terrestrial organic matter (TeOM) from the surrounding rainforest. Despite this TeOM is typically recalcitrant (i.e. resistant to degradation), only a small fraction of it reaches the ocean, pointing to a substantial TeOM degradation by the river microbiome. Yet, microbial genes involved in TeOM degradation in the Amazon River were barely known. Here, we examined the Amazon River microbiome by analysing 106 metagenomes from 30 sampling points distributed along the river. RESULTS We constructed the Amazon River basin Microbial non-redundant Gene Catalogue (AMnrGC) that includes ~ 3.7 million non-redundant genes, affiliating mostly to bacteria. We found that the Amazon River microbiome contains a substantial gene-novelty compared to other relevant known environments (rivers and rainforest soil). Genes encoding for proteins potentially involved in lignin degradation pathways were correlated to tripartite tricarboxylates transporters and hemicellulose degradation machinery, pointing to a possible priming effect. Based on this, we propose a model on how the degradation of recalcitrant TeOM could be modulated by labile compounds in the Amazon River waters. Our results also suggest changes of the microbial community and its genomic potential along the river course. CONCLUSIONS Our work contributes to expand significantly our comprehension of the world's largest river microbiome and its potential metabolism related to TeOM degradation. Furthermore, the produced gene catalogue (AMnrGC) represents an important resource for future research in tropical rivers. Video abstract.
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Affiliation(s)
- Célio Dias Santos-Júnior
- Molecular Biology Laboratory, Department of Genetics and Evolution – DGE, Universidade Federal de São Carlos – UFSCar, Rod. Washington Luis KM 235 - Monjolinho, São Carlos, SP 13565-905 Brazil
- Institute of Science and Technology for Brain-Inspired Intelligence – ISTBI, Fudan University, Handan Rd 220, Wu Jiao Chang, Yangpu, Shanghai, 200433 China
| | - Hugo Sarmento
- Laboratory of Microbial Processes & Biodiversity, Department of Hydrobiology – DHB, Universidade Federal de São Carlos – UFSCar, Via Washington Luis KM 235 - Monjolinho, São Carlos, SP 13565-905 Brazil
| | - Fernando Pellon de Miranda
- Centro de Pesquisas e Desenvolvimento Leopoldo Américo Miguez de Mello, Petróleo Brasileiro S.A. (Petrobras), Av. Horácio Macedo 950, Rio de Janeiro, RJ 21941-915 Brazil
| | - Flávio Henrique-Silva
- Molecular Biology Laboratory, Department of Genetics and Evolution – DGE, Universidade Federal de São Carlos – UFSCar, Rod. Washington Luis KM 235 - Monjolinho, São Carlos, SP 13565-905 Brazil
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta 37-49, ES08003, Barcelona, Catalonia Spain
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Kuznetsova EV, Kosolapov DB, Kosolapova NG. Taxonomic and Size–Morphological Groups of Bacterioplankton in Two Mongolian Reservoirs. BIOL BULL+ 2020. [DOI: 10.1134/s1062359019060104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Broman E, Asmala E, Carstensen J, Pinhassi J, Dopson M. Distinct Coastal Microbiome Populations Associated With Autochthonous- and Allochthonous-Like Dissolved Organic Matter. Front Microbiol 2019; 10:2579. [PMID: 31787958 PMCID: PMC6854034 DOI: 10.3389/fmicb.2019.02579] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/24/2019] [Indexed: 11/16/2022] Open
Abstract
Coastal zones are important transitional areas between the land and sea, where both terrestrial and phytoplankton supplied dissolved organic matter (DOM) are respired or transformed. As climate change is expected to increase river discharge and water temperatures, DOM from both allochthonous and autochthonous sources is projected to increase. As these transformations are largely regulated by bacteria, we analyzed microbial community structure data in relation to a 6-month long time-series dataset of DOM characteristics from Roskilde Fjord and adjacent streams, Denmark. The results showed that the microbial community composition in the outer estuary (closer to the sea) was largely associated with salinity and nutrients, while the inner estuary formed two clusters linked to either nutrients plus allochthonous DOM or autochthonous DOM characteristics. In contrast, the microbial community composition in the streams was found to be mainly associated with allochthonous DOM characteristics. A general pattern across the land-to-sea interface was that Betaproteobacteria were strongly associated with humic-like DOM [operational taxonomic units (OTUs) belonging to family Comamonadaceae], while distinct populations were instead associated with nutrients or abiotic variables such as temperature (Cyanobacteria genus Synechococcus) and salinity (Actinobacteria family Microbacteriaceae). Furthermore, there was a stark shift in the relative abundance of OTUs between stream and marine stations. This indicates that as DOM travels through the land-to-sea interface, different bacterial guilds continuously degrade it.
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Affiliation(s)
- Elias Broman
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Eero Asmala
- Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
| | | | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
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10
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Highly diverse fungal communities in carbon-rich aquifers of two contrasting lakes in Northeast Germany. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.04.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Deng L, Ngo HH, Guo W, Zhang H. Pre-coagulation coupled with sponge-membrane filtration for organic matter removal and membrane fouling control during drinking water treatment. WATER RESEARCH 2019; 157:155-166. [PMID: 30953850 DOI: 10.1016/j.watres.2019.03.052] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 03/19/2019] [Accepted: 03/25/2019] [Indexed: 06/09/2023]
Abstract
A new hybrid system was developed in this study for the treatment of drinking water consisting of pre-coagulation using polyaluminium chloride (PACl) and membrane filtration (MF) with sponge cubes acting as biomass carriers (P-SMF). When compared to a conventional MF (CMF) and a MF after coagulation by utilizing PACl (P-MF), better removal of nutrients, UV254 and dissolved organic carbon (DOC) (>65%) was obtained from the P-SMF. The accumulation of biopolymers (including polysaccharides and proteins), humic substances, hydrophilic organics, and other small molecular weight (MW) organic matter in the CMF led to the most severe membrane fouling coupled with the highest pore blocking and cake resistance. Pre-coagulation was ineffective in eliminating small MW and hydrophilic organic matter. Conversely, the larger MW organics (i.e. biopolymers and humic substances), small MW organics and hydrophilic organic compounds could be removed in significantly larger quantities in the P-SMF by PACl coagulation. This was achieved via adsorption and the biodegradation by attached biomass on these sponges and by the suspended sludge. Further analyses of the microbial community indicated that the combined addition of PACl and sponges generated a high enrichment of Zoolgloea, Amaricoccus and Reyranella leading to the reduction of biopolymers, and Flexibacter and Sphingobium were linked to the degradation of humic substances. Moreover, some members of Alphaproteobacteria in the P-SMF may be responsible for the removal of low MW organics. These results suggest that the pre-coagulation process coupled with adding sponge in the MF system is a promising technology for mitigating membrane fouling.
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Affiliation(s)
- Lijuan Deng
- State Key Laboratory of Separation Membranes and Membrane Process, Tianjin Polytechnic University, Tianjin, 300387, China; School of Environmental and Chemical Engineering, Tianjin Polytechnic University, Tianjin, 300387, China.
| | - Huu-Hao Ngo
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Wenshan Guo
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Hongwei Zhang
- State Key Laboratory of Separation Membranes and Membrane Process, Tianjin Polytechnic University, Tianjin, 300387, China; School of Environmental and Chemical Engineering, Tianjin Polytechnic University, Tianjin, 300387, China.
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12
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Yu S, He R, Song A, Huang Y, Jin Z, Liang Y, Li Q, Wang X, Müller WEG, Cao J. Spatial and temporal dynamics of bacterioplankton community composition in a subtropical dammed karst river of southwestern China. Microbiologyopen 2019; 8:e00849. [PMID: 31058472 PMCID: PMC6741127 DOI: 10.1002/mbo3.849] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 12/03/2022] Open
Abstract
River damming influences the hydro‐physicochemical variations in karst water; however, such disruption in bacterioplankton communities has seldom been studied. Here, three sampling sites (city‐river section, reservoir area, and outflow area) of the Ca2+–Mg2+–HCO3−–SO42− water type in the dammed Liu River were selected to investigate the bacterioplankton community composition as identified by high‐throughput 16S rRNA gene sequencing. In the dammed Liu River, thermal regimes have been altered, which has resulted in considerable spatial‐temporal differences in total dissolved solids (TDSs), oxidation‐reduction potential (Eh), dissolved oxygen (DO), and pH and in a different microenvironment for bacterioplankton. Among the dominant bacterioplankton phyla, Proteobacteria, Actinobacteria, Bacteroidetes, and Cyanobacteria account for 38.99%–87.24%, 3.75%–36.55%, 4.77%–38.90%, and 0%–14.44% of the total reads (mean relative frequency), respectively. Bacterioplankton communities are dominated by Brevundimonas, Novosphingobium, Zymomonas, the Actinobacteria hgcIclade, the CL500‐29 marine group, Sediminibacterium, Flavobacterium, Pseudarcicella, Cloacibacterium, and Prochlorococcus. Their abundances covary with spatial‐temporal variations in hydro‐physicochemical factors, as also demonstrated by beta diversity analyses. In addition, temperature plays a pivotal role in maintaining bacterioplankton biodiversity and hydro‐physicochemical variations. This result also highlights the concept that ecological niches for aquatic bacteria in dammed karst rivers do not accidentally occur but are the result of a suite of environmental forces. In addition, bacterioplankton can alter the aquatic carbon/nitrogen cycle and contribute to karst river metabolism.
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Affiliation(s)
- Shi Yu
- Key Laboratory of Karst Dynamics, MLR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, China.,International Research Center on Karst under the Auspices of UNESCO, Guilin, China
| | - Ruoxue He
- Key Laboratory of Karst Dynamics, MLR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, China.,International Research Center on Karst under the Auspices of UNESCO, Guilin, China.,Chengdu Technological University, Chengdu, China
| | - Ang Song
- Key Laboratory of Karst Dynamics, MLR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, China.,International Research Center on Karst under the Auspices of UNESCO, Guilin, China
| | - Yadan Huang
- Graduate School of Guilin Medical University, Guilin, China
| | - Zhenjiang Jin
- Environmental Science and Engineering College, Guilin University of Technology, Guilin, China
| | - Yueming Liang
- Key Laboratory of Karst Dynamics, MLR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, China.,International Research Center on Karst under the Auspices of UNESCO, Guilin, China
| | - Qiang Li
- Key Laboratory of Karst Dynamics, MLR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, China.,International Research Center on Karst under the Auspices of UNESCO, Guilin, China
| | - Xiaohong Wang
- ERC Advanced Investigator Grant Research Group at Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Werner E G Müller
- ERC Advanced Investigator Grant Research Group at Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Jianhua Cao
- Key Laboratory of Karst Dynamics, MLR & GZAR, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, China.,International Research Center on Karst under the Auspices of UNESCO, Guilin, China
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13
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Zoccarato L, Grossart HP. Relationship Between Lifestyle and Structure of Bacterial Communities and Their Functionality in Aquatic Systems. ADVANCES IN ENVIRONMENTAL MICROBIOLOGY 2019. [DOI: 10.1007/978-3-030-16775-2_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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14
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Lew S, Glińska-Lewczuk K. Environmental controls on the abundance of methanotrophs and methanogens in peat bog lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 645:1201-1211. [PMID: 30248845 DOI: 10.1016/j.scitotenv.2018.07.141] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 07/11/2018] [Accepted: 07/11/2018] [Indexed: 06/08/2023]
Abstract
The aim of the present study was to identify the factors that influence the composition of methanogens and methanotrophs in the background prokaryotic community in peat bog lakes. We hypothesized that the microbial composition is a function of the physicochemical conditions of the water and a function of depth-dependent oxygen (DO) concentrations. To address this aim, we collected water samples from subsurface and near-bottom layers, representing oxic and anoxic conditions in 4 peat bog lakes in NE Poland. The structure of methanogenic Archaea and methane-oxidizing bacteria (MOB) was determined with double labeled-fluorescence in situ hybridization (DOPE-FISH). The results showed significant differences in Procaryota communities between the oxic (subsurface) and suboxic/anoxic (near-bottom) layers in peat bog lakes (t-test, p < 0.05). The methanogens from the Archaea domain were observed in anoxic periods, while methanotrophs were present regardless of water depth and season. The abundance of methanogens was inversely correlated with DO and CO2. Methanotrophs adapted better to the changing habitat conditions. The nonmetrical multidimensional scaling (NMS) and partial least square regression (PLS-R) models showed that the methanotrophs in subsurface layers are positively associated with temperature, DOC, and TON while negatively associated with pH. The DO availability is not a prerequisite condition for the presence of methanothrophs. The most important factors for MOB at the bottom were CO2 and TON. Due to a significant role of methanotrophs in the control of the methane emission flux rates, there is a need for further research on factors responsible for methanotroph development in peat bog lakes.
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Affiliation(s)
- Sylwia Lew
- University of Warmia and Mazury in Olsztyn, Department of Microbiology and Mycology, Oczapowskiego str. 1a, 10-719 Olsztyn, Poland.
| | - Katarzyna Glińska-Lewczuk
- University of Warmia and Mazury in Olsztyn, Department of Water Resources, Climatology and Environmental Management, Plac Łódzki 2, 10-719 Olsztyn, Poland.
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15
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Kolmakova OV, Gladyshev MI, Fonvielle JA, Ganzert L, Hornick T, Grossart HP. Effects of zooplankton carcasses degradation on freshwater bacterial community composition and implications for carbon cycling. Environ Microbiol 2018; 21:34-49. [PMID: 30246449 DOI: 10.1111/1462-2920.14418] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 08/30/2018] [Accepted: 09/07/2018] [Indexed: 11/27/2022]
Abstract
Non-predatory mortality of zooplankton provides an abundant, yet, little studied source of high quality labile organic matter (LOM) in aquatic ecosystems. Using laboratory microcosms, we followed the decomposition of organic carbon of fresh 13 C-labelled Daphnia carcasses by natural bacterioplankton. The experimental setup comprised blank microcosms, that is, artificial lake water without any organic matter additions (B), and microcosms either amended with natural humic matter (H), fresh Daphnia carcasses (D) or both, that is, humic matter and Daphnia carcasses (HD). Most of the carcass carbon was consumed and respired by the bacterial community within 15 days of incubation. A shift in the bacterial community composition shaped by labile carcass carbon and by humic matter was observed. Nevertheless, we did not observe a quantitative change in humic matter degradation by heterotrophic bacteria in the presence of LOM derived from carcasses. However, carcasses were the main factor driving the bacterial community composition suggesting that the presence of large quantities of dead zooplankton might affect the carbon cycling in aquatic ecosystems. Our results imply that organic matter derived from zooplankton carcasses is efficiently remineralized by a highly specific bacterial community, but does not interfere with the bacterial turnover of more refractory humic matter.
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Affiliation(s)
- Olesya V Kolmakova
- Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia.,Siberian Federal University, Institute of Fundamental Biology and Biotechnology, Krasnoyarsk, Russia.,Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Michail I Gladyshev
- Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia.,Siberian Federal University, Institute of Fundamental Biology and Biotechnology, Krasnoyarsk, Russia
| | - Jérémy André Fonvielle
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Lars Ganzert
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.,GFZ German Research Centre for Geosciencess, Section 5.3 Geomicrobiology, Potsdam, Germany.,Experimental Phycology and Culture Collection of Algae (SAG), University of Göttingen, Göttingen, Germany
| | - Thomas Hornick
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.,Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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16
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Wang J, Wang C, Li J, Bai P, Li Q, Shen M, Li R, Li T, Zhao J. Comparative Genomics of Degradative Novosphingobium Strains With Special Reference to Microcystin-Degrading Novosphingobium sp. THN1. Front Microbiol 2018; 9:2238. [PMID: 30319567 PMCID: PMC6167471 DOI: 10.3389/fmicb.2018.02238] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/03/2018] [Indexed: 12/21/2022] Open
Abstract
Bacteria in genus Novosphingobium associated with biodegradation of substrates are prevalent in environments such as lakes, soil, sea, wood and sediments. To better understand the characteristics linked to their wide distribution and metabolic versatility, we report the whole genome sequence of Novosphingobium sp. THN1, a microcystin-degrading strain previously isolated by Jiang et al. (2011) from cyanobacteria-blooming water samples from Lake Taihu, China. We performed a genomic comparison analysis of Novosphingobium sp. THN1 with 21 other degradative Novosphingobium strains downloaded from GenBank. Phylogenetic trees were constructed using 16S rRNA genes, core genes, protein-coding sequences, and average nucleotide identity of whole genomes. Orthologous protein analysis showed that the 22 genomes contained 674 core genes and each strain contained a high proportion of distributed genes that are shared by a subset of strains. Inspection of their genomic plasticity revealed a high number of insertion sequence elements and genomic islands that were distributed on both chromosomes and plasmids. We also compared the predicted functional profiles of the Novosphingobium protein-coding genes. The flexible genes and all protein-coding genes produced the same heatmap clusters. The COG annotations were used to generate a dendrogram correlated with the compounds degraded. Furthermore, the metabolic profiles predicted from KEGG pathways showed that the majority of genes involved in central carbon metabolism, nitrogen, phosphate, sulfate metabolism, energy metabolism and cell mobility (above 62.5%) are located on chromosomes. Whereas, a great many of genes involved in degradation pathways (21-50%) are located on plasmids. The abundance and distribution of aromatics-degradative mono- and dioxygenases varied among 22 Novosphingoibum strains. Comparative analysis of the microcystin-degrading mlr gene cluster provided evidence for horizontal acquisition of this cluster. The Novosphingobium sp. THN1 genome sequence contained all the functional genes crucial for microcystin degradation and the mlr gene cluster shared high sequence similarity (≥85%) with the sequences of other microcystin-degrading genera isolated from cyanobacteria-blooming water. Our results indicate that Novosphingobium species have high genomic and functional plasticity, rearranging their genomes according to environment variations and shaping their metabolic profiles by the substrates they are exposed to, to better adapt to their environments.
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Affiliation(s)
- Juanping Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jionghui Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Bai
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Mengyuan Shen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Renhui Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Tao Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jindong Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Protein and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, China
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17
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Arias-Andres M, Kettner MT, Miki T, Grossart HP. Microplastics: New substrates for heterotrophic activity contribute to altering organic matter cycles in aquatic ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 635:1152-1159. [PMID: 29710570 DOI: 10.1016/j.scitotenv.2018.04.199] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/15/2018] [Accepted: 04/15/2018] [Indexed: 05/21/2023]
Abstract
Heterotrophic microbes with the capability to process considerable amounts of organic matter can colonize microplastic particles (MP) in aquatic ecosystems. Weather colonization of microorganisms on MP will alter ecological niche and functioning of microbial communities remains still unanswered. Therefore, we compared the functional diversity of biofilms on microplastics when incubated in three lakes in northeastern Germany differing in trophy and limnological features. For all lakes, we compared heterotrophic activities of MP biofilms with those of microorganisms in the surrounding water by using Biolog® EcoPlates and assessed their oxygen consumption in microcosm assays with and without MP. The present study found that the total biofilm biomass was higher in the oligo-mesotrophic and dystrophic lakes than in the eutrophic lake. In all lakes, functional diversity profiles of MP biofilms consistently differed from those in the surrounding water. However, solely in the oligo-mesotrophic lake MP biofilms had a higher functional richness compared to the ambient water. These results demonstrate that the functionality and hence the ecological role of MP-associated microbial communities are context-dependent, i.e. different environments lead to substantial changes in biomass build up and heterotrophic activities of MP biofilms. We propose that MP surfaces act as new niches for aquatic microorganisms and that the constantly increasing MP pollution has the potential to globally impact carbon dynamics of pelagic environments by altering heterotrophic activities.
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Affiliation(s)
- Maria Arias-Andres
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Dept. Experimental Limnology, Alte Fischerhuette 2, D-16775 Stechlin, Germany; Potsdam University, Inst. of Biochemistry and Biology, Maulbeerallee 2, D-14469 Potsdam, Germany; Central American Institute for Studies on Toxic Substances (IRET), Universidad Nacional, Campus Omar Dengo, P.O. Box 86-3000, Heredia, Costa Rica
| | - Marie Therese Kettner
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Dept. Experimental Limnology, Alte Fischerhuette 2, D-16775 Stechlin, Germany; Potsdam University, Inst. of Biochemistry and Biology, Maulbeerallee 2, D-14469 Potsdam, Germany
| | - Takeshi Miki
- Institute of Oceanography, National Taiwan University, No. 1 Sec. 4 Roosevelt Rd, Taipei 10617, Taiwan; Research Center for Environmental Changes, Academia Sinica, 128 Academia Road, Section 2, Nankang, 11529 Taipei, Taiwan
| | - Hans-Peter Grossart
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Dept. Experimental Limnology, Alte Fischerhuette 2, D-16775 Stechlin, Germany; Potsdam University, Inst. of Biochemistry and Biology, Maulbeerallee 2, D-14469 Potsdam, Germany.
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18
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Salmaso N, Albanese D, Capelli C, Boscaini A, Pindo M, Donati C. Diversity and Cyclical Seasonal Transitions in the Bacterial Community in a Large and Deep Perialpine Lake. MICROBIAL ECOLOGY 2018; 76:125-143. [PMID: 29192335 DOI: 10.1007/s00248-017-1120-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 11/22/2017] [Indexed: 06/07/2023]
Abstract
High-throughput sequencing (HTS) was used to analyze the seasonal variations in the bacterioplankton community composition (BCC) in the euphotic layer of a large and deep lake south of the Alps (Lake Garda). The BCC was analyzed throughout two annual cycles by monthly samplings using the amplification and sequencing of the V3-V4 hypervariable region of the 16S rRNA gene by the MiSeq Illumina platform. The dominant and most diverse bacterioplankton phyla were among the more frequently reported in freshwater ecosystems, including the Proteobacteria, Cyanobacteria, Bacteroidetes, Verrucomicrobia, Actinobacteria, and Planctomycetes. As a distinctive feature, the development of the BCC showed a cyclical temporal pattern in the two analyzed years and throughout the euphotic layer. The recurring temporal development was controlled by the strong seasonality in water temperature and thermal stratification, and by cyclical temporal changes in nutrients and, possibly, by the remarkable annual cyclical development of cyanobacteria and eukaryotic phytoplankton hosting bacterioplankton that characterizes Lake Garda. Further downstream analyses of operational taxonomic units associated to cyanobacteria allowed confirming the presence of the most abundant taxa previously identified by microscopy and/or phylogenetic analyses, as well as the presence of other small Synechococcales/Chroococcales and rare Nostocales never identified so far in the deep lakes south of the Alps. The implications of the high diversity and strong seasonality are relevant, opening perspectives for the definition of common and discriminating patterns characterizing the temporal and spatial distribution in the BCC, and for the application of the new sequencing technologies in the monitoring of water quality in large and deep lakes.
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Affiliation(s)
- Nico Salmaso
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010, San Michele all'Adige, Italy.
| | - Davide Albanese
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Camilla Capelli
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Adriano Boscaini
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Massimo Pindo
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Claudio Donati
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010, San Michele all'Adige, Italy
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19
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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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20
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Echeverría-Vega A, Chong G, Serrano AE, Guajardo M, Encalada O, Parro V, Blanco Y, Rivas L, Rose KC, Moreno-Paz M, Luque JA, Cabrol NA, Demergasso CS. Watershed-Induced Limnological and Microbial Status in Two Oligotrophic Andean Lakes Exposed to the Same Climatic Scenario. Front Microbiol 2018; 9:357. [PMID: 29556224 PMCID: PMC5844981 DOI: 10.3389/fmicb.2018.00357] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 02/14/2018] [Indexed: 12/04/2022] Open
Abstract
Laguna Negra and Lo Encañado are two oligotrophic Andean lakes forming part of the system fed by meltwater from distinct glacial tongues of the Echaurren glacier in central Chile, which is in a recession period. The recent increase in temperature and decline in precipitation have led to an increase of glacial meltwater and sediments entering these lakes. Although the lacustrine systems are also hydrogeologically connected, the limnology of the lakes is strongly controlled by the surface processes related to the respective sub-watersheds and hydrology. Watershed characteristics (area and length, slope, lithology, resistance to erosion, among others) affect the chemical and physical characteristics of both lakes (e.g., nutrient concentration and turbidity). We studied physical and chemical variables and performed 16S rRNA amplicon sequencing to determine the specific microbial signature of the lakes. The transparency, temperature, turbidity and concentrations of chlorophyll-a, dissolved organic matter, nutrients and the total number of cells, revealed the different status of both lakes at the time of sampling. The predominant bacterial groups in both lakes were Proteobacteria, Verrucomicrobia, and Bacteroidetes. Interestingly, the contribution of phototrophs was significantly higher in LN compared to LE (13 and 4% respectively) and the major fraction corresponded to Anoxygenic Phototrophs (AP) represented by Chloroflexi, Alpha, and Betaproteobacteria. Multivariate analyses showed that the nutrient levels and the light availability of both lakes, which finally depend on the hydrological characteristics of the respective watersheds, explain the differential community composition/function. The abundance of a diverse photoheterotrophic bacterioplankton community suggests that the ability to utilize solar energy along with organic and inorganic substrates is a key function in these oligotrophic mountain lakes.
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Affiliation(s)
| | - Guillermo Chong
- Departamento de Ciencias Geológicas, Universidad Católica de Norte, Antofagasta, Chile
| | - Antonio E Serrano
- Centro de Biotecnología, Universidad Católica del Norte, Antofagasta, Chile
| | - Mariela Guajardo
- Centro de Investigación Científica y Tecnológica para la Minería, Antofagasta, Chile
| | - Olga Encalada
- Centro de Biotecnología, Universidad Católica del Norte, Antofagasta, Chile
| | - Victor Parro
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Yolanda Blanco
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Luis Rivas
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Kevin C Rose
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Mercedes Moreno-Paz
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - José A Luque
- Departamento de Ciencias Geológicas, Universidad Católica de Norte, Antofagasta, Chile.,Centro de Investigación Tecnológica del Agua en el Desierto (CEITSAZA), Universidad Católica del Norte, Antofagasta, Chile
| | - Nathalie A Cabrol
- Carl Sagan Center, SETI Institute, Mountain View, CA, United States.,Space Science Division, NASA Ames Research Center, Moffett Field, CA, United States
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21
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Li Q, Yu S, Li L, Liu G, Gu Z, Liu M, Liu Z, Ye Y, Xia Q, Ren L. Microbial Communities Shaped by Treatment Processes in a Drinking Water Treatment Plant and Their Contribution and Threat to Drinking Water Safety. Front Microbiol 2017; 8:2465. [PMID: 29312177 PMCID: PMC5733044 DOI: 10.3389/fmicb.2017.02465] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 11/27/2017] [Indexed: 12/02/2022] Open
Abstract
Bacteria play an important role in water purification in drinking water treatment systems. On one hand, bacteria present in the untreated water may help in its purification through biodegradation of the contaminants. On the other hand, some bacteria may be human pathogens and pose a threat to consumers. The present study investigated bacterial communities using Illumina MiSeq sequencing of 16S rRNA genes and their functions were predicted using PICRUSt in a treatment system, including the biofilms on sand filters and biological activated carbon (BAC) filters, in 4 months. In addition, quantitative analyses of specific bacterial populations were performed by real-time quantitative polymerase chain reaction (qPCR). The bacterial community composition of post-ozonation effluent, BAC effluent and disinfected water varied with sampling time. However, the bacterial community structures at other treatment steps were relatively stable, despite great variations of source water quality, resulting in stable treatment performance. Illumina MiSeq sequencing illustrated that Proteobacteria was dominant bacterial phylum. Chlorine disinfection significantly influenced the microbial community structure, while other treatment processes were synergetic. Bacterial communities in water and biofilms were distinct, and distinctions of bacterial communities also existed between different biofilms. By contrast, the functional composition of biofilms on different filters were similar. Some functional genes related to pollutant degradation were found widely distributed throughout the treatment processes. The distributions of Mycobacterium spp. and Legionella spp. in water and biofilms were revealed by real-time quantitative polymerase chain reaction (qPCR). Most bacteria, including potential pathogens, could be effectively removed by chlorine disinfection. However, some bacteria presented great resistance to chlorine. qPCRs showed that Mycobacterium spp. could not be effectively removed by chlorine. These resistant bacteria and, especially potential pathogens should receive more attention. Redundancy analysis (RDA) showed that turbidity, ammonia nitrogen and total organic carbon (TOC) exerted significant effects on community profiles. Overall, this study provides insight into variations of microbial communities in the treatment processes and aids the optimization of drinking water treatment plant design and operation for public health.
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Affiliation(s)
- Qi Li
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Shuili Yu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Lei Li
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Guicai Liu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Zhengyang Gu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Minmin Liu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Zhiyuan Liu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Yubing Ye
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Qing Xia
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Liumo Ren
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China
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Kim S, Rossmassler K, Broeckling CD, Galloway S, Prenni J, De Long SK. Impact of inoculum sources on biotransformation of pharmaceuticals and personal care products. WATER RESEARCH 2017; 125:227-236. [PMID: 28865372 DOI: 10.1016/j.watres.2017.08.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 08/04/2017] [Accepted: 08/18/2017] [Indexed: 05/25/2023]
Abstract
Limited knowledge of optimal microbial community composition for PPCP biotreatment, and of the microbial phylotypes that drive biotransformation within mixed microbial communities, has hindered the rational design and operation of effective and reliable biological PPCP treatment technologies. Herein, bacterial community composition was investigated as an isolated variable within batch biofilm reactors via comparison of PPCP removals for three distinct inocula. Inocula pre-acclimated to model PPCPs were derived from activated sludge (AS), ditch sediment historically-impacted by wastewater treatment plant effluent (Sd), and material from laboratory-scale soil aquifer treatment (SAT) columns. PPCP removals were found to be substantially higher for AS- and Sd-derived inocula compared to the SAT-derived inocula despite comparable biomass. Removal patterns differed among the 6 model compounds examined (diclofenac, 5-fluorouracil, gabapentin, gemfibrozil, ibuprofen, and triclosan) indicating differences in biotransformation mechanisms. Sphingomonas, Beijerinckia, Methylophilus, and unknown Cytophagaceae were linked with successful PPCP biodegradation via next-generation sequencing of 16S rRNA genes over time. Results indicate the criticality of applying engineering approaches to control bacterial community compositions in biotreatment systems.
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Affiliation(s)
- Sunah Kim
- Colorado State University, Department of Civil and Environmental Engineering, USA
| | - Karen Rossmassler
- Colorado State University, Department of Civil and Environmental Engineering, USA
| | | | - Sarah Galloway
- Colorado State University, Proteomics and Metabolomics Facility, USA
| | - Jessica Prenni
- Colorado State University, Proteomics and Metabolomics Facility, USA
| | - Susan K De Long
- Colorado State University, Department of Civil and Environmental Engineering, USA.
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23
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Paliaga P, Korlević M, Ivančić I, Najdek M. Limited influence of primary treated sewage waters on bacterial abundance, production and community composition in coastal seawaters. MARINE ENVIRONMENTAL RESEARCH 2017; 131:215-226. [PMID: 29032852 DOI: 10.1016/j.marenvres.2017.09.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 09/12/2017] [Accepted: 09/14/2017] [Indexed: 06/07/2023]
Abstract
The response of bacteria in terms of abundance, production and community structure to changes induced by the discharge of primary treated sewage waters was investigated combining microbiological, chemical and molecular tools. The primary treatment did not affect substantially the bacterial community structure in wastewaters and did not reduce the concentrations of fecal indicators. The spatial distribution of the sewage plume was governed by vertical stratification and currents. Bacterial abundance and production in the sea receiving waste waters depended predominantly on environmental conditions. In the waters with the highest concentration of fecal pollution indicators the bacterial community was characterized by allochthonous bacteria belonging to Epsilonproteobacteria, Firmicutes, Gammaproteobacteria and Bacteroidetes. The latter two taxa were also present in unpolluted waters but had a different structure, typical for oligotrophic environments. Although the impact of primary treated sewage waters was limited, a sanitary risk persisted due to the relevant presence of potentially pathogenic bacteria.
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Affiliation(s)
- Paolo Paliaga
- Center for Marine Research, Ruđer Bošković Institute, G. Paliaga 5, 52210 Rovinj, Croatia.
| | - Marino Korlević
- Center for Marine Research, Ruđer Bošković Institute, G. Paliaga 5, 52210 Rovinj, Croatia.
| | - Ingrid Ivančić
- Center for Marine Research, Ruđer Bošković Institute, G. Paliaga 5, 52210 Rovinj, Croatia.
| | - Mirjana Najdek
- Center for Marine Research, Ruđer Bošković Institute, G. Paliaga 5, 52210 Rovinj, Croatia.
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24
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Lau MP, Hupfer M, Grossart HP. Reduction-oxidation cycles of organic matter increase bacterial activity in the pelagic oxycline. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:257-267. [PMID: 28217926 DOI: 10.1111/1758-2229.12526] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Dissolved organic matter (DOM) in aquatic ecosystems contains redox-active moieties, which are prone to oxidation and reduction reactions. Oxidized moieties feature reduction potentials Eh , so that the moieties may be used as terminal electron acceptors (TEAs) in microbial respiration with a thermodynamic energy yield between nitrate and sulfate reduction. Here, we study the response of pelagic freshwater bacteria to exposure to native DOM with varying availabilities of oxidized moieties and hence redox state. Our results show that the prevalence of oxidized DOM favors microbial production and growth in anoxic waters. Reduced DOM in stratified lakes may be oxidized when fluctuations of the oxycline expose DOM in previously anoxic water to epilimnetic oxygen. The resulting oxidized DOM may be rapidly used as TEAs in microbial respiration during subsequent periods of anoxia. We further investigate if the prevalence of these organic electron sinks in anaerobic incubations can induce changes in the microbial community. Our results reveal that DOM traversing transient redox interfaces selects for species that profit from such spatially confined and cyclically restored TEA reservoirs.
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Affiliation(s)
- Maximilian P Lau
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Chemical Analytics and Biogeochemistry, Mueggelseedamm 301, Berlin, Germany
- Universität Greifswald, Institute of Biochemistry, Felix-Hausdorff-Straße 4, 17487, Greifswald, Germany
| | - Michael Hupfer
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Chemical Analytics and Biogeochemistry, Mueggelseedamm 301, Berlin, Germany
| | - Hans-Peter Grossart
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Experimental Limnology, Alte Fischerhuette 2, 16775, Stechlin, Berlin, Germany
- University of Potsdam, Institute of Biology and Biochemistry, Karl-Liebknecht-Straße 24-25, 14476, Potsdam, Germany
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25
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Hayer M, Schwartz E, Marks JC, Koch BJ, Morrissey EM, Schuettenberg AA, Hungate BA. Identification of growing bacteria during litter decomposition in freshwater through H218O quantitative stable isotope probing. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:975-982. [PMID: 27657357 DOI: 10.1111/1758-2229.12475] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 09/15/2016] [Indexed: 06/06/2023]
Abstract
Identification of microorganisms that facilitate the cycling of nutrients in freshwater is paramount to understanding how these ecosystems function. Here, we identify growing aquatic bacteria using H218O quantitative stable isotope probing. During 8 day incubations in 97 atom % H218O, 54% of the taxa grew. The most abundant phyla among growing taxa were Proteobacteria (45%), Bacteroidetes (30%) and Firmicutes (10%). Taxa differed in isotopic enrichment, reflecting variation in DNA replication of bacterial populations. At the class level, the highest atom fraction excess was observed for OPB41 and δ-Proteobacteria. There was no linear relationship between 18 O incorporation and abundance of taxa. δ-Proteobacteria and OPB41 were not abundant, yet the DNA of both taxa was highly enriched in 18 O. Bacteriodetes, in contrast, were abundant but not highly enriched. Our study shows that a large proportion of the bacterial taxa found on decomposing leaf litter grew slowly, and several low abundance taxa were highly enriched. These findings indicating that rare organisms may be important for the decomposition of leaf litter in streams, and that quantitative stable isotope probing with H218O can be used to advance our understanding of microorganisms in freshwater by identifying species that are growing in complex communities.
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Affiliation(s)
- Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86001, USA
| | - Jane C Marks
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86001, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Ember M Morrissey
- Division of Plant and Soil, West Virginia University, Morgantown, WV, 26506, USA
| | - Alexa A Schuettenberg
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86001, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86001, USA
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26
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Gendaszewska D, Liwarska-Bizukojc E. Adaptation of microbial communities in activated sludge to 1-decyl-3-methylimidazolium bromide. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2016; 74:1227-1234. [PMID: 27642842 DOI: 10.2166/wst.2016.317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The effects of 1-decyl-3-methylimidazolium bromide on activated sludge process and microbial composition were investigated. Ionic liquid (IL) was dosed continuously to the laboratory activated sludge system at an influent concentration from 1 to 20 mg l(-1) for about 1 month. As compared to the control test, mean values of degree of chemical oxygen demand removal and degree of biochemical oxygen demand removal were almost remaining constant at a high level, equaling 92.6% and 98.1%, respectively. In addition, no influence of IL on size and shape of flocs was observed. The values of the sludge biotic index indicate that sludge exposed on IL was stable and very well colonized with good biological activity. Increases in Proteobacteria (mainly Variovorax sp., Vogesella sp., Hydrogenophaga sp.), Bacteroidetes (mainly Lewinella sp., Haliscomenobacter sp., Runella sp.) and Nitrospirae were detected in sludge adapted to IL compared to the control system. The results showed that activated sludge can adapt to IL present in wastewater.
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Affiliation(s)
| | - Ewa Liwarska-Bizukojc
- Lodz University of Technology, Institute of Environmental Engineering and Building Installations, Al. Politechniki 6, Lodz 90-924, Poland
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27
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Ramachandran A, Walsh DA. Investigation of XoxF methanol dehydrogenases reveals new methylotrophic bacteria in pelagic marine and freshwater ecosystems. FEMS Microbiol Ecol 2015; 91:fiv105. [DOI: 10.1093/femsec/fiv105] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2015] [Indexed: 11/14/2022] Open
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28
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Sosa OA, Gifford SM, Repeta DJ, DeLong EF. High molecular weight dissolved organic matter enrichment selects for methylotrophs in dilution to extinction cultures. ISME JOURNAL 2015; 9:2725-39. [PMID: 25978545 PMCID: PMC4817625 DOI: 10.1038/ismej.2015.68] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/04/2015] [Accepted: 03/18/2015] [Indexed: 02/06/2023]
Abstract
The role of bacterioplankton in the cycling of marine dissolved organic matter (DOM) is central to the carbon and energy balance in the ocean, yet there are few model organisms available to investigate the genes, metabolic pathways, and biochemical mechanisms involved in the degradation of this globally important carbon pool. To obtain microbial isolates capable of degrading semi-labile DOM for growth, we conducted dilution to extinction cultivation experiments using seawater enriched with high molecular weight (HMW) DOM. In total, 93 isolates were obtained. Amendments using HMW DOM to increase the dissolved organic carbon concentration 4x (280 μM) or 10x (700 μM) the ocean surface water concentrations yielded positive growth in 4–6% of replicate dilutions, whereas <1% scored positive for growth in non-DOM-amended controls. The majority (71%) of isolates displayed a distinct increase in cell yields when grown in increasing concentrations of HMW DOM. Whole-genome sequencing was used to screen the culture collection for purity and to determine the phylogenetic identity of the isolates. Eleven percent of the isolates belonged to the gammaproteobacteria including Alteromonadales (the SAR92 clade) and Vibrio. Surprisingly, 85% of isolates belonged to the methylotrophic OM43 clade of betaproteobacteria, bacteria thought to metabolically specialize in degrading C1 compounds. Growth of these isolates on methanol confirmed their methylotrophic phenotype. Our results indicate that dilution to extinction cultivation enriched with natural sources of organic substrates has a potential to reveal the previously unsuspected relationships between naturally occurring organic nutrients and the microorganisms that consume them.
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Affiliation(s)
- Oscar A Sosa
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, USA.,Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Scott M Gifford
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Daniel J Repeta
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Edward F DeLong
- Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, USA.,Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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29
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Fauteux L, Cottrell MT, Kirchman DL, Borrego CM, Garcia-Chaves MC, del Giorgio PA. Patterns in Abundance, Cell Size and Pigment Content of Aerobic Anoxygenic Phototrophic Bacteria along Environmental Gradients in Northern Lakes. PLoS One 2015; 10:e0124035. [PMID: 25927833 PMCID: PMC4415779 DOI: 10.1371/journal.pone.0124035] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 03/10/2015] [Indexed: 11/19/2022] Open
Abstract
There is now evidence that aerobic anoxygenic phototrophic (AAP) bacteria are widespread across aquatic systems, yet the factors that determine their abundance and activity are still not well understood, particularly in freshwaters. Here we describe the patterns in AAP abundance, cell size and pigment content across wide environmental gradients in 43 temperate and boreal lakes of Québec. AAP bacterial abundance varied from 1.51 to 5.49 x 105 cells mL-1, representing <1 to 37% of total bacterial abundance. AAP bacteria were present year-round, including the ice-cover period, but their abundance relative to total bacterial abundance was significantly lower in winter than in summer (2.6% and 7.7%, respectively). AAP bacterial cells were on average two-fold larger than the average bacterial cell size, thus AAP cells made a greater relative contribution to biomass than to abundance. Bacteriochlorophyll a (BChla) concentration varied widely across lakes, and was not related to AAP bacterial abundance, suggesting a large intrinsic variability in the cellular pigment content. Absolute and relative AAP bacterial abundance increased with dissolved organic carbon (DOC), whereas cell-specific BChla content was negatively related to chlorophyll a (Chla). As a result, both the contribution of AAP bacteria to total prokaryotic abundance, and the cell-specific BChla pigment content were positively correlated with the DOC:Chla ratio, both peaking in highly colored, low-chlorophyll lakes. Our results suggest that photoheterotrophy might represent a significant ecological advantage in highly colored, low-chlorophyll lakes, where DOC pool is chemically and structurally more complex.
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Affiliation(s)
- Lisa Fauteux
- Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Département des sciences biologiques, Université du Québec à Montréal, CP 8888, Montréal, Québec, Canada
| | - Matthew T. Cottrell
- School of Marine Science and Policy, University of Delaware, 700 Pilottown Rd., Lewes, DE 19958, United States of America
| | - David L. Kirchman
- School of Marine Science and Policy, University of Delaware, 700 Pilottown Rd., Lewes, DE 19958, United States of America
| | - Carles M. Borrego
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Campus de Montilivi, E-17071, Girona, Spain
| | - Maria Carolina Garcia-Chaves
- Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Département des sciences biologiques, Université du Québec à Montréal, CP 8888, Montréal, Québec, Canada
| | - Paul A. del Giorgio
- Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Département des sciences biologiques, Université du Québec à Montréal, CP 8888, Montréal, Québec, Canada
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30
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Llirós M, Inceoğlu Ö, García-Armisen T, Anzil A, Leporcq B, Pigneur LM, Viroux L, Darchambeau F, Descy JP, Servais P. Bacterial community composition in three freshwater reservoirs of different alkalinity and trophic status. PLoS One 2014; 9:e116145. [PMID: 25541975 PMCID: PMC4277477 DOI: 10.1371/journal.pone.0116145] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 12/03/2014] [Indexed: 11/21/2022] Open
Abstract
In order to investigate the factors controlling the bacterial community composition (BCC) in reservoirs, we sampled three freshwater reservoirs with contrasted physical and chemical characteristics and trophic status. The BCC was analysed by 16S rRNA gene amplicon 454 pyrosequencing. In parallel, a complete dataset of environmental parameters and phytoplankton community composition was also collected. BCC in the analysed reservoirs resembled that of epilimnetic waters of natural freshwater lakes with presence of Actinobacteria, Alpha- and Betaproteobacteria, Cytophaga–Flavobacteria–Bacteroidetes (CFB) and Verrucomicrobia groups. Our results evidenced that the retrieved BCC in the analysed reservoirs was strongly influenced by pH, alkalinity and organic carbon content, whereas comparatively little change was observed among layers in stratified conditions.
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Affiliation(s)
- Marc Llirós
- Laboratory of Freshwater Ecology, University of Namur, Namur, Belgium
| | - Özgül Inceoğlu
- Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Adriana Anzil
- Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Brussels, Belgium
| | - Bruno Leporcq
- Laboratory of Freshwater Ecology, University of Namur, Namur, Belgium
| | | | - Laurent Viroux
- Laboratory of Freshwater Ecology, University of Namur, Namur, Belgium
| | | | - Jean-Pierre Descy
- Laboratory of Freshwater Ecology, University of Namur, Namur, Belgium
| | - Pierre Servais
- Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Brussels, Belgium
- * E-mail:
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31
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Lew S, Koblížek M, Lew M, Medová H, Glińska-Lewczuk K, Owsianny PM. Seasonal changes of microbial communities in two shallow peat bog lakes. Folia Microbiol (Praha) 2014; 60:165-75. [PMID: 25331011 DOI: 10.1007/s12223-014-0352-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 09/24/2014] [Indexed: 11/24/2022]
Abstract
Peat bog lakes represent important ecosystems in temperate and boreal zones. We investigated the seasonal dynamics of the microbial community in two small peat bog lakes, Kuźnik Olsowy and Kuźnik Bagienny, located in western Poland. Fluorescence in situ hybridization analyses revealed that the bacterial community was dominated by Proteobacteria and Actinobacteria, in addition to a substantial number of archaea. An infrared epifluorescence analysis demonstrated that aerobic anoxygenic phototrophs (AAPs) constituted a significant fraction of bacterial plankton (1-19%). All the bacterial groups exhibited large seasonal changes whose course differed between the studied lakes. While chlorophyll had its maximum during winter or early summer, AAPs peaked in summer, when the growth of this group was stimulated by higher irradiance and elevated water temperatures.
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Affiliation(s)
- Sylwia Lew
- Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1a, 10-957, Olsztyn, Poland,
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Neuenschwander SM, Pernthaler J, Posch T, Salcher MM. Seasonal growth potential of rare lake water bacteria suggest their disproportional contribution to carbon fluxes. Environ Microbiol 2014; 17:781-95. [DOI: 10.1111/1462-2920.12520] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 05/29/2014] [Indexed: 11/30/2022]
Affiliation(s)
| | - Jakob Pernthaler
- Limnological Station; Institute of Plant Biology; University of Zurich; Kilchberg Switzerland
| | - Thomas Posch
- Limnological Station; Institute of Plant Biology; University of Zurich; Kilchberg Switzerland
| | - Michaela M. Salcher
- Limnological Station; Institute of Plant Biology; University of Zurich; Kilchberg Switzerland
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33
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Wurzbacher C, Rösel S, Rychła A, Grossart HP. Importance of saprotrophic freshwater fungi for pollen degradation. PLoS One 2014; 9:e94643. [PMID: 24732324 PMCID: PMC3986395 DOI: 10.1371/journal.pone.0094643] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 03/17/2014] [Indexed: 11/18/2022] Open
Abstract
Fungi and bacteria are the major organic matter (OM) decomposers in aquatic ecosystems. While bacteria are regarded as primary mineralizers in the pelagic zone of lakes and oceans, fungi dominate OM decomposition in streams and wetlands. Recent findings indicate that fungal communities are also active in lakes, but little is known about their diversity and interactions with bacteria. Therefore, the decomposer niche overlap of saprotrophic fungi and bacteria was studied on pollen (as a seasonally recurring source of fine particulate OM) by performing microcosm experiments with three different lake types. Special emphasis was placed on analysis of fungal community composition and diversity. We hypothesized that (I) pollen select for small saprotrophic fungi and at the same time for typical particle-associated bacteria; (II) fungal communities form specific free-living and attached sub-communities in each lake type; (III) the ratio between fungi or bacteria on pollen is controlled by the lake's chemistry. Bacteria-to-fungi ratios were determined by quantitative PCR (qPCR), and bacterial and fungal diversity were studied by clone libraries and denaturing gradient gel electrophoresis (DGGE) fingerprints. A protease assay was used to identify functional differences between treatments. For generalization, systematic differences in bacteria-to-fungi ratios were analyzed with a dataset from the nearby Baltic Sea rivers. High abundances of Chytridiomycota as well as occurrences of Cryptomycota and yeast-like fungi confirm the decomposer niche overlap of saprotrophic fungi and bacteria on pollen. As hypothesized, microbial communities consistently differed between the lake types and exhibited functional differences. Bacteria-to-fungi ratios correlated well with parameters such as organic carbon and pH. The importance of dissolved organic carbon and nitrogen for bacteria-to-fungi ratios was supported by the Baltic Sea river dataset. Our findings highlight the fact that carbon-to-nitrogen ratios may also control fungal contributions to OM decomposition in aquatic ecosystems.
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Affiliation(s)
- Christian Wurzbacher
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department Experimental Limnology, Stechlin, Brandenburg, Germany
- * E-mail:
| | - Stefan Rösel
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department Experimental Limnology, Stechlin, Brandenburg, Germany
| | - Anna Rychła
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department Experimental Limnology, Stechlin, Brandenburg, Germany
| | - Hans-Peter Grossart
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department Experimental Limnology, Stechlin, Brandenburg, Germany
- Potsdam University, Institute for Biochemistry and Biology, Potsdam, Brandenburg, Germany
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Contrasting effects of singlet oxygen and hydrogen peroxide on bacterial community composition in a humic lake. PLoS One 2014; 9:e92518. [PMID: 24667441 PMCID: PMC3965437 DOI: 10.1371/journal.pone.0092518] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 02/24/2014] [Indexed: 11/24/2022] Open
Abstract
Light excitation of humic matter generates reactive oxygen species (ROS) in surface waters of aquatic ecosystems. Abundant ROS generated in humic matter rich lakes include singlet oxygen (1O2) and hydrogen peroxide (H2O2). Because these ROS differ in half-life time and toxicity, we compared their effects on microbial activity (14C-Leucine incorporation) and bacterial community composition (BCC) in surface waters of humic Lake Grosse Fuchskuhle (North-eastern Germany). For this purpose, experiments with water samples collected from the lake were conducted in July 2006, September 2008 and August 2009. Artificially increased 1O2 and H2O2 concentrations inhibited microbial activity in water samples to a similar extent, but the effect of the respective ROS on BCC varied strongly. BCC analysis by 16S rRNA gene clone libraries and RT-PCR DGGE revealed ROS specific changes in relative abundance and activity of major bacterial groups and composition of dominating phylotypes. These changes were consistent in the three experiments performed in different years. The relative abundance of Polynucleobacter necessarius, Limnohabitans-related phylotypes (Betaproteobacteria), and Novosphingobium acidiphilum (Alphaproteobacteria) increased or was not affected by photo-sensitized 1O2 exposure, but decreased after H2O2 exposure. The opposite pattern was found for Actinobacteria of the freshwater AcI-B cluster which were highly sensitive to 1O2 but not to H2O2 exposure. Furthermore, group-specific RT-PCR DGGE analysis revealed that particle-attached P. necessarius and Limnohabitans-related phylotypes exhibit higher resistance to 1O2 exposure compared to free-living populations. These results imply that 1O2 acts as a factor in niche separation of closely affiliated Polynucleobacter and Limnohabitans-related phylotypes. Consequently, oxidative stress caused by photochemical ROS generation should be regarded as an environmental variable determining abundance, activity, and phylotype composition of environmentally relevant bacterial groups, in particular in illuminated and humic matter rich waters.
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Livermore JA, Emrich SJ, Tan J, Jones SE. Freshwater bacterial lifestyles inferred from comparative genomics. Environ Microbiol 2013; 16:746-58. [PMID: 23889754 DOI: 10.1111/1462-2920.12199] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 04/28/2013] [Accepted: 06/19/2013] [Indexed: 11/28/2022]
Abstract
While micro-organisms actively mediate and participate in freshwater ecosystem services, we know little about freshwater microbial genetic diversity. Genome sequences are available for many bacteria from the human microbiome and the ocean (over 800 and 200, respectively), but only two freshwater genomes are currently available: the streamlined genomes of Polynucleobacter necessarius ssp. asymbioticus and the Actinobacterium AcI-B1. Here, we sequenced and analysed draft genomes of eight phylogentically diverse freshwater bacteria exhibiting a range of lifestyle characteristics. Comparative genomics of these bacteria reveals putative freshwater bacterial lifestyles based on differences in predicted growth rate, capability to respond to environmental stimuli and diversity of useable carbon substrates. Our conceptual model based on these genomic characteristics provides a foundation on which further ecophysiological and genomic studies can be built. In addition, these genomes greatly expand the diversity of existing genomic context for future studies on the ecology and genetics of freshwater bacteria.
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Affiliation(s)
- Joshua A Livermore
- Notre Dame Environmental Change Initiative, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN, 46556, USA
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Boeuf D, Cottrell MT, Kirchman DL, Lebaron P, Jeanthon C. Summer community structure of aerobic anoxygenic phototrophic bacteria in the western Arctic Ocean. FEMS Microbiol Ecol 2013; 85:417-32. [PMID: 23560623 DOI: 10.1111/1574-6941.12130] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 04/02/2013] [Accepted: 04/02/2013] [Indexed: 11/26/2022] Open
Abstract
Aerobic anoxygenic phototrophic (AAP) bacteria are found in a range of aquatic and terrestrial environments, potentially playing unique roles in biogeochemical cycles. Although known to occur in the Arctic Ocean, their ecology and the factors that govern their community structure and distribution in this extreme environment are poorly understood. Here, we examined summer AAP abundance and diversity in the North East Pacific and the Arctic Ocean with emphasis on the southern Beaufort Sea. AAP bacteria comprised up to 10 and 14% of the prokaryotic community in the bottom nepheloid layer and surface waters of the Mackenzie plume, respectively. However, relative AAP abundances were low in offshore waters. Environmental pufM clone libraries revealed that AAP bacteria in the Alphaproteobacteria and Betaproteobacteria classes dominated in offshore and in river-influenced surface waters, respectively. The most frequent AAP group was a new uncultivated betaproteobacterial clade whose abundance decreased along the salinity gradient of the Mackenzie plume even though its photosynthetic genes were actively expressed in offshore waters. Our data indicate that AAP bacterial assemblages represented a mixture of freshwater and marine taxa mostly restricted to the Arctic Ocean and highlight the substantial influence of riverine inputs on their distribution in coastal environments.
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Affiliation(s)
- Dominique Boeuf
- UPMC, Univ Paris VI, UMR 7144, Adaptation et Diversité en Milieu Marin, Station Biologique, Roscoff, France
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Llames ME, Del Giorgio PA, Zagarese H, Ferraro M, Izaguirre I. Alternative states drive the patterns in the bacterioplankton composition in shallow Pampean lakes (Argentina). ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:310-321. [PMID: 23584972 DOI: 10.1111/1758-2229.12020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 10/12/2012] [Accepted: 11/22/2012] [Indexed: 06/02/2023]
Abstract
We assessed the influence of environmental factors in shaping the free-living bacterial community structure in a set of shallow lakes characterized by contrasting stable state patterns (clear-vegetated, inorganic-turbid and phytoplankton-turbid). Six temperate shallow lakes from the Pampa Plain (Argentina) were sampled over an annual cycle, and two fingerprinting techniques were applied: a 16S rDNA analysis was performed using denaturing gradient gel electrophoresis (DGGE) profiles, and a 16S-23S internally transcribed spacer region analysis was conducted by means of automated ribosomal intergenic spacer analysis (ARISA) profiles. Our results show that the steady state that characterized the different shallow lakes played a major role in structuring the community: the composition of free-living bacteria differed significantly between clear-vegetated, inorganic-turbid and phytoplankton-turbid shallow lakes. The state of the system was more important in determining these patterns than seasonality, geographical location or degree of hydrological connectivity. Moreover, this strong environmental control was particularly evident in the pattern observed in one of the lakes, which shifted from a clear to a turbid state over the course of the study. This lake showed a directional selection of species from a typical clear-like to a turbid-like community. The combined DGGE/ARISA approach revealed not only broad patterns among different alternative steady states, but also more subtle differences within different regimes.
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Affiliation(s)
- Maria E Llames
- Laboratorio de Ecología y Fotobiología Acuática, Instituto de Investigaciones Biotecnológicas, Instituto Tecnológico Chascomús, CONICET, UNSAM, Camino de Circunvalación Laguna Km 8, Chascomús, pcia. de Buenos Aires, Argentina, CP (B 7130 IWA).
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Zhang X, Fu L, Deng B, Liang Q, Zheng J, Sun J, Zhu H, Peng L, Wang Y, Wenying S, Li W. Bacillus subtilis SC02 supplementation causes alterations of the microbial diversity in grass carp water. World J Microbiol Biotechnol 2013; 29:1645-53. [DOI: 10.1007/s11274-013-1327-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 03/18/2013] [Indexed: 10/27/2022]
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Pajares S, Bonilla-Rosso G, Travisano M, Eguiarte LE, Souza V. Mesocosms of aquatic bacterial communities from the Cuatro Cienegas Basin (Mexico): a tool to test bacterial community response to environmental stress. MICROBIAL ECOLOGY 2012; 64:346-358. [PMID: 22460437 DOI: 10.1007/s00248-012-0045-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 03/08/2012] [Indexed: 05/31/2023]
Abstract
Microbial communities are responsible for important ecosystem processes, and their activities are regulated by environmental factors such as temperature and solar ultraviolet radiation. Here we investigate changes in aquatic microbial community structure, diversity, and evenness in response to changes in temperature and UV radiation. For this purpose, 15 mesocosms were seeded with both microbial mat communities and plankton from natural pools within the Cuatro Cienegas Basin (Mexico). Clone libraries (16S rRNA) were obtained from water samples at the beginning and at the end of the experiment (40 days). Phylogenetic analysis indicated substantial changes in aquatic community composition and structure in response to temperature and UV radiation. Extreme treatments with elevation in temperature or UV radiation reduced diversity in relation to the Control treatments, causing a reduction in richness and increase in dominance, with a proliferation of a few resistant operational taxonomic units. Each phylum was affected differentially by the new conditions, which translates in a differential modification of ecosystem functioning. This suggests that the impact of environmental stress, at least at short term, will reshape the aquatic bacterial communities of this unique ecosystem. This work also demonstrates the possibility of designing manageable synthetic microbial community ecosystems where controlled environmental variables can be manipulated. Therefore, microbial model systems offer a complementary approach to field and laboratory studies of global research problems associated with the environment.
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Affiliation(s)
- Silvia Pajares
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), AP 70-275, CU, Coyoacán, 04510, Mexico City, Mexico
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Peura S, Eiler A, Hiltunen M, Nykänen H, Tiirola M, Jones RI. Bacterial and phytoplankton responses to nutrient amendments in a boreal lake differ according to season and to taxonomic resolution. PLoS One 2012; 7:e38552. [PMID: 22715392 PMCID: PMC3371014 DOI: 10.1371/journal.pone.0038552] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 05/11/2012] [Indexed: 11/18/2022] Open
Abstract
Nutrient limitation and resource competition in bacterial and phytoplankton communities may appear different when considering different levels of taxonomic resolution. Nutrient amendment experiments conducted in a boreal lake on three occasions during one open water season revealed complex responses in overall bacterioplankton and phytoplankton abundance and biovolume. In general, bacteria were dominant in spring, while phytoplankton was clearly the predominant group in autumn. Seasonal differences in the community composition of bacteria and phytoplankton were mainly related to changes in observed taxa, while the differences across nutrient treatments within an experiment were due to changes in relative contributions of certain higher- and lower-level phylogenetic groups. Of the main bacterioplankton phyla, only Actinobacteria had a treatment response that was visible even at the phylum level throughout the season. With increasing resolution (from 75 to 99% sequence similarity) major responses to nutrient amendments appeared using 454 pyrosequencing data of 16S rRNA amplicons. This further revealed that OTUs (defined by 97% sequence similarity) annotated to the same highly resolved freshwater groups appeared to occur during different seasons and were showing treatment-dependent differentiation, indicating that OTUs within these groups were not ecologically coherent. Similarly, phytoplankton species from the same genera responded differently to nutrient amendments even though biovolumes of the majority of taxa increased when both nitrogen and phosphorus were added simultaneously. The bacterioplankton and phytoplankton community compositions showed concurrent trajectories that could be seen in synchronous succession patterns over the season. Overall, our data revealed that the response of both communities to nutrient changes was highly dependent on season and that contradictory results may be obtained when using different taxonomic resolutions.
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Affiliation(s)
- Sari Peura
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.
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Jezbera J, Jezberová J, Koll U, Horňák K, Šimek K, Hahn MW. Contrasting trends in distribution of four major planktonic betaproteobacterial groups along a pH gradient of epilimnia of 72 freshwater habitats. FEMS Microbiol Ecol 2012; 81:467-79. [PMID: 22452571 DOI: 10.1111/j.1574-6941.2012.01372.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 03/16/2012] [Accepted: 03/16/2012] [Indexed: 12/22/2022] Open
Abstract
The distribution and abundance of Betaproteobacteria and three of its genera - Limnohabitans (R-BT065 lineage), Polynucleobacter (including subclusters Polynucleobacter necessarius and Polynucleobacter acidiphobus/Polynucleobacter difficilis), and Methylophilus - across the epilimnia of 72 limnologically diverse freshwater habitats were investigated using fluorescence in situ hybridization. Moreover, seasonal development of Betaproteobacteria subgroups along the longitudinal axis of a reservoir was followed. Betaproteobacteria comprised on average 29.1%, Polynucleobacter 11.6%, P. necessarius 10.1%, P. acidiphobus/difficilis 0.5%, Limnohabitans 8.9%, and Methylophilus 0.9% of total bacterioplankton cells in the investigated habitats. Polynucleobacter necessarius and Limnohabitans coexisted in the majority of habitats but showed contrasting abundance patterns along the pH gradient of habitats (pH, 3.8-8.5). The observed distribution patterns could theoretically be explained by different preferences for substrate sources, that is, substances of humic origin in acidic waters and algal-derived substances in alkaline waters. However, substrate utilization patterns observed in laboratory experiments indicate no coherent group-specific differences in substrate preferences. Interestingly, similar distribution patterns were revealed for Limnohabitans and P. acidiphobus/difficilis, suggesting similar ecological adaptations of these distantly related taxa. Our findings further emphasize that at least two taxa of freshwater Betaproteobacteria represent ecologically diversified groups. Investigations at higher phylogenetic resolution are required for obtaining further insights into their ecology.
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Affiliation(s)
- Jan Jezbera
- Institute for Limnology, Austrian Academy of Sciences, Mondsee, Austria.
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Fujii M, Kojima H, Iwata T, Urabe J, Fukui M. Dissolved organic carbon as major environmental factor affecting bacterioplankton communities in mountain lakes of eastern Japan. MICROBIAL ECOLOGY 2012; 63:496-508. [PMID: 22109097 DOI: 10.1007/s00248-011-9983-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 11/05/2011] [Indexed: 05/31/2023]
Abstract
Relationships between environmental factors and bacterial communities were investigated in 41 freshwater lakes located in mountainous regions of eastern Japan. Bacterioplankton community composition (BCC) was determined by polymerase chain reaction-denaturing gradient gel electrophoresis of the 16S rRNA gene and then evaluated on the basis of physicochemical and biological variables of the lakes. Canonical correspondence analysis revealed that BCC of oligotrophic lakes was significantly influenced by dissolved organic carbon (DOC) content, but its effect was not apparent in the analysis covering all lakes including mesotrophic and eutrophic ones. The generalized linear model showed the negative association of DOC on the taxon richness of bacterioplankton communities. DOC was positively correlated with the catchment area per lake volume, suggesting that a large fraction of DOC supplied to the lake was derived from terrestrial sources. These results suggest that allochthonous DOC has a significant effect on bacterioplankton communities especially in oligotrophic lakes. The genus Polynucleobacter was detected most frequently. The occurrence of Polynucleobacter species was positively associated with DOC and negatively associated with total phosphorus (TP) levels. In addition, TP had a stronger effect than DOC, suggesting that oligotrophy is the most important factor on the occurrence of this genus.
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Affiliation(s)
- Masanori Fujii
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan
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Bauer N, Zwirnmann E, Grossart HP, Hilt S. TRANSFORMATION AND ALLELOPATHY OF NATURAL DISSOLVED ORGANIC CARBON AND TANNIC ACID ARE AFFECTED BY SOLAR RADIATION AND BACTERIA(1). JOURNAL OF PHYCOLOGY 2012; 48:355-364. [PMID: 27009725 DOI: 10.1111/j.1529-8817.2012.01134.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The aim of this study was to test whether abiotic and biotic factors may affect allelopathic properties. Therefore, we investigated how solar radiation and bacteria influence allelopathic effects of the plant-derived, polyphenolic tannic acid (TA) on microalgae. Using a block design, lake water samples with and without TA were exposed to solar radiation or kept in darkness with or without bacteria for 3 weeks. Dissolved organic carbon (DOC), specific size fractions of DOC analyzed by chromatography-organic carbon detection (LC-OCD), and concentrations of total phenolic compounds (TPC) were measured to follow the fate of TA in lake water with natural DOC exposed to photolytic and microbial degradation. DOC and TPC decreased in dark-incubated lake water with TA and bacteria indicating microbial degradation. In contrast, exposure to solar radiation of lake water with TA and bacteria did not decrease DOC. Chromatographic analyses documented an accumulation of DOC mean size fraction designated as humic substances (HS) in sunlit water samples with TA. The recalcitrance of the humic fraction indicates that photolytic degradation may contribute to a DOC less available for bacterial degradation. Subsequent growth tests with Desmodesmus armatus (Chodat) E. Hegewald showed low but reproducible difference in algal growth with lower algal growth rate cultured in photolytically and microbially degraded TA in lake water than cultured in respective dark treatments. This finding highlights the importance of photolytic processes and microbial degradation influencing allelopathic effects and may explain the high potential of allelochemicals for structuring the phytoplankton community composition in naturally illuminated surface waters.
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Affiliation(s)
- Nadine Bauer
- Department of Shallow Lakes, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, 12587 Berlin, GermanyCentral Chemical Laboratory, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, 12587 Berlin, GermanyDepartment of Limnology of Stratified Lakes, Leibniz Institute of Freshwater Ecology and Inland Fisheries Alte Fischerhütte 2, 16775 Stechlin, GermanyDepartment of Shallow Lakes, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, 12587 Berlin, Germany
| | - Elke Zwirnmann
- Department of Shallow Lakes, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, 12587 Berlin, GermanyCentral Chemical Laboratory, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, 12587 Berlin, GermanyDepartment of Limnology of Stratified Lakes, Leibniz Institute of Freshwater Ecology and Inland Fisheries Alte Fischerhütte 2, 16775 Stechlin, GermanyDepartment of Shallow Lakes, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, 12587 Berlin, Germany
| | - Hans-Peter Grossart
- Department of Shallow Lakes, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, 12587 Berlin, GermanyCentral Chemical Laboratory, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, 12587 Berlin, GermanyDepartment of Limnology of Stratified Lakes, Leibniz Institute of Freshwater Ecology and Inland Fisheries Alte Fischerhütte 2, 16775 Stechlin, GermanyDepartment of Shallow Lakes, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, 12587 Berlin, Germany
| | - Sabine Hilt
- Department of Shallow Lakes, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, 12587 Berlin, GermanyCentral Chemical Laboratory, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, 12587 Berlin, GermanyDepartment of Limnology of Stratified Lakes, Leibniz Institute of Freshwater Ecology and Inland Fisheries Alte Fischerhütte 2, 16775 Stechlin, GermanyDepartment of Shallow Lakes, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, 12587 Berlin, Germany
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Rocker D, Brinkhoff T, Grüner N, Dogs M, Simon M. Composition of humic acid-degrading estuarine and marine bacterial communities. FEMS Microbiol Ecol 2012; 80:45-63. [PMID: 22133061 DOI: 10.1111/j.1574-6941.2011.01269.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 11/17/2011] [Accepted: 11/21/2011] [Indexed: 11/27/2022] Open
Abstract
We examined the bacterial decomposition of humic acids (HA) in two flow-through culture experiments, one inoculated by marine and one by estuarine bacterial communities. In both experiments, the cultures were fed with HA media of salinities of 28 and 14, close to their ambient and a distinctly different, foreign salinity. HA were decomposed to > 60% of the initial concentration within 70 days, and the foreign salinity yielded the highest decomposition. A detrended correspondence analysis of denaturing gradient gel electrophoresis (DGGE) banding patterns showed that during incubation, the bacterial community composition underwent distinct changes. A phylogenetic analysis of DGGE bands excised and bacteria isolated at the end on HA as the sole carbon source showed that Alphaproteobacteria and Gammaproteobacteria largely dominated the communities in the marine flow-through cultures, whereas Gammaproteobacteria, Actinobacteria and Alphaproteobacteria dominated the estuarine communities. Eleven of 13 isolates obtained from both experiments were able to grow on HA as the sole carbon source, seven on phenol and three, affiliated to the Roseobacter clade, on various aromatic acids. The bacteria retrieved from the flow-through cultures were closely (96-99%) affiliated to organisms capable of degrading humic matter, aromatic and aliphatic compounds and also to other bacteria reported previously from the Wadden Sea and Weser estuary.
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Affiliation(s)
- Dagmar Rocker
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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Zhang SY, Wang QF, Wan R, Xie SG. Changes in bacterial community of anthracene bioremediation in municipal solid waste composting soil. J Zhejiang Univ Sci B 2012; 12:760-8. [PMID: 21887852 DOI: 10.1631/jzus.b1000440] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are common contaminants in a municipal solid waste (MSW) composting site. Knowledge of changes in microbial structure is useful to identify particular PAH degraders. However, the microbial community in the MSW composting soil and its change associated with prolonged exposure to PAHs and subsequent biodegradation remain largely unknown. In this study, anthracene was selected as a model compound. The bacterial community structure was investigated using terminal restriction fragment length polymorphism (TRFLP) and 16S rRNA gene clone library analysis. The two bimolecular tools revealed a large shift of bacterial community structure after anthracene amendment and subsequent biodegradation. Genera Methylophilus, Mesorhizobium, and Terrimonas had potential links to anthracene biodegradation, suggesting a consortium playing an active role.
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Affiliation(s)
- Shu-ying Zhang
- College of Environmental Sciences and Engineering, Peking University, Beijing, China
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Salka I, Cuperová Z, Mašín M, Koblížek M, Grossart HP. Rhodoferax-related pufM gene cluster dominates the aerobic anoxygenic phototrophic communities in German freshwater lakes. Environ Microbiol 2011; 13:2865-75. [PMID: 21895915 DOI: 10.1111/j.1462-2920.2011.02562.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The presence of aerobic anoxygenic phototrophs (AAPs) has been repeatedly reported from various marine environments, but their distribution in freshwater lakes was neglected until recently. We investigated the phylogenetic composition of AAP communities in 10 lakes in Northeastern Germany with different trophic status including oligotrophic Lake Stechlin and humic matter rich Lake Grosse Fuchskuhle. The AAP community was composed by members of Alpha- and Betaproteobacteria, but their contribution varied largely among the studied lakes. Our results show that AAP community composition in the studied lakes was affected mostly by pH and humic matter content. While alkaline lakes were mostly composed of Betaproteobacteria, the acidic and humic matter rich south-west (SW) basin of Lake Grosse Fuchskule was dominated (87%) by Alphaproteobacteria. The most frequent group within Betaproteobacteria was a cluster of pufM genes which was phylogenetically related to Rhodoferax representing 38.5% of all retrieved sequences. Alphaproteobacteria-related sequences had a broader phylogenetic diversity including six different taxa dominated by Sphingomonas- and Rhodobacter-like bacteria in lakes with alkaline to neutral pH. In the acidic and humic matter-rich SW basin of Lake Grosse Fuchskuhle, however, Methylobacterium-related sequences dominated the AAP community. We suggest that the variable AAP community structure might reflect the potential of these bacteria to cope with the contrasting conditions in freshwater environments.
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Affiliation(s)
- Ivette Salka
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, 16775 Stechlin, Germany
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Newton RJ, Jones SE, Eiler A, McMahon KD, Bertilsson S. A guide to the natural history of freshwater lake bacteria. Microbiol Mol Biol Rev 2011; 75:14-49. [PMID: 21372319 PMCID: PMC3063352 DOI: 10.1128/mmbr.00028-10] [Citation(s) in RCA: 867] [Impact Index Per Article: 66.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Freshwater bacteria are at the hub of biogeochemical cycles and control water quality in lakes. Despite this, little is known about the identity and ecology of functionally significant lake bacteria. Molecular studies have identified many abundant lake bacteria, but there is a large variation in the taxonomic or phylogenetic breadths among the methods used for this exploration. Because of this, an inconsistent and overlapping naming structure has developed for freshwater bacteria, creating a significant obstacle to identifying coherent ecological traits among these groups. A discourse that unites the field is sorely needed. Here we present a new freshwater lake phylogeny constructed from all published 16S rRNA gene sequences from lake epilimnia and propose a unifying vocabulary to discuss freshwater taxa. With this new vocabulary in place, we review the current information on the ecology, ecophysiology, and distribution of lake bacteria and highlight newly identified phylotypes. In the second part of our review, we conduct meta-analyses on the compiled data, identifying distribution patterns for bacterial phylotypes among biomes and across environmental gradients in lakes. We conclude by emphasizing the role that this review can play in providing a coherent framework for future studies.
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Affiliation(s)
- Ryan J. Newton
- Great Lakes WATER Institute, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, Limnology/Department of Ecology & Genetics, Uppsala University, Uppsala, Sweden, Departments of Bacteriology and Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin
| | - Stuart E. Jones
- Great Lakes WATER Institute, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, Limnology/Department of Ecology & Genetics, Uppsala University, Uppsala, Sweden, Departments of Bacteriology and Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin
| | - Alexander Eiler
- Great Lakes WATER Institute, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, Limnology/Department of Ecology & Genetics, Uppsala University, Uppsala, Sweden, Departments of Bacteriology and Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin
| | - Katherine D. McMahon
- Great Lakes WATER Institute, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, Limnology/Department of Ecology & Genetics, Uppsala University, Uppsala, Sweden, Departments of Bacteriology and Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin
| | - Stefan Bertilsson
- Great Lakes WATER Institute, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, Limnology/Department of Ecology & Genetics, Uppsala University, Uppsala, Sweden, Departments of Bacteriology and Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin
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Glaeser SP, Grossart HP, Glaeser J. Singlet oxygen, a neglected but important environmental factor: short-term and long-term effects on bacterioplankton composition in a humic lake. Environ Microbiol 2010; 12:3124-36. [DOI: 10.1111/j.1462-2920.2010.02285.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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49
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Kampe H, Dziallas C, Grossart HP, Kamjunke N. Similar bacterial community composition in acidic mining lakes with different pH and lake chemistry. MICROBIAL ECOLOGY 2010; 60:618-627. [PMID: 20495796 DOI: 10.1007/s00248-010-9679-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Accepted: 04/19/2010] [Indexed: 05/29/2023]
Abstract
As extreme environmental conditions strongly affect bacterial community composition (BCC), we examined whether differences in pH-even at low pH-and in iron and sulfate concentrations lead to changes in BCC of acidic mining lakes. Thereby, we tested the following hypotheses: (1) diversity of the bacterial community in acidic lakes decreases with reducing pH, (2) BCC differs between epilimnion and hypolimnion, and (3) BCC in extremely acidic environments does not vary much over time. Therefore, we investigated the BCC of three acidic lakes with different pH values (2.3, 2.7, and 3.2) by denaturing gradient gel electrophoresis (DGGE) and subsequent sequencing of DGGE bands as well as catalyzed reporter deposition-FISH (CARD-FISH). BCC did not significantly vary among the studied lakes nor differ much between water layers. In contrast, BCC significantly changed over time, which is contradictory to our hypotheses. Bacterial communities were dominated by Alpha-, Beta-, and Gammaproteobacteria, whereas Actino- and Acidobacteria rarely occurred. Cell numbers of both free and attached bacteria were positively related to DOC concentration. Overall, low pH and extreme chemical conditions of the studied lakes led to similar assemblages of bacteria with pronounced temporal differences. This notion indicates that temporal changes in environmental conditions including food web structure also affect unique communities of bacteria thriving at low pH.
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Affiliation(s)
- Heike Kampe
- Institute of Biochemistry and Biology, University of Potsdam, Am Neuen Palais 10, 14469 Potsdam, Germany
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