1
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Li S, Diao M, Wang S, Zhu X, Dong X, Strous M, Ji G. Distinct oxygen isotope fractionations driven by different electron donors during microbial nitrate reduction in lake sediments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:812-821. [PMID: 35691702 DOI: 10.1111/1758-2229.13101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
Microbial nitrate reduction can be driven by organic carbon oxidation, as well as by inorganic electron donors, such as reduced forms of sulfur and iron. An apparent inverse oxygen isotope fractionation effect was observed during nitrate reduction in sediment incubations from five sampling sites of a freshwater lake, Hongze Lake, China. Incubations with organic and inorganic electron donor additions were performed. Especially, the inverse oxygen isotope effect was intensified after glucose addition, whereas the incubations with sulfide and Fe2+ showed normal fractionation factors. Nitrate reductase encoding genes, napA and narG, were analysed with metagenomics. Higher napA/narG ratios were associated with higher oxygen fractionation factors. The most abundant clade (59%) of NapA in the incubation with glucose was affiliated with Rhodocyclales. In contrast, it only accounted for 8%-9% of NapA in the incubations with sulfide and Fe2+ . Differences in nitrate reductases might explain different oxygen isotope effects. Our findings also suggested that large variance of O-nitrate isotope fractionations might have to be considered in the interpretation of natural isotope records.
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Affiliation(s)
- Shengjie Li
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, China
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Muhe Diao
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Shuo Wang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, China
| | - Xianfang Zhu
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, China
| | - Xiaoli Dong
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, China
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2
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Vega M, Ontiveros-Valencia A, Vargas IT, Nerenberg R. Chlorate addition enhances perchlorate reduction in denitrifying membrane-biofilm reactors. Appl Microbiol Biotechnol 2022; 106:4341-4350. [PMID: 35612628 DOI: 10.1007/s00253-022-11976-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 11/29/2022]
Abstract
Perchlorate is a widespread drinking water contaminant with regulatory standards ranging from 2 to 18 μg/L. The hydrogen-based membrane-biofilm reactor (MBfR) can effectively reduce perchlorate, but it is challenging to achieve low-µg/L levels. We explored chlorate addition to increase the abundance of perchlorate-reducing bacteria (PRB) and improve removals. MBfR reactors were operated with and without chlorate addition. Results show that chlorate doubled the abundance of putative PRB (e.g., Rhodocyclales) and improved perchlorate reduction to 23 ± 17 µg/L, compared to 53 ± 37 µg/L in the control. Sulfate reduction was substantially inhibited during chlorate addition, but quickly recovered once suspended. Our results suggest that chlorate addition can enhance perchlorate reduction by providing a selective pressure for PRB. It also decreases net sulfate reduction. KEY POINTS: • Chlorate increased the abundance of perchlorate-reducing bacteria • Chlorate addition improved perchlorate removal • Chlorate appeared to suppress sulfate reduction.
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Affiliation(s)
- Marcela Vega
- Departamento de Ingeniería Hidráulica y Ambiental, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile.,Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, 156 Fitzpatrick Hall of Engineering, South Bend, IN, 46556, USA.,Centro de Desarrollo Urbano Sustentable (CEDEUS), Av. Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - Aura Ontiveros-Valencia
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, 156 Fitzpatrick Hall of Engineering, South Bend, IN, 46556, USA.,División de Ciencias Ambientales, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa de San José 2055, CP 78216, San Luis Potosí, México
| | - Ignacio T Vargas
- Departamento de Ingeniería Hidráulica y Ambiental, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile.,Centro de Desarrollo Urbano Sustentable (CEDEUS), Av. Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - Robert Nerenberg
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, 156 Fitzpatrick Hall of Engineering, South Bend, IN, 46556, USA.
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3
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Zilius M, Bonaglia S, Broman E, Chiozzini VG, Samuiloviene A, Nascimento FJA, Cardini U, Bartoli M. N 2 fixation dominates nitrogen cycling in a mangrove fiddler crab holobiont. Sci Rep 2020; 10:13966. [PMID: 32811860 PMCID: PMC7435186 DOI: 10.1038/s41598-020-70834-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 08/03/2020] [Indexed: 12/20/2022] Open
Abstract
Mangrove forests are among the most productive and diverse ecosystems on the planet, despite limited nitrogen (N) availability. Under such conditions, animal-microbe associations (holobionts) are often key to ecosystem functioning. Here, we investigated the role of fiddler crabs and their carapace-associated microbial biofilm as hotspots of microbial N transformations and sources of N within the mangrove ecosystem. 16S rRNA gene and metagenomic sequencing provided evidence of a microbial biofilm dominated by Cyanobacteria, Alphaproteobacteria, Actinobacteria, and Bacteroidota with a community encoding both aerobic and anaerobic pathways of the N cycle. Dinitrogen (N2) fixation was among the most commonly predicted process. Net N fluxes between the biofilm-covered crabs and the water and microbial N transformation rates in suspended biofilm slurries portray these holobionts as a net N2 sink, with N2 fixation exceeding N losses, and as a significant source of ammonium and dissolved organic N to the surrounding environment. N stable isotope natural abundances of fiddler crab carapace-associated biofilms were within the range expected for fixed N, further suggesting active microbial N2 fixation. These results extend our knowledge on the diversity of invertebrate-microbe associations, and provide a clear example of how animal microbiota can mediate a plethora of essential biogeochemical processes in mangrove ecosystems.
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Affiliation(s)
- Mindaugas Zilius
- Marine Research Institute, Klaipėda University, Klaipeda, Lithuania. .,Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
| | - Stefano Bonaglia
- Marine Research Institute, Klaipėda University, Klaipeda, Lithuania.,Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.,Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Elias Broman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.,Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | | | | | - Francisco J A Nascimento
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.,Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Ulisse Cardini
- Marine Research Institute, Klaipėda University, Klaipeda, Lithuania.,Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Napoli, Italy
| | - Marco Bartoli
- Marine Research Institute, Klaipėda University, Klaipeda, Lithuania.,Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parma, Italy
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4
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Soil Water Contents Control the Responses of Dissolved Nitrogen Pools and Bacterial Communities to Freeze-Thaw in Temperate Soils. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6867081. [PMID: 32258137 PMCID: PMC7086428 DOI: 10.1155/2020/6867081] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 01/30/2020] [Accepted: 02/26/2020] [Indexed: 11/18/2022]
Abstract
Background Freeze-thaw influences soil-dissolved nitrogen (N) pools due to variations in bacterial communities in temperate regions. The availability of soil water is important to soil biogeochemical cycles under frozen conditions. However, it is unclear how soil water content (SWC) mediates the effects of freeze-thaw on soil-dissolved N pools and bacterial communities. Method In this study, freeze-thaw microcosms were incubated at three levels of SWC, including 10% (air-dried soils), 15% (natural SWC), and 30% (wet soils). In addition to measuring soil-dissolved N pools, variations in bacterial communities were examined using high-throughput sequencing. Results and Conclusions. Total dissolved N (TDN), NO3 --N, NH4 +-N, microbial biomass N (MBN), and net N mineralization rate (NNMR) were significantly influenced by SWC, freeze-thaw, and their interaction (NH4 +-N excluded). N immobilization was inhibited under both low and high SWC, which was accompanied by varied bacterial community composition. However, only higher SWC substantially modified the freeze-thaw effects on the soil-dissolved N pools, characterized by a decrease in N mineralization (especially for the content of NO3 --N and NNMR) and an increase in N immobilization (MBN). These scenarios could be significantly correlated to variations in bacterial community composition based on redundancy analysis, especially by species belonging to Bacteroidetes, Nitrospirae, Alphaproteobacteria, Gemmatimonadetes, and Verrucomicrobia (Spearman's correlations). In conclusion, bacterial species passed through biotic (bacterial species) and abiotic filters (soil N pools) in response to freeze-thaw under varied SWC.Bacteroidetes, Nitrospirae, Alphaproteobacteria, Gemmatimonadetes, and Verrucomicrobia (Spearman's correlations). In conclusion, bacterial species passed through biotic (bacterial species) and abiotic filters (soil N pools) in response to freeze-thaw under varied SWC.Nitrospirae, Alphaproteobacteria, Gemmatimonadetes, and Verrucomicrobia (Spearman's correlations). In conclusion, bacterial species passed through biotic (bacterial species) and abiotic filters (soil N pools) in response to freeze-thaw under varied SWC.Alphaproteobacteria, Gemmatimonadetes, and Verrucomicrobia (Spearman's correlations). In conclusion, bacterial species passed through biotic (bacterial species) and abiotic filters (soil N pools) in response to freeze-thaw under varied SWC.Gemmatimonadetes, and Verrucomicrobia (Spearman's correlations). In conclusion, bacterial species passed through biotic (bacterial species) and abiotic filters (soil N pools) in response to freeze-thaw under varied SWC.Verrucomicrobia (Spearman's correlations). In conclusion, bacterial species passed through biotic (bacterial species) and abiotic filters (soil N pools) in response to freeze-thaw under varied SWC.
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5
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Gao X, Luo W, Luo X, Li C, Zhang X, Wang Y. Indigenous microbes induced fluoride release from aquifer sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 252:580-590. [PMID: 31185346 DOI: 10.1016/j.envpol.2019.05.118] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 04/17/2019] [Accepted: 05/14/2019] [Indexed: 06/09/2023]
Abstract
Release of fluoride from Quaternary sediments produces F-contaminated groundwater which threatens the health of millions of people worldwide. Despite the mechanisms of fluoride release from sediments are documented by numerous studies, it remains poorly understood that whether indigenous microbes participate in or not for the formation of F-rich groundwater by releasing fluoride from aquifer sediments. A microcosm-based approach, geochemistry and techniques of microbiology and molecular ecology were conducted together to investigate these mechanisms. Results show that microbes are abundant in high [F] groundwater containing at least 1129 operational taxonomic units (OTUs), and indigenous microbes can have an essential role in the mobilization of fluoride in sediments collected from aquifers in a typical fluorosis area in China. It also shows that for the sediments in this study, fluoride release (ca. 2 mg/L) is coupled with elevated concentrations of Ca (△ = 75 mg/L), Mg (△ = 33 mg/L), Al (△ = 0.2 mg/L) and Mn (△ = 1.4 mg/L). This suggests that the fluoride may source from the dissolution of F-bearing carbonate minerals and/or Al-Mn hydroxides in a local acidic environment. The findings provide additional insights into the biogeochemical circulation of fluoride in natural environment, especially in groundwater system and the development of effective strategies for the management of F-contaminated groundwater worldwide.
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Affiliation(s)
- Xubo Gao
- State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences, Wuhan, 430074, PR China
| | - Wenting Luo
- State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences, Wuhan, 430074, PR China
| | - Xuesong Luo
- College of Resources and Environment, Huangzhong Agriculture University, Wuhan, 430070, PR China; State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences, Wuhan, 430074, PR China
| | - Chengcheng Li
- State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences, Wuhan, 430074, PR China.
| | - Xin Zhang
- State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences, Wuhan, 430074, PR China
| | - Yanxin Wang
- State Key Laboratory of Biogeology and Environmental Geology & School of Environmental Studies, China University of Geosciences, Wuhan, 430074, PR China
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6
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Ecology and Biotechnological Potential of Bacteria Belonging to the Genus Pseudovibrio. Appl Environ Microbiol 2018; 84:AEM.02516-17. [PMID: 29453252 DOI: 10.1128/aem.02516-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Members of the genus Pseudovibrio have been isolated worldwide from a great variety of marine sources as both free-living and host-associated bacteria. So far, the available data depict a group of alphaproteobacteria characterized by a versatile metabolism, which allows them to use a variety of substrates to meet their carbon, nitrogen, sulfur, and phosphorous requirements. Additionally, Pseudovibrio-related bacteria have been shown to proliferate under extreme oligotrophic conditions, tolerate high heavy-metal concentrations, and metabolize potentially toxic compounds. Considering this versatility, it is not surprising that they have been detected from temperate to tropical regions and are often the most abundant isolates obtained from marine invertebrates. Such an association is particularly recurrent with marine sponges and corals, animals that play a key role in benthic marine systems. The data so far available indicate that these bacteria are mainly beneficial to the host, and besides being involved in major nutrient cycles, they could provide the host with both vitamins/cofactors and protection from potential pathogens via the synthesis of antimicrobial secondary metabolites. In fact, the biosynthetic abilities of Pseudovibrio spp. have been emerging in recent years, and both genomic and analytic studies have underlined how these organisms promise novel natural products of biotechnological value.
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7
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Huang L, Chen Z, Wen Q, Zhao L, Lee DJ, Yang L, Wang Y. Insights into Feast-Famine polyhydroxyalkanoate (PHA)-producer selection: Microbial community succession, relationships with system function and underlying driving forces. WATER RESEARCH 2018; 131:167-176. [PMID: 29281810 DOI: 10.1016/j.watres.2017.12.033] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 06/07/2023]
Abstract
The Feast-Famine (FF) process has been frequently used to select polyhydroxyalkanoate (PHA)-accumulating mixed cultures (MCs), but there has been little insight into the ecophysiology of the microbial community during the selection process. In three FF systems with well-defined conditions, synchronized variations in higher-order properties of MCs and complicate microbial community succession mainly including enrichment and elimination of non-top competitors and unexpected turnover of top competitors, were observed. Quantification of PHA-accumulating function genes (phaC) revealed that the top competitors maintained the PHA synthesis by playing consecutive roles when the highly dynamic turnover occurred. Due to its specific physiological characteristics during the PHA-accumulating process, Thauera strain OTU 7 was found to be responsible for the fluctuating SVI, which threatened the robustness of the FF system. This trait was also responsible for its later competitive exclusion by the other PHA-producer, Paracoccus strain OTU 1. Deterministic processes dominated the entire FF system, resulting in the inevitable microbial community succession in the acclimation phase and maintenance of the stable PHA-accumulating function in the maturation phase. However, neutral processes, likely caused by predation from bacterial phages, also occurred, which led to the unpredictable temporal dynamics of the top competitors.
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Affiliation(s)
- Long Huang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Zhiqiang Chen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Qinxue Wen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Lizhi Zhao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106, Taiwan; Department of Chemical Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Lian Yang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yao Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
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8
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Flynn TM, Koval JC, Greenwald SM, Owens SM, Kemner KM, Antonopoulos DA. Parallelized, Aerobic, Single Carbon-Source Enrichments from Different Natural Environments Contain Divergent Microbial Communities. Front Microbiol 2017; 8:2321. [PMID: 29234312 PMCID: PMC5712364 DOI: 10.3389/fmicb.2017.02321] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 11/10/2017] [Indexed: 12/31/2022] Open
Abstract
Microbial communities that inhabit environments such as soil can contain thousands of distinct taxa, yet little is known about how this diversity is maintained in response to environmental perturbations such as changes in the availability of carbon. By utilizing aerobic substrate arrays to examine the effect of carbon amendment on microbial communities taken from six distinct environments (soil from a temperate prairie and forest, tropical forest soil, subalpine forest soil, and surface water and soil from a palustrine emergent wetland), we examined how carbon amendment and inoculum source shape the composition of the community in each enrichment. Dilute subsamples from each environment were used to inoculate 96-well microtiter plates containing triplicate wells amended with one of 31 carbon sources from six different classes of organic compounds (phenols, polymers, carbohydrates, carboxylic acids, amines, amino acids). After incubating each well aerobically in the dark for 72 h, we analyzed the composition of the microbial communities on the substrate arrays as well as the initial inocula by sequencing 16S rRNA gene amplicons using the Illumina MiSeq platform. Comparisons of alpha and beta diversity in these systems showed that, while the composition of the communities that grow to inhabit the wells in each substrate array diverges sharply from that of the original community in the inoculum, these enrichment communities are still strongly affected by the inoculum source. We found most enrichments were dominated by one or several OTUs most closely related to aerobes or facultative anaerobes from the Proteobacteria (e.g., Pseudomonas, Burkholderia, and Ralstonia) or Bacteroidetes (e.g., Chryseobacterium). Comparisons within each substrate array based on the class of carbon source further show that the communities inhabiting wells amended with a carbohydrate differ significantly from those enriched with a phenolic compound. Selection therefore seems to play a role in shaping the communities in the substrate arrays, although some stochasticity is also seen whereby several replicate wells within a single substrate array display strongly divergent community compositions. Overall, the use of highly parallel substrate arrays offers a promising path forward to study the response of microbial communities to perturbations in a changing environment.
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Affiliation(s)
- Theodore M Flynn
- Biosciences Division, Argonne National Laboratory, Argonne, IL, United States
| | - Jason C Koval
- Biosciences Division, Argonne National Laboratory, Argonne, IL, United States
| | | | - Sarah M Owens
- Biosciences Division, Argonne National Laboratory, Argonne, IL, United States
| | - Kenneth M Kemner
- Biosciences Division, Argonne National Laboratory, Argonne, IL, United States
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9
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Yu T, Li M, Niu M, Fan X, Liang W, Wang F. Difference of nitrogen-cycling microbes between shallow bay and deep-sea sediments in the South China Sea. Appl Microbiol Biotechnol 2017; 102:447-459. [DOI: 10.1007/s00253-017-8594-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 10/05/2017] [Accepted: 10/09/2017] [Indexed: 11/29/2022]
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10
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Saad S, Bhatnagar S, Tegetmeyer HE, Geelhoed JS, Strous M, Ruff SE. Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate-reducing benthic microbial populations. Environ Microbiol 2017; 19:4866-4881. [PMID: 28836729 PMCID: PMC5763382 DOI: 10.1111/1462-2920.13895] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/07/2017] [Accepted: 08/15/2017] [Indexed: 12/01/2022]
Abstract
For the anaerobic remineralization of organic matter in marine sediments, sulfate reduction coupled to fermentation plays a key role. Here, we enriched sulfate‐reducing/fermentative communities from intertidal sediments under defined conditions in continuous culture. We transiently exposed the cultures to oxygen or nitrate twice daily and investigated the community response. Chemical measurements, provisional genomes and transcriptomic profiles revealed trophic networks of microbial populations. Sulfate reducers coexisted with facultative nitrate reducers or aerobes enabling the community to adjust to nitrate or oxygen pulses. Exposure to oxygen and nitrate impacted the community structure, but did not suppress fermentation or sulfate reduction as community functions, highlighting their stability under dynamic conditions. The most abundant sulfate reducer in all cultures, related to Desulfotignum balticum, appeared to have coupled both acetate‐ and hydrogen oxidation to sulfate reduction. We describe a novel representative of the widespread uncultured candidate phylum Fermentibacteria (formerly candidate division Hyd24‐12). For this strictly anaerobic, obligate fermentative bacterium, we propose the name ‘USabulitectum silens’ and identify it as a partner of sulfate reducers in marine sediments. Overall, we provide insights into the function of fermentative, as well as sulfate‐reducing microbial communities and their adaptation to a dynamic environment.
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Affiliation(s)
- Sainab Saad
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Srijak Bhatnagar
- UC Davis Genome Center, University of California Davis, Davis, CA, USA
| | - Halina E Tegetmeyer
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Institute for Genome Research and Systems Biology, Center for Biotechnology, University of Bielefeld, Bielefeld, Germany
| | - Jeanine S Geelhoed
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Department of Ecosystem Studies, NIOZ Royal Netherlands Institute for Sea Research, Yerseke, The Netherlands
| | - Marc Strous
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Institute for Genome Research and Systems Biology, Center for Biotechnology, University of Bielefeld, Bielefeld, Germany.,Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - S Emil Ruff
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Department of Geoscience, University of Calgary, Calgary, AB, Canada
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11
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Wittorf L, Bonilla-Rosso G, Jones CM, Bäckman O, Hulth S, Hallin S. Habitat partitioning of marine benthic denitrifier communities in response to oxygen availability. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:486-492. [PMID: 26929183 DOI: 10.1111/1758-2229.12393] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/27/2015] [Accepted: 02/12/2016] [Indexed: 06/05/2023]
Abstract
Denitrification is of global significance for the marine nitrogen budget and the main process for nitrogen loss in coastal sediments. This facultative anaerobic respiratory pathway is modular in nature and the final step, the reduction of nitrous oxide (N2 O), is performed by microorganisms with a complete denitrification pathway as well as those only capable of N2 O reduction. Fluctuating oxygen availability is a significant driver of denitrification in sediments, but the effects on the overall N2 O-reducing community that ultimately controls the emission of N2 O from marine sediments is not well known. To investigate the effects of different oxygen regimes on N2 O reducing communities, coastal marine surface sediment was incubated in microcosms under oxic, anoxic or oscillating oxygen conditions in the overlying water for 137 days. Quantification of the genetic potential for denitrification, anammox and respiratory ammonification indicated that denitrification supported nitrogen removal in these sediments. Furthermore, denitrifiers with a complete pathway were identified as the dominant community involved in N2 O reduction, rather than organisms that are only N2 O reducers. Specific lineages within each group were associated with different oxygen regimes suggesting that oxygen availability in the overlying water is associated with habitat partitioning of N2 O reducers in coastal marine surface sediments.
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Affiliation(s)
- Lea Wittorf
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Germán Bonilla-Rosso
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Christopher M Jones
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ola Bäckman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Stefan Hulth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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12
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Fan Z, Han RM, Ma J, Wang GX. Submerged macrophytes shape the abundance and diversity of bacterial denitrifiers in bacterioplankton and epiphyton in the Shallow Fresh Lake Taihu, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:14102-14114. [PMID: 27048324 DOI: 10.1007/s11356-016-6390-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 02/29/2016] [Indexed: 06/05/2023]
Abstract
nirK and nirS genes are important functional genes involved in the denitrification pathway. Recent studies about these two denitrifying genes are focusing on sediment and wastewater microbe. In this study, we conducted a comparative analysis of the abundance and diversity of denitrifiers in the epiphyton of submerged macrophytes Potamogeton malaianus and Ceratophyllum demersum as well as in bacterioplankton in the shallow fresh lake Taihu, China. Results showed that nirK and nirS genes had significant different niches in epiphyton and bacterioplankton. Bacterioplankton showed greater abundance of nirK gene in terms of copy numbers and lower abundance of nirS gene. Significant difference in the abundance of nirK and nirS genes also existed between the epiphyton from different submerged macrophytes. Similar community diversity yet different community abundance was observed between epiphytic bacteria and bacterioplankton. No apparent seasonal variation was found either in epiphytic bacteria or bacterioplankton; however, environmental parameters seemed to have direct relevancy with nirK and nirS genes. Our study suggested that submerged macrophytes have greater influence than seasonal parameters in shaping the presence and abundance of bacterial denitrifiers. Further investigation needs to focus on the potential contact and relative contribution between denitrifiers and environmental factors.
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Affiliation(s)
- Zhou Fan
- Jiangsu Key Laboratory of Environmental Change and Ecological Construction, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, School of Geography Science, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, Nanjing Normal University, Nanjing, 210023, China
| | - Rui-Ming Han
- Jiangsu Key Laboratory of Environmental Change and Ecological Construction, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, School of Geography Science, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, Nanjing Normal University, Nanjing, 210023, China
| | - Jie Ma
- Jiangsu Key Laboratory of Environmental Change and Ecological Construction, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, School of Geography Science, Nanjing Normal University, Nanjing, 210023, China
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, Nanjing Normal University, Nanjing, 210023, China
| | - Guo-Xiang Wang
- Jiangsu Key Laboratory of Environmental Change and Ecological Construction, Nanjing Normal University, Nanjing, 210023, China.
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, School of Geography Science, Nanjing Normal University, Nanjing, 210023, China.
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control, Nanjing Normal University, Nanjing, 210023, China.
- Nanjing Normal University, School of Geography Science, Wenyuan Road 1, Nanjing, 210023, China.
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Winkel M, Salman-Carvalho V, Woyke T, Richter M, Schulz-Vogt HN, Flood BE, Bailey JV, Mußmann M. Single-cell Sequencing of Thiomargarita Reveals Genomic Flexibility for Adaptation to Dynamic Redox Conditions. Front Microbiol 2016; 7:964. [PMID: 27446006 PMCID: PMC4914600 DOI: 10.3389/fmicb.2016.00964] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 06/03/2016] [Indexed: 11/25/2022] Open
Abstract
Large, colorless sulfur-oxidizing bacteria (LSB) of the family Beggiatoaceae form thick mats at sulfidic sediment surfaces, where they efficiently detoxify sulfide before it enters the water column. The genus Thiomargarita harbors the largest known free-living bacteria with cell sizes of up to 750 μm in diameter. In addition to their ability to oxidize reduced sulfur compounds, some Thiomargarita spp. are known to store large amounts of nitrate, phosphate and elemental sulfur internally. To date little is known about their energy yielding metabolic pathways, and how these pathways compare to other Beggiatoaceae. Here, we present a draft single-cell genome of a chain-forming “Candidatus Thiomargarita nelsonii Thio36”, and conduct a comparative analysis to five draft and one full genome of other members of the Beggiatoaceae. “Ca. T. nelsonii Thio36” is able to respire nitrate to both ammonium and dinitrogen, which allows them to flexibly respond to environmental changes. Genes for sulfur oxidation and inorganic carbon fixation confirmed that “Ca. T. nelsonii Thio36” can function as a chemolithoautotroph. Carbon can be fixed via the Calvin–Benson–Bassham cycle, which is common among the Beggiatoaceae. In addition we found key genes of the reductive tricarboxylic acid cycle that point toward an alternative CO2 fixation pathway. Surprisingly, “Ca. T. nelsonii Thio36” also encodes key genes of the C2-cycle that convert 2-phosphoglycolate to 3-phosphoglycerate during photorespiration in higher plants and cyanobacteria. Moreover, we identified a novel trait of a flavin-based energy bifurcation pathway coupled to a Na+-translocating membrane complex (Rnf). The coupling of these pathways may be key to surviving long periods of anoxia. As other Beggiatoaceae “Ca. T. nelsonii Thio36” encodes many genes similar to those of (filamentous) cyanobacteria. In summary, the genome of “Ca. T. nelsonii Thio36” provides additional insight into the ecology of giant sulfur-oxidizing bacteria, and reveals unique genomic features for the Thiomargarita lineage within the Beggiatoaceae.
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Affiliation(s)
- Matthias Winkel
- Molecular Ecology Group, Department of Molecular Ecology, Max Planck Institute for Marine MicrobiologyBremen, Germany; Section Geomicrobiology, GFZ German Research Centre for Geoscience, Helmholtz Centre PotsdamPotsdam, Germany
| | - Verena Salman-Carvalho
- HGF MPG Joint Research Group for Deep-sea Ecology and Technology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Walnut Creek CA, USA
| | - Michael Richter
- Microbial Genomics and Bioinformatics Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | | | - Beverly E Flood
- Department of Earth Sciences, University of Minnesota, Minneapolis MN, USA
| | - Jake V Bailey
- Department of Earth Sciences, University of Minnesota, Minneapolis MN, USA
| | - Marc Mußmann
- Molecular Ecology Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology Bremen, Germany
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14
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Stenuit B, Agathos SN. Deciphering microbial community robustness through synthetic ecology and molecular systems synecology. Curr Opin Biotechnol 2015; 33:305-17. [PMID: 25880923 DOI: 10.1016/j.copbio.2015.03.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 03/16/2015] [Accepted: 03/22/2015] [Indexed: 01/09/2023]
Abstract
Microbial ecosystems exhibit specific robustness attributes arising from the assembly and interaction networks of diverse, heterogeneous communities challenged by fluctuating environmental conditions. Synthetic ecology provides new insights into key biodiversity-stability relationships and robustness determinants of host-associated or environmental microbiomes. Driven by the advances of meta-omics technologies and bioinformatics, community-centered approaches (defined as molecular systems synecology) combined with the development of dynamic and mechanistic mathematical models make it possible to decipher and predict the outcomes of microbial ecosystems under disturbances. Beyond discriminating the normal operating range and natural, intrinsic dynamics of microbial processes from systems-level responses to environmental forcing, predictive modeling is poised to be integrated within prescriptive analytical frameworks and thus provide guidance in decision-making and proactive microbial resource management.
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Affiliation(s)
- Ben Stenuit
- Université catholique de Louvain, Earth & Life Institute, Bioengineering Laboratory, Place Croix du Sud 2, bte. L07.05.19, B-1348 Louvain-la-Neuve, Belgium.
| | - Spiros N Agathos
- Université catholique de Louvain, Earth & Life Institute, Bioengineering Laboratory, Place Croix du Sud 2, bte. L07.05.19, B-1348 Louvain-la-Neuve, Belgium
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15
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Intergenomic comparisons highlight modularity of the denitrification pathway and underpin the importance of community structure for N2O emissions. PLoS One 2014; 9:e114118. [PMID: 25436772 PMCID: PMC4250227 DOI: 10.1371/journal.pone.0114118] [Citation(s) in RCA: 227] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 11/05/2014] [Indexed: 11/19/2022] Open
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas and the predominant ozone depleting substance. The only enzyme known to reduce N2O is the nitrous oxide reductase, encoded by the nosZ gene, which is present among bacteria and archaea capable of either complete denitrification or only N2O reduction to di-nitrogen gas. To determine whether the occurrence of nosZ, being a proxy for the trait N2O reduction, differed among taxonomic groups, preferred habitats or organisms having either NirK or NirS nitrite reductases encoded by the nirK and nirS genes, respectively, 652 microbial genomes across 18 phyla were compared. Furthermore, the association of different co-occurrence patterns with enzymes reducing nitric oxide to N2O encoded by nor genes was examined. We observed that co-occurrence patterns of denitrification genes were not randomly distributed across taxa, as specific patterns were found to be more dominant or absent than expected within different taxonomic groups. The nosZ gene had a significantly higher frequency of co-occurrence with nirS than with nirK and the presence or absence of a nor gene largely explained this pattern, as nirS almost always co-occurred with nor. This suggests that nirS type denitrifiers are more likely to be capable of complete denitrification and thus contribute less to N2O emissions than nirK type denitrifiers under favorable environmental conditions. Comparative phylogenetic analysis indicated a greater degree of shared evolutionary history between nosZ and nirS. However 30% of the organisms with nosZ did not possess either nir gene, with several of these also lacking nor, suggesting a potentially important role in N2O reduction. Co-occurrence patterns were also non-randomly distributed amongst preferred habitat categories, with several habitats showing significant differences in the frequencies of nirS and nirK type denitrifiers. These results demonstrate that the denitrification pathway is highly modular, thus underpinning the importance of community structure for N2O emissions.
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