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Yao S, Zhang K, Yang S, Li Z, Wang Y, Ma F, Chen P, Zhu T. A novel coupling process to replace the traditional multi-stage anammox process-sulfur autotrophic denitrification coupled anammox system. Biodegradation 2024; 35:565-582. [PMID: 38844743 DOI: 10.1007/s10532-024-10077-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/16/2024] [Indexed: 07/14/2024]
Abstract
A novel coupling process to replace the traditional multi-stage anammox process-sulfur autotrophic denitrification (SAD) coupled anaerobic ammonium oxidation (anammox) system was designed, which solved problems of nitrate produced in anammox process and low nitrate conversion rate caused by nitrite accumulation in SAD process. Different filter structures (SAD filter and anammox granular sludge) were investigated to further explore the excellent performance of the novel integrated reactor. The results of sequential batch experiments indicated that nitrite accumulation occurred during SAD, which inhibited the conversion of nitrate to dinitrogen gas. When SAD filter and anammox granular sludge were added to packed bed reactor simultaneously, the nitrate removal rate increased by 37.21% and effluent nitrite concentration decreased by 100% compared to that achieved using SAD. The stratified filter structure solved groove flow. Different proportion influence of SAD filter and anammox granular sludge on the stratified filter structure was evaluated. More suitable ratio of SAD filter to anammox granular sludge was 2:1. Proteobacteria (57.26%), Bacteroidetes (20.12%) and Chloroflexi (9.95%) were the main phyla. The dominant genera of denitrification functional bacteria were Thiobacillus (39.80%), Chlorobaculum (3.99%), norank_f_PHOs-HE36 (2.90%) and Ignavibacterium (2.64%). The dominant genus of anammox bacterium was Candidatus_Kuenenia (3.05%).
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Affiliation(s)
- Sai Yao
- Institute of Process Equipment and Environmental Engineering, School of Mechanical Engineering and Automation, Northeastern University, 3-11, Wenhua Road, Heping District, Shenyang, 110004, People's Republic of China
| | - Kuo Zhang
- College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, People's Republic of China
| | - Song Yang
- Liaoning Coning Testing Co., Ltd, No. 603, 16-6, Wensu Street, Hunnan District, Shenyang, 110170, People's Republic of China
| | - Zijun Li
- Institute of Process Equipment and Environmental Engineering, School of Mechanical Engineering and Automation, Northeastern University, 3-11, Wenhua Road, Heping District, Shenyang, 110004, People's Republic of China
| | - Youzhao Wang
- Institute of Process Equipment and Environmental Engineering, School of Mechanical Engineering and Automation, Northeastern University, 3-11, Wenhua Road, Heping District, Shenyang, 110004, People's Republic of China
| | - Feng Ma
- Institute of Process Equipment and Environmental Engineering, School of Mechanical Engineering and Automation, Northeastern University, 3-11, Wenhua Road, Heping District, Shenyang, 110004, People's Republic of China
| | - Pu Chen
- Institute of Process Equipment and Environmental Engineering, School of Mechanical Engineering and Automation, Northeastern University, 3-11, Wenhua Road, Heping District, Shenyang, 110004, People's Republic of China
| | - Tong Zhu
- Institute of Process Equipment and Environmental Engineering, School of Mechanical Engineering and Automation, Northeastern University, 3-11, Wenhua Road, Heping District, Shenyang, 110004, People's Republic of China.
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2
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Fournier C, Fiedler A, Weidele M, Kautz H, Schleheck D. Description of a 'plankton filtration bias' in sequencing-based bacterial community analysis and of an Arduino microcontroller-based flowmeter device that can help to resolve it. PLoS One 2024; 19:e0303937. [PMID: 38805423 PMCID: PMC11132488 DOI: 10.1371/journal.pone.0303937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 05/03/2024] [Indexed: 05/30/2024] Open
Abstract
Diversity studies of aquatic picoplankton (bacterioplankton) communities using size-class filtration, DNA extraction, PCR and sequencing of phylogenetic markers, require a robust methodological pipeline, since biases have been demonstrated essentially at all levels, including DNA extraction, primer choice and PCR. Even different filtration volumes of the same plankton sample and, thus, different biomass loading of the filters, can distort the sequencing results. In this study, we designed an Arduino microcontroller-based flowmeter that records the decrease of initial (maximal) flowrate as proxy for increasing biomass loading and clogging of filters during plankton filtration. The device was tested using freshwater plankton of Lake Constance, and total DNA was extracted and an 16S rDNA amplicon was sequenced. We confirmed that different filtration volumes used for the same water sample affect the sequencing results. Differences were visible in alpha and beta diversities and across all taxonomic ranks. Taxa most affected were typical freshwater Actinobacteria and Bacteroidetes, increasing up to 38% and decreasing up to 29% in relative abundance, respectively. In another experiment, a lake water sample was filtered undiluted and three-fold diluted, and each filtration was stopped once the flowrate had reduced to 50% of initial flowrate, hence, at the same degree of filter clogging. The three-fold diluted sample required three-fold filtration volumes, while equivalent amounts of total DNA were extracted and differences across all taxonomic ranks were not statistically significant compared to the undiluted controls. In conclusion, this work confirms a volume/biomass-dependent bacterioplankton filtration bias for sequencing-based community analyses and provides an improved procedure for controlling biomass loading during filtrations and recovery of equivalent amounts of DNA from samples independent of the plankton density. The application of the device can also avoid the distorting of sequencing results as caused by the plankton filtration bias.
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Affiliation(s)
- Corentin Fournier
- Department of Biology, Microbial Ecology and Limnic Microbiology, Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Alexander Fiedler
- Department of Biology, Microbial Ecology and Limnic Microbiology, Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Maximilian Weidele
- Scientific Engineering and Manufacturing Services, University of Konstanz, Konstanz, Germany
| | - Harald Kautz
- Scientific Engineering and Manufacturing Services, University of Konstanz, Konstanz, Germany
| | - David Schleheck
- Department of Biology, Microbial Ecology and Limnic Microbiology, Limnological Institute, University of Konstanz, Konstanz, Germany
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Cram JA, Hollins A, McCarty AJ, Martinez G, Cui M, Gomes ML, Fuchsman CA. Microbial diversity and abundance vary along salinity, oxygen, and particle size gradients in the Chesapeake Bay. Environ Microbiol 2024; 26:e16557. [PMID: 38173306 DOI: 10.1111/1462-2920.16557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024]
Abstract
Marine snow and other particles are abundant in estuaries, where they drive biogeochemical transformations and elemental transport. Particles range in size, thereby providing a corresponding gradient of habitats for marine microorganisms. We used standard normalized amplicon sequencing, verified with microscopy, to characterize taxon-specific microbial abundances, (cells per litre of water and per milligrams of particles), across six particle size classes, ranging from 0.2 to 500 μm, along the main stem of the Chesapeake Bay estuary. Microbial communities varied in salinity, oxygen concentrations, and particle size. Many taxonomic groups were most densely packed on large particles (in cells/mg particles), yet were primarily associated with the smallest particle size class, because small particles made up a substantially larger portion of total particle mass. However, organisms potentially involved in methanotrophy, nitrite oxidation, and sulphate reduction were found primarily on intermediately sized (5-180 μm) particles, where species richness was also highest. All abundant ostensibly free-living organisms, including SAR11 and Synecococcus, appeared on particles, albeit at lower abundance than in the free-living fraction, suggesting that aggregation processes may incorporate them into particles. Our approach opens the door to a more quantitative understanding of the microscale and macroscale biogeography of marine microorganisms.
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Affiliation(s)
- Jacob A Cram
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
| | - Ashley Hollins
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
| | - Alexandra J McCarty
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
- Marine Advisory Program, Virginia Institute of Marine Science, Gloucester, Virginia, USA
| | | | - Minming Cui
- Earth and Planetary Sciences, Johns Hopkins University, Baltimore, Maryland, USA
| | - Maya L Gomes
- Earth and Planetary Sciences, Johns Hopkins University, Baltimore, Maryland, USA
| | - Clara A Fuchsman
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, Maryland, USA
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Cabrol L, Capo E, van Vliet DM, von Meijenfeldt FAB, Bertilsson S, Villanueva L, Sánchez-Andrea I, Björn E, G. Bravo A, Heimburger Boavida LE. Redox gradient shapes the abundance and diversity of mercury-methylating microorganisms along the water column of the Black Sea. mSystems 2023; 8:e0053723. [PMID: 37578240 PMCID: PMC10469668 DOI: 10.1128/msystems.00537-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 06/16/2023] [Indexed: 08/15/2023] Open
Abstract
In the global context of seawater deoxygenation triggered by climate change and anthropogenic activities, changes in redox gradients impacting biogeochemical transformations of pollutants, such as mercury, become more likely. Being the largest anoxic basin worldwide, with high concentrations of the potent neurotoxic methylmercury (MeHg), the Black Sea is an ideal natural laboratory to provide new insights about the link between dissolved oxygen concentration and hgcAB gene-carrying (hgc+) microorganisms involved in the formation of MeHg. We combined geochemical and microbial approaches to assess the effect of vertical redox gradients on abundance, diversity, and metabolic potential of hgc+ microorganisms in the Black Sea water column. The abundance of hgcA genes [congruently estimated by quantitative PCR (qPCR) and metagenomics] correlated with MeHg concentration, both maximal in the upper part of the anoxic water. Besides the predominant Desulfobacterales, hgc+ microorganisms belonged to a unique assemblage of diverse-previously underappreciated-anaerobic fermenters from Anaerolineales, Phycisphaerae (characteristic of the anoxic and sulfidic zone), Kiritimatiellales, and Bacteroidales (characteristic of the suboxic zone). The metabolic versatility of Desulfobacterota differed from strict sulfate reduction in the anoxic water to reduction of various electron acceptors in the suboxic water. Linking microbial activity and contaminant concentration in environmental studies is rare due to the complexity of biological pathways. In this study, we disentangle the role of oxygen in shaping the distribution of Hg-methylating microorganisms consistently with MeHg concentration, and we highlight their taxonomic and metabolic niche partitioning across redox gradients, improving the prediction of the response of marine communities to the expansion of oxygen-deficient zones. IMPORTANCE Methylmercury (MeHg) is a neurotoxin detected at high concentrations in certain marine ecosystems, posing a threat to human health. MeHg production is mainly mediated by hgcAB gene-carrying (hgc+) microorganisms. Oxygen is one of the main factors controlling Hg methylation; however, its effect on the diversity and ecology of hgc+ microorganisms remains unknown. Under the current context of seawater deoxygenation, mercury cycling is expected to be disturbed. Here, we show the strong effect of oxygen gradients on the distribution of potential Hg methylators. In addition, we show for the first time the significant contribution of a unique assemblage of potential fermenters from Anaerolineales, Phycisphaerae, and Kiritimatiellales to Hg methylation, stratified in different redox niches along the Black Sea gradient. Our results considerably expand the known taxonomic diversity and ecological niches prone to the formation of MeHg and contribute to better apprehend the consequences of oxygen depletion in seawater.
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Affiliation(s)
- Léa Cabrol
- Aix Marseille University, Univ. Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France
- Institute of Ecology and Biodiversity (IEB), University of Chile, Santiago, Chile
| | - Eric Capo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, Barcelona, Spain
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
| | - Daan M. van Vliet
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
- Wageningen Food and Biobased Research, Wageningen, the Netherlands
| | - F. A. Bastiaan von Meijenfeldt
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, the Netherlands
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, the Netherlands
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, Utrecht, the Netherlands
| | - Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Erik Björn
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Andrea G. Bravo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, Barcelona, Spain
| | - Lars-Eric Heimburger Boavida
- Aix Marseille University, Univ. Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France
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Hamdan HZ, Ahmad FA, Zayyat RM, Salam DA. Spatio-temporal variation of the microbial community of the coast of Lebanon in response to petroleum hydrocarbon pollution. MARINE POLLUTION BULLETIN 2023; 192:115037. [PMID: 37201353 DOI: 10.1016/j.marpolbul.2023.115037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 05/20/2023]
Abstract
In this study, the coast of Lebanon was analyzed for the dynamic changes in sediment microbial communities in response to a major petroleum oil spill and tar contamination that occurred in the summer of 2021. Spatio-temporal variations in the microbial structure along the shores of Lebanon were assessed in comparison to baseline microbial structure determined in 2017. Microbial community structure and diversity were determined using Illumina MiSeq technology and DADA2 pipeline. The results show a significant diversity of microbial populations along the Lebanese shore, and a significant change in the sediment microbial structure within four years. Namely, Woeseia, Blastopirellula, and Muriicola were identified in sediment samples collected in year 2017, while a higher microbial diversity was observed in 2021 with Woeseia, Halogranum, Bacillus, and Vibrio prevailing in beach sediments. In addition, the results demonstrate a significant correlation between certain hydrocarbon degraders, such as Marinobacter and Vibrio, and measured hydrocarbon concentrations.
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Affiliation(s)
- Hamdan Z Hamdan
- Department of Natural Sciences, School of Arts & Sciences, Lebanese American University, Beirut, Lebanon
| | - Farah Ali Ahmad
- Department of Civil and Environmental Engineering, Maroun Semaan Faculty of Engineering and Architecture, American University of Beirut, Beirut, Lebanon
| | - Ramez M Zayyat
- Department of Civil and Environmental Engineering, Maroun Semaan Faculty of Engineering and Architecture, American University of Beirut, Beirut, Lebanon
| | - Darine A Salam
- Department of Civil and Environmental Engineering, Maroun Semaan Faculty of Engineering and Architecture, American University of Beirut, Beirut, Lebanon.
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Geller-McGrath D, Mara P, Taylor GT, Suter E, Edgcomb V, Pachiadaki M. Diverse secondary metabolites are expressed in particle-associated and free-living microorganisms of the permanently anoxic Cariaco Basin. Nat Commun 2023; 14:656. [PMID: 36746960 PMCID: PMC9902471 DOI: 10.1038/s41467-023-36026-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/12/2023] [Indexed: 02/08/2023] Open
Abstract
Secondary metabolites play essential roles in ecological interactions and nutrient acquisition, and are of interest for their potential uses in medicine and biotechnology. Genome mining for biosynthetic gene clusters (BGCs) can be used for the discovery of new compounds. Here, we use metagenomics and metatranscriptomics to analyze BGCs in free-living and particle-associated microbial communities through the stratified water column of the Cariaco Basin, Venezuela. We recovered 565 bacterial and archaeal metagenome-assembled genomes (MAGs) and identified 1154 diverse BGCs. We show that differences in water redox potential and microbial lifestyle (particle-associated vs. free-living) are associated with variations in the predicted composition and production of secondary metabolites. Our results indicate that microbes, including understudied clades such as Planctomycetota, potentially produce a wide range of secondary metabolites in these anoxic/euxinic waters.
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Affiliation(s)
| | - Paraskevi Mara
- Geology & Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Elizabeth Suter
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
- Biology, Chemistry and Environmental Studies Department, Molloy College, Rockville Centre, NY, USA
| | - Virginia Edgcomb
- Geology & Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| | - Maria Pachiadaki
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
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7
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Ren ZQ, Wang H, Zhang LG, Du XN, Huang BC, Jin RC. A review of anammox-based nitrogen removal technology: From microbial diversity to engineering applications. BIORESOURCE TECHNOLOGY 2022; 363:127896. [PMID: 36070811 DOI: 10.1016/j.biortech.2022.127896] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
The anaerobic ammonium oxidation (anammox) process has the advantages of high efficiency and low energy consumption, so it has broad application prospects in biological denitrification of wastewater. However, the application of anammox technology to existing wastewater treatment is still challenging. The main problems are the insufficient supply of nitrite and the susceptibility of anammox bacteria to environmental factors. In this paper, from the perspective of the diversity of anammox bacteria, the habitats and characteristics of anammox bacteria of different genera were compared. At the same time, laboratory research and engineering applications of anammox technology in treating wastewater from different sources were reviewed, and the progress of and obstacles to the practical application of anammox technology were clarified. Finally, a focus for future research was proposed to intensively study the water quality barrier factors of anammox and its regulation strategies. Meanwhile, a combined process was developed and optimized on this basis.
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Affiliation(s)
- Zhi-Qi Ren
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Hao Wang
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Li-Ge Zhang
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Xue-Ning Du
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Bao-Cheng Huang
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; School of Engineering, Hangzhou Normal University, Hangzhou 310018, China
| | - Ren-Cun Jin
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; School of Engineering, Hangzhou Normal University, Hangzhou 310018, China.
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8
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Zheng G, Cheng Y, Zhu Y, Yang J, Wang L, Chen T. Correlation of microbial dynamics to odor production and emission in full-scale sewage sludge composting. BIORESOURCE TECHNOLOGY 2022; 360:127597. [PMID: 35835422 DOI: 10.1016/j.biortech.2022.127597] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/03/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Odor is inevitably produced during sewage sludge composting, and the subsequent pollution hinders the further development of composting technologies. Third-generation high-throughput sequencing was used to analyze microbial community succession, and the correlations between odor and microbial communities were evaluated. Hydrogen sulfide (47.5-87.9 %) and ammonia (9.4-49.9 %) contributed majorly to odor emissions, accounting for 93.7-98.5 % of the emissions. Volatile sulfur compounds were mainly produced in the mesophilic and pre-thermophilic phases (43.0-83.4 %), whereas ammonia was mainly produced in the thermophilic phase (52.1-59.4 %). Microorganisms dominant in the mesophilic and thermophilic phases correlated positively with odor production in the following order: Rhodocyclaceae > Clostridiaceae_1 > Hyphomicrobiaceae > Acidimicrobiales > Family_XI, whereas those dominant in the cooling phase showed negative correlations with odor production in the following order: Bacillus > Sphingobacteriaceae > Pseudomonadaceae > DSSF69 > Chitinophagaceae. The back mixing of mature compost is expected to serve as an economical measure for controlling odor during sewage sludge composting.
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Affiliation(s)
- Guodi Zheng
- Center for Environmental Remediation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yuan Cheng
- Center for Environmental Remediation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanli Zhu
- Center for Environmental Remediation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junxing Yang
- Center for Environmental Remediation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Wang
- College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Tongbin Chen
- Center for Environmental Remediation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
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Marois C, Girard C, Klanten Y, Vincent WF, Culley AI, Antoniades D. Local Habitat Filtering Shapes Microbial Community Structure in Four Closely Spaced Lakes in the High Arctic. Front Microbiol 2022; 13:779505. [PMID: 35222324 PMCID: PMC8873593 DOI: 10.3389/fmicb.2022.779505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 01/20/2022] [Indexed: 11/13/2022] Open
Abstract
Arctic lakes are experiencing increasingly shorter periods of ice cover due to accelerated warming at northern high latitudes. Given the control of ice cover thickness and duration over many limnological processes, these changes will have pervasive effects. However, due to their remote and extreme locations even first-order data on lake ecology is lacking for many ecosystems. The aim of this study was to characterize and compare the microbial communities of four closely spaced lakes in Stuckberry Valley (northern Ellesmere Island, Canadian Arctic Archipelago), in the coastal margin zone of the Last Ice Area, that differed in their physicochemical, morphological and catchment characteristics. We performed high-throughput amplicon sequencing of the V4 16S rRNA gene to provide inter- and intra-lake comparisons. Two deep (>25 m) and mostly oxygenated lakes showed highly similar community assemblages that were distinct from those of two shallower lakes (<10 m) with anoxic bottom waters. Proteobacteria, Verrucomicrobia, and Planctomycetes were the major phyla present in the four water bodies. One deep lake contained elevated proportions of Cyanobacteria and Thaumarchaeota that distinguished it from the others, while the shallow lakes had abundant communities of predatory bacteria, as well as microbes in their bottom waters that contribute to sulfur and methane cycles. Despite their proximity, our data suggest that local habitat filtering is the primary determinant of microbial diversity in these systems. This study provides the first detailed examination of the microbial assemblages of the Stuckberry lakes system, resulting in new insights into the microbial ecology of the High Arctic.
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Affiliation(s)
- Catherine Marois
- Département de Biochimie, Microbiologie et Bio-Informatique, Université Laval, Québec, QC, Canada
- Centre d’Études Nordiques (CEN), Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Catherine Girard
- Centre d’Études Nordiques (CEN), Université Laval, Québec, QC, Canada
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC, Canada
| | - Yohanna Klanten
- Centre d’Études Nordiques (CEN), Université Laval, Québec, QC, Canada
- Département de Géographie, Université Laval, Québec, QC, Canada
| | - Warwick F. Vincent
- Centre d’Études Nordiques (CEN), Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Département de Biologie, Université Laval, Québec, QC, Canada
| | - Alexander I. Culley
- Département de Biochimie, Microbiologie et Bio-Informatique, Université Laval, Québec, QC, Canada
- Centre d’Études Nordiques (CEN), Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Dermot Antoniades
- Centre d’Études Nordiques (CEN), Université Laval, Québec, QC, Canada
- Département de Géographie, Université Laval, Québec, QC, Canada
- *Correspondence: Dermot Antoniades,
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Liu L, Lv AP, Narsing Rao MP, Ming YZ, Salam N, Li MM, Liu ZT, Zhang XT, Zhang JY, Xian WD, Jiao JY, Li WJ. Diversity and Distribution of Anaerobic Ammonium Oxidation Bacteria in Hot Springs of Conghua, China. Front Microbiol 2022; 12:739234. [PMID: 35145488 PMCID: PMC8822059 DOI: 10.3389/fmicb.2021.739234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 12/07/2021] [Indexed: 11/13/2022] Open
Abstract
Anaerobic ammonium oxidation (anammox) is an important process of the nitrogen cycle, and the anammox bacteria have been studied in a wide variety of environments. However, the distribution, diversity, and abundance of anammox bacteria in hot springs remain enigmatic. In this study, the anammox process was firstly investigated in hot springs of Conghua, China. Anammox-like bacterial sequences that closely affiliated to “Candidatus Brocadia,” “Candidatus Kuenenia,” “Candidatus Scalindua,” “Candidatus Anammoxoglobus,” and “Candidatus Jettenia” were detected. Several operational taxonomic units (OTUs) from this study shared low sequence identities to the 16S rRNA gene of the known anammox bacteria, suggesting that they might be representing putative novel anammox bacteria. A quantitative PCR analysis of anammox-specific 16S rRNA gene confirmed that the abundance of anammox bacteria ranged from 1.60 × 104 to 1.20 × 107 copies L–1. Nitrate was a key environmental factor defining the geographical distribution of the anammox bacterial community in the hot spring ecosystem. Dissolved inorganic carbon had a significant influence on anammox bacterial biodiversity. Our findings for the first time revealed that the diverse anammox bacteria, including putative novel anammox bacterial candidates, were present in Conghua hot spring, which extended the existence of anammox bacteria to the hot springs in China and expands our knowledge of the biogeography of anammox bacteria. This work filled up the research lacuna of anammox bacteria in Chinese hot spring habitat and would guide for enrichment strategies of anammox bacteria of Conghua hot springs.
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Affiliation(s)
- Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ai-Ping Lv
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yu-Zhen Ming
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Nimaichand Salam
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ze-Tao Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiao-Tong Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jing-Yi Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Jian-Yu Jiao,
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
- *Correspondence: Wen-Jun Li,
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11
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Fuchsman CA, Cherubini L, Hays MD. An analysis of protists in Pacific oxygen deficient zones: implications for Prochlorococcus and N 2 -producing bacteria. Environ Microbiol 2022; 24:1790-1804. [PMID: 34995411 DOI: 10.1111/1462-2920.15893] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 11/26/2022]
Abstract
Ocean oxygen deficient zones (ODZs) host 30%-50% of marine N2 production. Cyanobacteria photosynthesizing in the ODZ create a secondary chlorophyll maximum and provide organic matter to N2 -producing bacteria. This chlorophyll maximum is thought to occur due to reduced grazing in anoxic waters. We first examine ODZ protists with long amplicon reads. We then use non-primer-based methods to examine the composition and relative abundance of protists in metagenomes from the Eastern Tropical North and South Pacific ODZs and compare these data to the oxic Hawaii Ocean Time-series (HOT) in the North Pacific. We identify and quantify protists in proportion to the total microbial community. From metagenomic data, we see a large drop in abundance of fungi and protists such as choanoflagellates, radiolarians, cercozoa and ciliates in the ODZs but not in the oxic mesopelagic at HOT. Diplonemid euglenozoa were the only protists that increased in the ODZ. Dinoflagellates and foraminifera reads were also present in the ODZ though less abundant compared to oxic waters. Denitrification has been found in foraminifera but not yet in dinoflagellates. DNA techniques cannot separate dinoflagellate cells and cysts. Metagenomic analysis found taxonomic groups missed by amplicon sequencing and identified trends in abundance.
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Affiliation(s)
- Clara A Fuchsman
- University of Maryland Center for Environmental Science Horn Point Laboratory, Cambridge, MD, 21613, USA
| | - Luca Cherubini
- Maryland Sea Grant College, College Park, MD, 20740, USA
| | - Matthew D Hays
- University of Maryland Center for Environmental Science Horn Point Laboratory, Cambridge, MD, 21613, USA
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12
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Lodha T, Narvekar S, Karodi P. Classification of uncultivated anammox bacteria and Candidatus Uabimicrobium into new classes and provisional nomenclature as Candidatus Brocadiia classis nov. and Candidatus Uabimicrobiia classis nov. of the phylum Planctomycetes and novel family Candidatus Scalinduaceae fam. nov to accommodate the genus Candidatus Scalindua. Syst Appl Microbiol 2021; 44:126272. [PMID: 34735804 DOI: 10.1016/j.syapm.2021.126272] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 11/26/2022]
Abstract
The phylum Planctomycetes is metabolically unique group of bacteria divided in two classes Planctomycetia and Phycisphaerae. Anaerobic ammonia-oxidizing (anammox) bacteria are the uncultured representatives of the phylum Planctomycetes. Anammox bacterial genera are placed in the family Candidatus (Ca.) Brocadiaceae of the order Ca. Brocadiales, assigned to the class Planctomycetia. Phylogenetic analysis, showed that the anammox bacteria and Ca. Uabimicrobium form a divergent clade from the rest of the cultured representatives of the phylum Planctomycetes. The phylogenetic study, pairwise distance and Average Amino acid Identity (AAI) showed that anammox bacteria don't belong to the classes Planctomycetia and Phycisphaerae. Anammox bacteria and Ca. Uabimicrobium form a deep-branching third clade in the phylogenetic analysis indicating that it is the most ancient third class within the phylum Planctomycetes. Phenotypic characters also separate anammox bacteria from classes Planctomycetia and Phycisphaerae. Therefore, based on phenotypic, phylogenetic, pairwise distance, AAI and phylogenomic analysis we propose a novel class Ca. Brocadiia to accommodate the order Ca. Brocadiales of anammox bacteria except Ca. Anammoximicrobium. Genera Ca. Jettenia, Ca. Anammoxoglobus, Ca. Kuenenia and Ca. Brocadia show their phylogenetic affiliation to the family Ca. Brocadiaceae. However, Ca. Scalindua showed a distant relationship with the family Ca. Brocadiaceae. Therefore, we suggest the exclusion of the genus Ca. Scalindua from the family Ca. Brocadiaceae; and propose its inclusion under a novel family with a provisional name as Ca. Scalinduaceae fam. nov. Similarly, Ca. Uabimicrobium amporphum showed distinct phylogenetic affiliation, therefore we propose a novel class Ca. Uabimicrobiia classis nov. to accommodate the genus Ca. Uabimicrobium.
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Affiliation(s)
- Tushar Lodha
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411021, India.
| | - Simran Narvekar
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411021, India
| | - Prachi Karodi
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411021, India
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13
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Li Y, Zhang M, Xu D, Shan X, Zheng P. Potential of anammox process towards high-efficient nitrogen removal in wastewater treatment: Theoretical analysis and practical case with a SBR. CHEMOSPHERE 2021; 281:130729. [PMID: 34022604 DOI: 10.1016/j.chemosphere.2021.130729] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 04/13/2021] [Accepted: 04/24/2021] [Indexed: 06/12/2023]
Abstract
Anammox process has been widely applied in the wastewater nitrogen removal for its high rate and low cost. However, few researches reported the process potential in treating low-strength nitrogen wastewater. In this study, a sequencing batch reactor (SBR) was taken to explore the feasibility of low-strength nitrogen wastewater treatment by anammox process in theory and practice. The practical operation indicated that the effluent with satisfactory quality (1.90 ± 0.70 mg-TN·L-1) could be achieved, when the SBR was fed with low-strength nitrogen influent (6.20 ± 0.45 mg-NH4+-N·L-1 and 7.96 ± 0.59 mg-NO2--N·L-1). The hydraulic retention time (HRT), nitrogen removal efficiency, nitrogen removal rate (NRR) and hydraulic loading rate of SBR were 5.42 h, 86.5%, 0.054 kg-N·m-3·d-1 and 4.43 m3·m-3·d-1 during the 79-day operation, respectively. The theoretical analysis revealed the potential of anammox SBR. When SBR is stably operated, the maximum NRR would be 0.062 kg-N·m-3·d-1 if the effluent nitrogen was required to be as low as 3 mg·L-1. The NRR value is feasible for engineering. However, considering the lower specific substrates utilization rate in practice, the maximum stable NRR was calibrated and found inefficient afterwards. In order to improve the potential of anammox process, the reactors without back mixing and with periodic bioaugmentation should be taken in priority for the engineering applications. In particular, the bioaugmentation frequency and single addition amount were calculated as 7 d and 0.3 g-VSS·L-1, respectively. The results may provide guidance for the development of high-efficient and stable nitrogen removal process under low-strength condition.
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Affiliation(s)
- Yiyu Li
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Meng Zhang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Dongdong Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Xiaoyu Shan
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, USA
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China.
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14
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Pavlovska M, Prekrasna I, Dykyi E, Zotov A, Dzhulai A, Frolova A, Slobodnik J, Stoica E. Niche partitioning of bacterial communities along the stratified water column in the Black Sea. Microbiologyopen 2021; 10:e1195. [PMID: 34180601 PMCID: PMC8217838 DOI: 10.1002/mbo3.1195] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 11/22/2022] Open
Abstract
The Black Sea is the largest semi‐closed permanently anoxic basin on our planet with long‐term stratification. The study aimed at describing the Black Sea microbial community taxonomic and functional composition within the range of depths spanning across oxic/anoxic interface, and to uncover the factors behind both their vertical and regional differentiation. 16S rRNA gene MiSeq sequencing was applied to get the data on microbial community taxonomy, and the PICRUSt pipeline was used to infer their functional profile. The normoxic zone was mainly inhabited by primary producers and heterotrophic prokaryotes (e.g., Flavobacteriaceae, Rhodobacteraceae, Synechococcaceae) whereas the euxinic zone—by heterotrophic and chemoautotrophic taxa (e.g., MSBL2, Piscirickettsiaceae, and Desulfarculaceae). Assimilatory sulfate reduction and oxygenic photosynthesis were prevailing within the normoxic zone, while the role of nitrification, dissimilatory sulfate reduction, and anoxygenic photosynthesis increased in the oxygen‐depleted water column part. Regional differentiation of microbial communities between the Ukrainian shelf and offshore zone was detected as well, yet it was significantly less pronounced than the vertical one. It is suggested that regional differentiation within a well‐oxygenated zone is driven by the difference in phytoplankton communities providing various substrates for the prokaryotes, whereas redox stratification is the main driving force behind microbial community vertical structure.
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Affiliation(s)
- Mariia Pavlovska
- State Institution National Antarctic Scientific Center, Kyiv, Ukraine.,Ukrainian Scientific Center of Ecology of the Sea, Odesa, Ukraine.,National University of Life and Environmental Sciences of Ukraine, Kyiv, Ukraine
| | | | - Evgen Dykyi
- State Institution National Antarctic Scientific Center, Kyiv, Ukraine.,Ukrainian Scientific Center of Ecology of the Sea, Odesa, Ukraine
| | - Andrii Zotov
- State Institution National Antarctic Scientific Center, Kyiv, Ukraine.,State Institution Institute of Marine Biology of the NAS of Ukraine, Odesa, Ukraine
| | - Artem Dzhulai
- State Institution National Antarctic Scientific Center, Kyiv, Ukraine
| | - Alina Frolova
- Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | | | - Elena Stoica
- National Institute for Marine Research and Development "Grigore Antipa", Constanta, Romania
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15
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Suominen S, Doorenspleet K, Sinninghe Damsté JS, Villanueva L. Microbial community development on model particles in the deep sulfidic waters of the Black Sea. Environ Microbiol 2021; 23:2729-2746. [PMID: 32291864 PMCID: PMC8359284 DOI: 10.1111/1462-2920.15024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/01/2020] [Accepted: 04/12/2020] [Indexed: 12/31/2022]
Abstract
Microorganisms attached to particles have been shown to be different from free-living microbes and to display diverse metabolic activities. However, little is known about the ecotypes associated with particles and their substrate preference in anoxic marine waters. Here, we investigate the microbial community colonizing particles in the anoxic and sulfide-rich waters of the Black Sea. We incubated beads coated with different substrates in situ at 1000 and 2000 m depth. After 6 h, the particle-attached microbes were dominated by Gamma- and Alpha-proteobacteria, and groups related to the phyla Latescibacteria, Bacteroidetes, Planctomycetes and Firmicutes, with substantial variation across the bead types, indicating that the attaching communities were selected by the substrate. Further laboratory incubations for 7 days suggested the presence of a community of highly specialized taxa. After incubation for 35 days, the microbial composition across all beads and depths was similar and primarily composed of putative sulfur cycling microbes. In addition to the major shared microbial groups, subdominant taxa on chitin and protein-coated beads were detected pointing to specialized microbial degraders. These results highlight the role of particles as sites for attachment and biofilm formation, while the composition of organic matter defined a secondary part of the microbial community.
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Affiliation(s)
- Saara Suominen
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityDen BurgThe Netherlands
| | - Karlijn Doorenspleet
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityDen BurgThe Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityDen BurgThe Netherlands
- Department of Earth Sciences, Faculty of GeosciencesUtrecht UniversityUtrecht, The Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityDen BurgThe Netherlands
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16
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Small sinking particles control anammox rates in the Peruvian oxygen minimum zone. Nat Commun 2021; 12:3235. [PMID: 34050175 PMCID: PMC8163745 DOI: 10.1038/s41467-021-23340-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 04/26/2021] [Indexed: 11/15/2022] Open
Abstract
Anaerobic oxidation of ammonium (anammox) in oxygen minimum zones (OMZs) is a major pathway of oceanic nitrogen loss. Ammonium released from sinking particles has been suggested to fuel this process. During cruises to the Peruvian OMZ in April–June 2017 we found that anammox rates are strongly correlated with the volume of small particles (128–512 µm), even though anammox bacteria were not directly associated with particles. This suggests that the relationship between anammox rates and particles is related to the ammonium released from particles by remineralization. To investigate this, ammonium release from particles was modelled and theoretical encounters of free-living anammox bacteria with ammonium in the particle boundary layer were calculated. These results indicated that small sinking particles could be responsible for ~75% of ammonium release in anoxic waters and that free-living anammox bacteria frequently encounter ammonium in the vicinity of smaller particles. This indicates a so far underestimated role of abundant, slow-sinking small particles in controlling oceanic nutrient budgets, and furthermore implies that observations of the volume of small particles could be used to estimate N-loss across large areas. Up to 40% of the ocean’s fixed nitrogen is lost in oxygen minimum zones (OMZs) by anammox, but despite the importance of this process, nitrogen loss patterns in OMZs are difficult to predict. Here the authors show that ammonium release from small particles is a major control of anammox in the Peruvian OMZ.
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17
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Invertebrate and Microbial Response to Hyporheic Restoration of an Urban Stream. WATER 2021. [DOI: 10.3390/w13040481] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
All cities face complex challenges managing urban stormwater while also protecting urban water bodies. Green stormwater infrastructure and process-based restoration offer alternative strategies that prioritize watershed connectivity. We report on a new urban floodplain restoration technique being tested in the City of Seattle, USA: an engineered hyporheic zone. The hyporheic zone has long been an overlooked component in floodplain restoration. Yet this subsurface area offers enormous potential for stormwater amelioration and is a critical component of healthy streams. From 2014 to 2017, we measured hyporheic temperature, nutrients, and microbial and invertebrate communities at three paired stream reaches with and without hyporheic restoration. At two of the three pairs, water temperature was significantly lower at the restored reach, while dissolved organic carbon and microbial metabolism were higher. Hyporheic invertebrate density and taxa richness were significantly higher across all three restored reaches. These are some of the first quantified responses of hyporheic biological communities to restoration. Our results complement earlier reports of enhanced hydrologic and chemical functioning of the engineered hyporheic zone. Together, this research demonstrates that incorporation of hyporheic design elements in floodplain restoration can enhance temperature moderation, habitat diversity, contaminant filtration, and the biological health of urban streams.
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18
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Hou D, Hong M, Wang K, Yan H, Wang Y, Dong P, Li D, Liu K, Zhou Z, Zhang D. Prokaryotic community succession and assembly on different types of microplastics in a mariculture cage. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 268:115756. [PMID: 33162209 DOI: 10.1016/j.envpol.2020.115756] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/25/2020] [Accepted: 09/26/2020] [Indexed: 06/11/2023]
Abstract
Microplastics have emerged as a new anthropogenic substrate that can readily be colonized by microorganisms. Nevertheless, microbial community succession and assembly among different microplastics in nearshore mariculture cages remains poorly understood. Using an in situ incubation experiment, 16S rRNA gene amplicon sequencing, and the neutral model, we investigated the prokaryotic communities attached to polyethylene terephthalate (PET), polyethylene (PE), and polypropylene (PP) in a mariculture cage in Xiangshan Harbor, China. The α-diversities and compositions of microplastic-attached prokaryotic communities were significantly distinct from free-living and small particle-attached communities in the surrounding water but relatively similar to the large particle-attached communities. Although a distinct prokaryotic community was developed on each type of microplastic, the communities on PE and PP more closely resembled each other. Furthermore, the prokaryotic community dissimilarity among all media (microplastics and water fractions) tended to decrease over time. Hydrocarbon-degrading bacteria Alcanivorax preferentially colonized PE, and the genus Vibrio with opportunistically pathogenic members has the potential to colonize PET. Additionally, neutral processes dominated the prokaryotic community assembly on PE and PP, while selection was more responsible for the prokaryotic assembly on PET. The assembly of Planctomycetaceae and Thaumarchaeota Marine Group I taxa on three microplastics were mainly governed by selection and neutral processes, respectively. Our study provides further understanding of microplastic-associated microbial ecology in mariculture environments.
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Affiliation(s)
- Dandi Hou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Man Hong
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Kai Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
| | - Huizhen Yan
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Yanting Wang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Pengsheng Dong
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Daoji Li
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China
| | - Kai Liu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China
| | - Zhiqiang Zhou
- Xiangshan Fisheries Technology Extension Center, Ningbo, 315700, China
| | - Demin Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China; School of Marine Sciences, Ningbo University, Ningbo, 315211, China
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19
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Kaboré OD, Godreuil S, Drancourt M. Planctomycetes as Host-Associated Bacteria: A Perspective That Holds Promise for Their Future Isolations, by Mimicking Their Native Environmental Niches in Clinical Microbiology Laboratories. Front Cell Infect Microbiol 2020; 10:519301. [PMID: 33330115 PMCID: PMC7734314 DOI: 10.3389/fcimb.2020.519301] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/27/2020] [Indexed: 01/22/2023] Open
Abstract
Traditionally recognized as environmental bacteria, Planctomycetes have just been linked recently to human pathology as opportunistic pathogens, arousing a great interest for clinical microbiologists. However, the lack of appropriate culture media limits our future investigations as no Planctomycetes have ever been isolated from patients' specimens despite several attempts. Several Planctomycetes have no cultivable members and are only recognized by 16S rRNA gene sequence detection and analysis. The cultured representatives are slow-growing fastidious bacteria and mostly difficult to culture on synthetic media. Accordingly, the provision of environmental and nutritional conditions like those existing in the natural habitat where yet uncultured/refractory bacteria can be detected might be an option for their potential isolation. Hence, we systematically reviewed the various natural habitats of Planctomycetes, to review their nutritional requirements, the physicochemical characteristics of their natural ecological niches, current methods of cultivation of the Planctomycetes and gaps, from a perspective of collecting data in order to optimize conditions and the protocols of cultivation of these fastidious bacteria. Planctomycetes are widespread in freshwater, seawater, and terrestrial environments, essentially associated to particles or organisms like macroalgae, marine sponges, and lichens, depending on the species and metabolizable polysaccharides by their sulfatases. Most Planctomycetes grow in nutrient-poor oligotrophic environments with pH ranging from 3.4 to 11, but a few strains can also grow in quite nutrient rich media like M600/M14. Also, a seasonality variation of abundance is observed, and bloom occurs in summer-early autumn, correlating with the strong growth of algae in the marine environments. Most Planctomycetes are mesophilic, but with a few Planctomycetes being thermophilic (50°C to 60°C). Commonly added nutrients are N-acetyl-glucosamine, yeast-extracts, peptone, and some oligo and macro-elements. A biphasic host-associated extract (macroalgae, sponge extract) conjugated with a diluted basal medium should provide favorable results for the success of isolation in pure culture.
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Affiliation(s)
- Odilon D. Kaboré
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Sylvain Godreuil
- Université de Montpellier UMR 1058 UMR MIVEGEC, UMR IRD 224-CNRS Inserm, Montpellier, France
| | - Michel Drancourt
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
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20
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Fuchsman CA, Stüeken EE. Using modern low-oxygen marine ecosystems to understand the nitrogen cycle of the Paleo- and Mesoproterozoic oceans. Environ Microbiol 2020; 23:2801-2822. [PMID: 32869502 DOI: 10.1111/1462-2920.15220] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 11/29/2022]
Abstract
During the productive Paleoproterozoic (2.4-1.8 Ga) and less productive Mesoproterozoic (1.8-1.0 Ga), the ocean was suboxic to anoxic and multicellular organisms had not yet evolved. Here, we link geologic information about the Proterozoic ocean to microbial processes in modern low-oxygen systems. High iron concentrations and rates of Fe cycling in the Proterozoic are the largest differences from modern oxygen-deficient zones. In anoxic waters, which composed most of the Paleoproterozoic and ~40% of the Mesoproterozoic ocean, nitrogen cycling dominated. Rates of N2 production by denitrification and anammox were likely linked to sinking organic matter fluxes and in situ primary productivity under anoxic conditions. Additionally autotrophic denitrifiers could have used reduced iron or methane. 50% of the Mesoproterozoic ocean may have been suboxic, promoting nitrification and metal oxidation in the suboxic water and N2 O and N2 production by partial and complete denitrification in anoxic zones in organic aggregates. Sulfidic conditions may have composed ~10% of the Mesoproterozoic ocean focused along continental margins. Due to low nitrate concentrations in offshore regions, anammox bacteria likely dominated N2 production immediately above sulfidic zones, but in coastal regions, higher nitrate concentrations probably promoted complete S-oxidizing autotrophic denitrification at the sulfide interface.
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Affiliation(s)
- Clara A Fuchsman
- Horn Point Laboratory, University of Maryland Center for Environmental Science, Cambridge, MD, 21613, USA
| | - Eva E Stüeken
- School of Earth & Environmental Sciences, University of St Andrews, St Andrews, KY16 9AL, Scotland, UK
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21
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Suter EA, Pachiadaki MG, Montes E, Edgcomb VP, Scranton MI, Taylor CD, Taylor GT. Diverse nitrogen cycling pathways across a marine oxygen gradient indicate nitrogen loss coupled to chemoautotrophic activity. Environ Microbiol 2020; 23:2747-2764. [PMID: 32761757 DOI: 10.1111/1462-2920.15187] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 08/01/2020] [Accepted: 08/02/2020] [Indexed: 11/28/2022]
Abstract
Genetic markers and geochemical assays of microbial nitrogen cycling processes, including autotrophic and heterotrophic denitrification, anammox, ammonia oxidation, and nitrite oxidation, were examined across the oxycline, suboxic, and anoxic zones of the Cariaco Basin, Venezuela. Ammonia and nitrite oxidation genes were expressed through the entire gradient. Transcripts associated with autotrophic and heterotrophic denitrifiers were mostly confined to the suboxic zone and below but were also present in particles in the oxycline. Anammox genes and transcripts were detected over a narrow depth range near the bottom of the suboxic zone and coincided with secondary NO2 - maxima and available NH4 + . Dissolved inorganic nitrogen (DIN) amendment incubations and comparisons between our sampling campaigns suggested that denitrifier activity may be closely coupled with NO3 - availability. Expression of denitrification genes at depths of high rates of chemoautotrophic carbon fixation and phylogenetic analyses of nitrogen cycling genes and transcripts indicated a diverse array of denitrifiers, including chemoautotrophs capable of using NO3 - to oxidize reduced sulfur species. Thus, results suggest that the Cariaco Basin nitrogen cycle is influenced by autotrophic carbon cycling in addition to organic matter oxidation and anammox.
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Affiliation(s)
- Elizabeth A Suter
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA.,Biology, Chemistry, and Environmental Studies Department, Center for Environmental Research and Coastal Oceans Monitoring, Molloy College, Rockville Centre, NY, USA.,Department of Biological Sciences, Wagner College, Staten Island, NY, USA
| | - Maria G Pachiadaki
- Woods Hole Oceanographic Institution, Woods Hole, MA, USA.,Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Enrique Montes
- College of Marine Science, University of South Florida, St. Petersburg, FL, USA
| | | | - Mary I Scranton
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Craig D Taylor
- Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
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Oren A, Garrity GM, Parker CT, Chuvochina M, Trujillo ME. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2020; 70:3956-4042. [DOI: 10.1099/ijsem.0.003789] [Citation(s) in RCA: 782] [Impact Index Per Article: 195.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M. Garrity
- NamesforLife, LLC, PO Box 769, Okemos MI 48805-0769, USA
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| | | | - Maria Chuvochina
- Australian Centre for Ecogenomics, University of Queensland, St. Lucia QLD 4072, Brisbane, Australia
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007, Salamanca, Spain
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Nsenga Kumwimba M, Lotti T, Şenel E, Li X, Suanon F. Anammox-based processes: How far have we come and what work remains? A review by bibliometric analysis. CHEMOSPHERE 2020; 238:124627. [PMID: 31548173 DOI: 10.1016/j.chemosphere.2019.124627] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/05/2019] [Accepted: 08/19/2019] [Indexed: 06/10/2023]
Abstract
Nitrogen contamination remains a severe environmental problem and a major threat to sustainable development worldwide. A systematic analysis of the literature indicates that the partial nitritation-anammox (PN/AMX) process is still actively studied as a viable option for energy-efficient and feasible technology for the sustainable treatment of N- rich wastewaters, since its initial discovery in 1990. Notably, the mainstream PN/AMX process application remains the most challenging bottleneck in AMX technology and fascinates the world's attention in AMX studies. This paper discusses the recent trends and developments of PN/AMX research and analyzes the results of recent years of research on the PN/AMX from lab-to full-scale applications. The findings would deeply improve our understanding of the major challenges under mainstream conditions and next-stage research on the PN/AMX process. A great deal of efforts has been made in the process engineering, PN/AMX bacteria populations, predictive modeling, and the full-scale implementations during the past 22 years. A series of new and excellent experimental findings at lab, pilot and full-scale levels including good nitrogen removal performance even under low temperature (15-10 °C) around the world were achieved. To date, pilot- and full-scale PN/AMX have been successfully used to treat different types of industrial sewage, including black wastewater, sludge digester liquids, landfill leachate, monosodium glutamate wastewater, etc. Supplementing the qualitative analysis, this review also provides a quantitative bibliometrics study and evaluates global perspectives on PN/AMX research published during the past 22 years. Finally, general trends in the development of PN/AMX research are summarized with the aim of conveying potential future trajectories. The current review offers a valuable orientation and global overview for scientists, engineers, readers and decision makers presently focusing on PN/AMX processes.
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Affiliation(s)
- Mathieu Nsenga Kumwimba
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510275, China; School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China; Faculty of Agronomy, Department of Natural Resources and Environmental Management, University of Lubumbashi, Congo
| | - Tommaso Lotti
- Civil and Environmental Engineering Department, University of Florence, Via di Santa Marta 3, 50139, Florence, Italy
| | - Engin Şenel
- Hitit University Faculty of Medicine, Department of Dermatology, Çorum, Turkey
| | - Xuyong Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Fidèle Suanon
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
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24
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Peng MW, Yu XL, Guan Y, Liu P, Yan P, Fang F, Guo J, Chen YP. Underlying Promotion Mechanism of High Concentration of Silver Nanoparticles on Anammox Process. ACS NANO 2019; 13:14500-14510. [PMID: 31794189 DOI: 10.1021/acsnano.9b08263] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Silver nanoparticles (AgNPs) are largely discharged into sewers and mostly accumulated in the sediments and sludge. The toxicity of AgNPs to environmental microorganisms has attracted great attention. However, the effect of AgNPs on anaerobic ammonium-oxidizing (anammox) granules remains unknown. Here we present the underlying promotion mechanism of AgNPs on anammox granules from a morphological and molecular biology perspective. Our results demonstrate a positive effect of AgNPs on the proliferation of anammox bacteria. AgNPs resulted in a change in the three-dimensional structure of anammox granules and led to larger pore size and higher porosity. In addition, the diffusion capacity of the substrate and metal ions was enhanced. Furthermore, the expression of anammox-related enzymes, such as nitrite oxidoreductase (NirS), hydrazine dehydrogenase (Hdh), and hydrazine synthase (HZS), was upregulated. Therefore, the growth rate and the nitrogen removal performance of the anammox granules were improved. Our findings clarify the underlying mechanism of AgNPs on anammox granules and provide a promising method for the treatment of AgNPs-rich wastewater.
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Affiliation(s)
- Meng-Wen Peng
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE , Chongqing University , Chongqing 400045 , China
| | - Xiu-Ling Yu
- Zhejiang Provincial Key Laboratory of Agricultural Resource and Environment , Zhejiang University , Hangzhou 310058 , China
| | - Yong Guan
- National Synchrotron Radiation Laboratory , University of Science and Technology of China , Hefei 230026 , China
| | - Peng Liu
- School of Environmental Studies , China University of Geosciences , Wuhan 430074 , China
| | - Peng Yan
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE , Chongqing University , Chongqing 400045 , China
| | - Fang Fang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE , Chongqing University , Chongqing 400045 , China
| | - Jinsong Guo
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE , Chongqing University , Chongqing 400045 , China
| | - You-Peng Chen
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE , Chongqing University , Chongqing 400045 , China
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Alves KJ, da Silva MCP, Cotta SR, Ottoni JR, van Elsas JD, de Oliveira VM, Andreote FD. Mangrove soil as a source for novel xylanase and amylase as determined by cultivation-dependent and cultivation-independent methods. Braz J Microbiol 2019; 51:217-228. [PMID: 31741310 DOI: 10.1007/s42770-019-00162-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 09/19/2019] [Indexed: 11/25/2022] Open
Abstract
Xylanase and α-amylase enzymes participate in the degradation of organic matter, acting in hemicellulose and starch mineralization, respectively, and are in high demand for industrial use. Mangroves represent a promising source for bioprospecting enzymes due to their unique characteristics, such as fluctuations in oxic/anoxic conditions and salinity. In this context, the present work aimed to bioprospect xylanases from mangrove soil using cultivation-dependent and cultivation-independent methods. Through screening from a metagenomic library, three potentially xylanolytic clones were obtained and sequenced, and reads were assembled into contigs and annotated. The contig MgrBr135 was affiliated with the Planctomycetaceae family and was one of 30 ORFs selected for subcloning that demonstrated only amylase activity. Through the cultivation method, 38 bacterial isolates with xylanolytic activity were isolated. Isolate 11 showed an enzymatic index of 10.9 using the plate assay method. Isolate 39 achieved an enzyme activity of 0.43 U/mL using the colorimetric method with 3,5-dinitrosalicylic acid. Isolate 39 produced xylanase on culture medium with salinity ranging from 1.25 to 5%. Partial 16S rRNA gene sequencing identified isolates in the Bacillus and Paenibacillus genera. The results of this study highlight the importance of mangroves as an enzyme source and show that bacterial groups can be used for starch and hemicellulose degradation.
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Affiliation(s)
- Kelly Jaqueline Alves
- Department of Soil Science, Laboratory of Soil Microbiology, University of Sao Paulo, Padua Dias Avenue, 11 CP 09, Piracicaba, São Paulo, 13418-900, Brazil.
| | - Mylenne Calciolari Pinheiro da Silva
- Department of Soil Science, Laboratory of Soil Microbiology, University of Sao Paulo, Padua Dias Avenue, 11 CP 09, Piracicaba, São Paulo, 13418-900, Brazil
| | - Simone Raposo Cotta
- Center for Nuclear Energy in Agriculture, University of São Paulo, Centenario Avenue, 303, Piracicaba, São Paulo, 13416-000, Brazil
| | - Júlia Ronzella Ottoni
- University Center Dinâmica das Cataratas, Castelo Branco Street, 349, Foz do Iguaçu, Paraná, 85852-010, Brazil
| | - Jan Dirk van Elsas
- Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, the Netherlands
| | - Valeria Maia de Oliveira
- Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Alexandre Cazellato Avenue, 999, Paulínia, São Paulo, 13140-000, Brazil
| | - Fernando Dini Andreote
- Department of Soil Science, Laboratory of Soil Microbiology, University of Sao Paulo, Padua Dias Avenue, 11 CP 09, Piracicaba, São Paulo, 13418-900, Brazil
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Zheng Y, Wu W, Hu G, Qiu L, Bing X, Chen J. Varieties of immunity activities and gut contents in tilapia with seasonal changes. FISH & SHELLFISH IMMUNOLOGY 2019; 90:466-476. [PMID: 31004800 DOI: 10.1016/j.fsi.2019.04.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/04/2019] [Accepted: 04/11/2019] [Indexed: 06/09/2023]
Abstract
We performed 16S rDNA sequencing of tilapia fecal samples to analyze changes in tilapia gut contents after cultivation of the fish in the presence of sandwich-like floating beds of Chinese medicinal herbs (5 and 10% planting-areas; 5% Polygonum cuspidatum). The interactive effects between water quality and blood and hepatic pro- and anti-inflammatory concentrations were also assessed. Our results showed that the water quality (i.e., NO3--N, NO2--N, TP removal rates) improved, and the abundance of Chloroflexi and Cyanobacteria increased. The abundance of Bacteroidetes, Verrucomicrobia, Saccharibacteria, and Actinobacteria showed both significant seasonal decreases and increases in the presence of P. cuspidatum (increases in August and decreases in July). Fish blood and hepatic IL-10 and IFN-γ levels (together with fish sampled in September) significantly increased in the P. cuspidatum group sampled in August, while those of TNF-α (10% sandwich-like, P. cuspidatum), IL-1β (P. cuspidatum), IL-8 (5% sandwich-like in September, S905S) significantly decreased. Heat shock proteins 60 and 70 levels significantly increased in the P. cuspidatum group, and complement C3 and C4 concentrations significantly increased in S905S. This study demonstrated that enhanced immunity through the regulation of pro- and anti-inflammatory proteins was sustained throughout development until harvest, particularly in fish grown with P. cuspidatum.
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Affiliation(s)
- Yao Zheng
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, No. 9 Shanshui East Rd., Wuxi, Jiangsu, 214081, China
| | - Wei Wu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, No. 9 Shanshui East Rd., Wuxi, Jiangsu, 214081, China
| | - Gengdong Hu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, No. 9 Shanshui East Rd., Wuxi, Jiangsu, 214081, China
| | - Liping Qiu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, No. 9 Shanshui East Rd., Wuxi, Jiangsu, 214081, China
| | - Xuwen Bing
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, No. 9 Shanshui East Rd., Wuxi, Jiangsu, 214081, China.
| | - Jiazhang Chen
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, No. 9 Shanshui East Rd., Wuxi, Jiangsu, 214081, China.
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Miao L, Yang G, Tao T, Peng Y. Recent advances in nitrogen removal from landfill leachate using biological treatments - A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 235:178-185. [PMID: 30682670 DOI: 10.1016/j.jenvman.2019.01.057] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/07/2019] [Accepted: 01/17/2019] [Indexed: 05/21/2023]
Abstract
Landfill leachate, generated from the wastes in a landfill, is a type of wastewater with high concentrations of ammonia and organics, causing a serious environmental pollution. Because of its complex and changing characteristics, it is difficult to remove nitrogen from landfill leachate economically and effectively. Hence, nitrogen removal is a significant research priority of landfill leachate treatment in recent years. Biological processes are known to be effective in nitrogen removal. In this work, the biological nitrogen removal treatments were divided into the following processes: conventional nitrification-denitrification process, nitritation-denitritation process, endogenous denitritation process, and anaerobic ammonium oxidation (Anammox) process. This manuscript summarized the theories and applications of these approaches in detail, and concluded that appropriate processes should be selected in accordance with different characteristics of landfill leachate, in order to effectively remove nitrogen from all stages of landfill leachate and reduce disposal costs. Finally, perspective on the challenges and opportunities of biological nitrogen removal from landfill leachate was also presented.
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Affiliation(s)
- Lei Miao
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan, PR China
| | - Gangqing Yang
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan, PR China
| | - Tao Tao
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan, PR China
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing, PR China.
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28
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Zhou Z, Wei Q, Yang Y, Li M, Gu JD. Practical applications of PCR primers in detection of anammox bacteria effectively from different types of samples. Appl Microbiol Biotechnol 2018; 102:5859-5871. [PMID: 29802476 DOI: 10.1007/s00253-018-9078-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/05/2018] [Accepted: 05/07/2018] [Indexed: 01/21/2023]
Abstract
Research on anammox (anaerobic ammonium oxidizing) bacteria is important due to their biogeochemical and industrial application significance since the first discovery made over two decades ago. By coupling NH4+ and NO2- biochemically to form N2 gas, anammox bacteria contribute significantly to global marine and terrestrial nitrogen balance (responsible for 50, 9~40, and 4~37% of the nitrogen loss for marine, lakes, and paddy soil) and are also useful in energy-conserving nitrogen removal in wastewater treatment. PCR-based detection and quantification of anammox bacteria are an easy, essential, and widely accessible technique used ubiquitously for studying them in many environmental niches. In this article, we make a summary on practical applications of 16S rRNA and functional gene PCR primers, including hydrazine dehydrogenase (Hzo), nitrite reductase (NirS), hydrazine synthase (Hzs), and cytochrome c biogenesis proteins (Ccs) in detection of them. PCR primer performances in both practical applications and tests in silico are also presented for comparison. For detecting general and specific anammox bacterial groups, selection of appropriate PCR primers for different environmental samples and practical application guidance on choice of appropriate primer pairs for different purposes are also offered. This article provides practical information on selection and application of PCR technique in detection of anammox bacteria from the diverse environments to further promote convenient applications of this technique in research and other purposes.
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Affiliation(s)
- Zhichao Zhou
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, Hong Kong, People's Republic of China
| | - Qiaoyan Wei
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, People's Republic of China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Yuchun Yang
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, Hong Kong, People's Republic of China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, People's Republic of China.
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, Hong Kong, People's Republic of China.
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, SAR, People's Republic of China.
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Suter EA, Pachiadaki M, Taylor GT, Astor Y, Edgcomb VP. Free‐living chemoautotrophic and particle‐attached heterotrophic prokaryotes dominate microbial assemblages along a pelagic redox gradient. Environ Microbiol 2017; 20:693-712. [DOI: 10.1111/1462-2920.13997] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 11/09/2017] [Accepted: 11/13/2017] [Indexed: 01/28/2023]
Affiliation(s)
- Elizabeth A. Suter
- School of Marine and Atmospheric SciencesStony Brook UniversityStony Brook NY USA
- Department of Biological SciencesWagner CollegeStaten Island NY 10301 USA
| | - Maria Pachiadaki
- Woods Hole Oceanographic InstitutionWoods Hole MA USA
- Bigelow Laboratory for Ocean SciencesEast Boothbay ME USA
| | - Gordon T. Taylor
- School of Marine and Atmospheric SciencesStony Brook UniversityStony Brook NY USA
| | - Yrene Astor
- Fundación La Salle de Ciencias Naturales, EDIMARPorlamar Nueva Esparta Venezuela
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Fuchsman CA, Devol AH, Saunders JK, McKay C, Rocap G. Niche Partitioning of the N Cycling Microbial Community of an Offshore Oxygen Deficient Zone. Front Microbiol 2017; 8:2384. [PMID: 29259587 PMCID: PMC5723336 DOI: 10.3389/fmicb.2017.02384] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/20/2017] [Indexed: 11/29/2022] Open
Abstract
Microbial communities in marine oxygen deficient zones (ODZs) are responsible for up to half of marine N loss through conversion of nutrients to N2O and N2. This N loss is accomplished by a consortium of diverse microbes, many of which remain uncultured. Here, we characterize genes for all steps in the anoxic N cycle in metagenomes from the water column and >30 μm particles from the Eastern Tropical North Pacific (ETNP) ODZ. We use an approach that allows for both phylogenetic identification and semi-quantitative assessment of gene abundances from individual organisms, and place these results in context of chemical measurements and rate data from the same location. Denitrification genes were enriched in >30 μm particles, even in the oxycline, while anammox bacteria were not abundant on particles. Many steps in denitrification were encoded by multiple phylotypes with different distributions. Notably three N2O reductases (nosZ), each with no cultured relative, inhabited distinct niches; one was free-living, one dominant on particles and one had a C terminal extension found in autotrophic S-oxidizing bacteria. At some depths >30% of the community possessed nitrite reductase nirK. A nirK OTU linked to SAR11 explained much of this abundance. The only bacterial gene found for NO reduction to N2O in the ODZ was a form of qnorB related to the previously postulated "nitric oxide dismutase," hypothesized to produce N2 directly while oxidizing methane. However, similar qnorB-like genes are also found in the published genomes of many bacteria that do not oxidize methane, and here the qnorB-like genes did not correlate with the presence of methane oxidation genes. Correlations with N2O concentrations indicate that these qnorB-like genes likely facilitate NO reduction to N2O in the ODZ. In the oxycline, qnorB-like genes were not detected in the water column, and estimated N2O production rates from ammonia oxidation were insufficient to support the observed oxycline N2O maximum. However, both qnorB-like and nosZ genes were present within particles in the oxycline, suggesting a particulate source of N2O and N2. Together, our analyses provide a holistic view of the diverse players in the low oxygen nitrogen cycle.
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Affiliation(s)
- Clara A. Fuchsman
- School of Oceanography, University of Washington, Seattle, WA, United States
| | | | | | | | - Gabrielle Rocap
- School of Oceanography, University of Washington, Seattle, WA, United States
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Bertagnolli AD, Padilla CC, Glass JB, Thamdrup B, Stewart FJ. Metabolic potential and
in situ
activity of marine Marinimicrobia bacteria in an anoxic water column. Environ Microbiol 2017; 19:4392-4416. [DOI: 10.1111/1462-2920.13879] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 07/17/2017] [Accepted: 07/26/2017] [Indexed: 11/29/2022]
Affiliation(s)
| | - Cory C. Padilla
- School of Biological SciencesGeorgia Institute of TechnologyAtlanta GA USA
| | - Jennifer B. Glass
- School of Earth and Atmospheric SciencesGeorgia Institute of TechnologyAtlanta GA USA
| | - Bo Thamdrup
- Department of Biology and Nordic Center for Earth Evolution (NordCEE)University of Southern DenmarkOdense Denmark
| | - Frank J. Stewart
- School of Biological SciencesGeorgia Institute of TechnologyAtlanta GA USA
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32
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Mao N, Ren H, Geng J, Ding L, Xu K. Engineering application of anaerobic ammonium oxidation process in wastewater treatment. World J Microbiol Biotechnol 2017; 33:153. [DOI: 10.1007/s11274-017-2313-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 06/13/2017] [Indexed: 10/19/2022]
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33
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Pereira AD, Cabezas A, Etchebehere C, Chernicharo CADL, de Araújo JC. Microbial communities in anammox reactors: a review. ACTA ACUST UNITED AC 2017. [DOI: 10.1080/21622515.2017.1304457] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Alyne Duarte Pereira
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Angela Cabezas
- Microbial Ecology Laboratory, Microbial Biochemistry and Genomics Department, Biological Research Institute ‘Clemente Estable’, Montevideo, Uruguay
| | - Claudia Etchebehere
- Microbial Ecology Laboratory, Microbial Biochemistry and Genomics Department, Biological Research Institute ‘Clemente Estable’, Montevideo, Uruguay
| | | | - Juliana Calábria de Araújo
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
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Bohórquez J, McGenity TJ, Papaspyrou S, García-Robledo E, Corzo A, Underwood GJC. Different Types of Diatom-Derived Extracellular Polymeric Substances Drive Changes in Heterotrophic Bacterial Communities from Intertidal Sediments. Front Microbiol 2017; 8:245. [PMID: 28289404 PMCID: PMC5326797 DOI: 10.3389/fmicb.2017.00245] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/06/2017] [Indexed: 11/18/2022] Open
Abstract
Intertidal areas support extensive diatom-rich biofilms. Such microphytobenthic (MPB) diatoms exude large quantities of extracellular polymeric substances (EPS) comprising polysaccharides, glycoproteins and other biopolymers, which represent a substantial carbon pool. However, degradation rates of different EPS components, and how they shape heterotrophic communities in sediments, are not well understood. An aerobic mudflat-sediment slurry experiment was performed in the dark with two different EPS carbon sources from a diatom-dominated biofilm: colloidal EPS (cEPS) and the more complex hot-bicarbonate-extracted EPS. Degradation rate constants determined over 9 days for three sediment fractions [dissolved organic carbon (DOC), total carbohydrates (TCHO), and (cEPS)] were generally higher in the colloidal-EPS slurries (0.105–0.123 d−1) compared with the hot-bicarbonate-extracted-EPS slurries (0.060–0.096 d−1). Addition of hot-bicarbonate-EPS resulted in large increases in dissolved nitrogen and phosphorous by the end of the experiment, indicating that the more complex EPS is an important source of regenerated inorganic nutrients. Microbial biomass increased ~4–6-fold over 9 days, and pyrosequencing of bacterial 16S rRNA genes revealed that the addition of both types of EPS greatly altered the bacterial community composition (from 0 to 9 days) compared to a control with no added EPS. Bacteroidetes (especially Tenacibaculum) and Verrucomicrobia increased significantly in relative abundance in both the hot-bicarbonate-EPS and colloidal-EPS treatments. These differential effects of EPS fractions on carbon-loss rates, nutrient regeneration and microbial community assembly improve our understanding of coastal-sediment carbon cycling and demonstrate the importance of diverse microbiota in processing this abundant pool of organic carbon.
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Affiliation(s)
- Julio Bohórquez
- Department of Biology, Faculty of Marine and Environmental Science, University of CádizPuerto Real, Spain; School of Biological Sciences, University of EssexColchester, UK
| | - Terry J McGenity
- School of Biological Sciences, University of Essex Colchester, UK
| | - Sokratis Papaspyrou
- Departamento de Biomedicina, Biotecnología y Salud Publica, Universidad de Cádiz Puerto Real, Spain
| | - Emilio García-Robledo
- Department of Biology, Faculty of Marine and Environmental Science, University of CádizPuerto Real, Spain; Microbiology Section, Department of Biosciences, University of AarhusAarhus, Denmark
| | - Alfonso Corzo
- Department of Biology, Faculty of Marine and Environmental Science, University of Cádiz Puerto Real, Spain
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35
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Gokal J, Awolusi OO, Enitan AM, Kumari S, Bux F. Chapter 4 Molecular Characterization and Quantification of Microbial Communities in Wastewater Treatment Systems. Microb Biotechnol 2016. [DOI: 10.1201/9781315367880-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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36
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Microbial communities within the water column of freshwater Lake Radok, East Antarctica: predominant 16S rDNA phylotypes and bacterial cultures. Polar Biol 2016. [DOI: 10.1007/s00300-016-2008-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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37
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Nozhevnikova AN, Botchkova EA, Plakunov VK. Multi-species biofilms in ecology, medicine, and biotechnology. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715060107] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Satinsky BM, Fortunato CS, Doherty M, Smith CB, Sharma S, Ward ND, Krusche AV, Yager PL, Richey JE, Moran MA, Crump BC. Metagenomic and metatranscriptomic inventories of the lower Amazon River, May 2011. MICROBIOME 2015; 3:39. [PMID: 26353777 PMCID: PMC4564970 DOI: 10.1186/s40168-015-0099-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 08/12/2015] [Indexed: 05/11/2023]
Abstract
BACKGROUND The Amazon River runs nearly 6500 km across the South American continent before emptying into the western tropical North Atlantic Ocean. In terms of both volume and watershed area, it is the world's largest riverine system, affecting elemental cycling on a global scale. RESULTS A quantitative inventory of genes and transcripts benchmarked with internal standards was obtained at five stations in the lower Amazon River during May 2011. At each station, metagenomes and metatranscriptomes were obtained in duplicate for two microbial size fractions (free-living, 0.2 to 2.0 μm; particle-associated, 2.0 to 297 μm) using 150 × 150 paired-end Illumina sequencing. Forty eight sample datasets were obtained, averaging 15 × 10(6) potential protein-encoding reads each (730 × 10(6) total). Prokaryotic metagenomes and metatranscriptomes were dominated by members of the phyla Actinobacteria, Planctomycetes, Betaproteobacteria, Verrucomicrobia, Nitrospirae, and Acidobacteria. The actinobacterium SCGC AAA027-L06 reference genome recruited the greatest number of reads overall, with this single bin contributing an average of 50 billion genes and 500 million transcripts per liter of river water. Several dominant taxa were unevenly distributed between the free-living and particle-associated size fractions, such as a particle-associated bias for reads binning to planctomycete Schlesneria paludicola and a free-living bias for actinobacterium SCGC AAA027-L06. Gene expression ratios (transcripts to gene copy ratio) increased downstream from Óbidos to Macapá and Belém, indicating higher per cell activity of Amazon River bacteria and archaea as river water approached the ocean. CONCLUSION This inventory of riverine microbial genes and transcripts, benchmarked with internal standards for full quantitation, provides an unparalleled window into microbial taxa and functions in the globally important Amazon River ecosystem.
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Affiliation(s)
- Brandon M Satinsky
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA.
| | - Caroline S Fortunato
- Horn Point, Laboratory University of Maryland Center for Environmental Science, Cambridge, MD, 21612, USA.
| | - Mary Doherty
- Horn Point, Laboratory University of Maryland Center for Environmental Science, Cambridge, MD, 21612, USA.
| | - Christa B Smith
- Department of Marine Sciences, University of Georgia, Athens, GA, 30605-3636, USA.
| | - Shalabh Sharma
- Department of Marine Sciences, University of Georgia, Athens, GA, 30605-3636, USA.
| | - Nicholas D Ward
- School of Oceanography, University of Washington, Seattle, WA, 98112, USA.
| | - Alex V Krusche
- CENA-USP, Avenida Centenário 303, 13416-000, Piracicaba, São Paulo, Brazil.
| | - Patricia L Yager
- Department of Marine Sciences, University of Georgia, Athens, GA, 30605-3636, USA
| | - Jeffrey E Richey
- School of Oceanography, University of Washington, Seattle, WA, 98112, USA.
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, 30605-3636, USA.
| | - Byron C Crump
- College of Earth, Ocean, and Atmospheric Science, Oregon State University, CEOAS Admin Bldg, Corvallis, OR, 97331-5503, USA.
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Žure M, Munn CB, Harder J. Diversity ofRhodopirellulaand related planctomycetes in a North Sea coastal sediment employingcarBas molecular marker. FEMS Microbiol Lett 2015; 362:fnv127. [DOI: 10.1093/femsle/fnv127] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2015] [Indexed: 01/28/2023] Open
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Padilla CC, Ganesh S, Gantt S, Huhman A, Parris DJ, Sarode N, Stewart FJ. Standard filtration practices may significantly distort planktonic microbial diversity estimates. Front Microbiol 2015; 6:547. [PMID: 26082766 PMCID: PMC4451414 DOI: 10.3389/fmicb.2015.00547] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/13/2015] [Indexed: 02/01/2023] Open
Abstract
Fractionation of biomass by filtration is a standard method for sampling planktonic microbes. It is unclear how the taxonomic composition of filtered biomass changes depending on sample volume. Using seawater from a marine oxygen minimum zone, we quantified the 16S rRNA gene composition of biomass on a prefilter (1.6 μm pore-size) and a downstream 0.2 μm filter over sample volumes from 0.05 to 5 L. Significant community shifts occurred in both filter fractions, and were most dramatic in the prefilter community. Sequences matching Vibrionales decreased from ~40 to 60% of prefilter datasets at low volumes (0.05–0.5 L) to less than 5% at higher volumes, while groups such at the Chromatiales and Thiohalorhabdales followed opposite trends, increasing from minor representation to become the dominant taxa at higher volumes. Groups often associated with marine particles, including members of the Deltaproteobacteria, Planctomycetes, and Bacteroidetes, were among those showing the greatest increase with volume (4 to 27-fold). Taxon richness (97% similarity clusters) also varied significantly with volume, and in opposing directions depending on filter fraction, highlighting potential biases in community complexity estimates. These data raise concerns for studies using filter fractionation for quantitative comparisons of aquatic microbial diversity, for example between free-living and particle-associated communities.
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Affiliation(s)
- Cory C Padilla
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Sangita Ganesh
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Shelby Gantt
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Alex Huhman
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Darren J Parris
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Neha Sarode
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Frank J Stewart
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
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41
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Fontanez KM, Eppley JM, Samo TJ, Karl DM, DeLong EF. Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre. Front Microbiol 2015; 6:469. [PMID: 26042105 PMCID: PMC4436931 DOI: 10.3389/fmicb.2015.00469] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 04/29/2015] [Indexed: 01/20/2023] Open
Abstract
Sinking particles mediate the transport of carbon and energy to the deep-sea, yet the specific microbes associated with sedimenting particles in the ocean's interior remain largely uncharacterized. In this study, we used particle interceptor traps (PITs) to assess the nature of particle-associated microbial communities collected at a variety of depths in the North Pacific Subtropical Gyre. Comparative metagenomics was used to assess differences in microbial taxa and functional gene repertoires in PITs containing a preservative (poisoned traps) compared to preservative-free traps where growth was allowed to continue in situ (live traps). Live trap microbial communities shared taxonomic and functional similarities with bacteria previously reported to be enriched in dissolved organic matter (DOM) microcosms (e.g., Alteromonas and Methylophaga), in addition to other particle and eukaryote-associated bacteria (e.g., Flavobacteriales and Pseudoalteromonas). Poisoned trap microbial assemblages were enriched in Vibrio and Campylobacterales likely associated with eukaryotic surfaces and intestinal tracts as symbionts, pathogens, or saprophytes. The functional gene content of microbial assemblages in poisoned traps included a variety of genes involved in virulence, anaerobic metabolism, attachment to chitinaceaous surfaces, and chitin degradation. The presence of chitinaceaous surfaces was also accompanied by the co-existence of bacteria which encoded the capacity to attach to, transport and metabolize chitin and its derivatives. Distinctly different microbial assemblages predominated in live traps, which were largely represented by copiotrophs and eukaryote-associated bacterial communities. Predominant sediment trap-assocaited eukaryotic phyla included Dinoflagellata, Metazoa (mostly copepods), Protalveolata, Retaria, and Stramenopiles. These data indicate the central role of eukaryotic taxa in structuring sinking particle microbial assemblages, as well as the rapid responses of indigenous microbial species in the degradation of marine particulate organic matter (POM) in situ in the ocean's interior.
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Affiliation(s)
- Kristina M Fontanez
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA
| | - John M Eppley
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA ; Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaii Honolulu, HI, USA ; Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii Honolulu, HI, USA
| | - Ty J Samo
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaii Honolulu, HI, USA ; Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii Honolulu, HI, USA ; Lawrence Livermore National Laboratory, Nuclear and Chemical Sciences Division Livermore, CA, USA
| | - David M Karl
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaii Honolulu, HI, USA ; Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii Honolulu, HI, USA
| | - Edward F DeLong
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology Cambridge, MA, USA ; Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaii Honolulu, HI, USA ; Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii Honolulu, HI, USA
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Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone. ISME JOURNAL 2015; 9:2682-96. [PMID: 25848875 DOI: 10.1038/ismej.2015.44] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 02/11/2015] [Accepted: 02/26/2015] [Indexed: 02/01/2023]
Abstract
The genetic composition of marine microbial communities varies at the microscale between particle-associated (PA; >1.6 μm) and free-living (FL; 0.2-1.6 μm) niches. It remains unclear, however, how metabolic activities differ between PA and FL fractions. We combined rate measurements with metatranscriptomics to quantify PA and FL microbial activity in the oxygen minimum zone (OMZ) of the Eastern Tropical North Pacific, focusing on dissimilatory processes of the nitrogen (N) cycle. Bacterial gene counts were 8- to 15-fold higher in the FL compared with the PA fraction. However, rates of all measured N cycle processes, excluding ammonia oxidation, declined significantly following particle (>1.6 μm) removal. Without particles, rates of nitrate reduction to nitrite (1.5-9.4nMNd(-1)) fell to zero and N2 production by denitrification (0.5-1.7nMNd(-1)) and anammox (0.3-1.9nMNd(-1)) declined by 53-85%. The proportional representation of major microbial taxa and N cycle gene transcripts in metatranscriptomes followed fraction-specific trends. Transcripts encoding nitrate reductase were uniform among PA and FL fractions, whereas anammox-associated transcripts were proportionately enriched up to 15-fold in the FL fraction. In contrast, transcripts encoding enzymes for N2O and N2 production by denitrification were enriched up to 28-fold in PA samples. These patterns suggest that the majority of N cycle activity, excluding N2O and N2 production by denitrification, is confined to a FL majority that is critically dependent on access to particles, likely as a source of organic carbon and inorganic N. Variable particle distributions may drive heterogeneity in N cycle activity and gene expression in OMZs.
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43
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Fonti V, Beolchini F, Rocchetti L, Dell'Anno A. Bioremediation of contaminated marine sediments can enhance metal mobility due to changes of bacterial diversity. WATER RESEARCH 2015; 68:637-50. [PMID: 25462769 DOI: 10.1016/j.watres.2014.10.035] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 09/12/2014] [Accepted: 10/19/2014] [Indexed: 05/25/2023]
Abstract
Bioremediation strategies applied to contaminated marine sediments can induce important changes in the mobility and bioavailability of metals with potential detrimental consequences on ecosystem health. In this study we investigated changes of bacterial abundance and diversity (by a combination of molecular fingerprinting and next generation sequencing analyses) during biostimulation experiments carried out on anoxic marine sediments characterized by high metal content. We provide evidence that the addition of organic (lactose and/or acetate) and/or inorganic compounds to contaminated sediments determines a significant increase of bacterial growth coupled with changes in bacterial diversity and assemblage composition. Experimental systems supplied only with organic substrates were characterized by an increase of the relative importance of sulfate reducing bacteria belonging to the families Desulfobacteraceae and Desulfobulbaceae with a concomitant decrease of taxa affiliated with Flavobacteriaceae. An opposite effect was observed in the experimental treatments supplied also with inorganic nutrients. The increase of bacterial metabolism coupled with the increase of bacterial taxa affiliated with Flavobacteriaceae were reflected in a significant decrease of Cd and Zn associated with sedimentary organic matter and Pb and As associated with the residual fraction of the sediment. However, independently from the experimental conditions investigated no dissolution of metals occurred, suggesting a role of bacterial assemblages in controlling metal solubilization processes. Overall results of this study have allowed to identify key biogeochemical interactions influencing the metal behavior and provide new insights for a better understanding of the potential consequences of bio-treatments on the metal fate in contaminated marine sediments.
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Affiliation(s)
- Viviana Fonti
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
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44
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Sonthiphand P, Hall MW, Neufeld JD. Biogeography of anaerobic ammonia-oxidizing (anammox) bacteria. Front Microbiol 2014; 5:399. [PMID: 25147546 PMCID: PMC4123730 DOI: 10.3389/fmicb.2014.00399] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 07/15/2014] [Indexed: 02/01/2023] Open
Abstract
Anaerobic ammonia-oxidizing (anammox) bacteria are able to oxidize ammonia and reduce nitrite to produce N2 gas. After being discovered in a wastewater treatment plant (WWTP), anammox bacteria were subsequently characterized in natural environments, including marine, estuary, freshwater, and terrestrial habitats. Although anammox bacteria play an important role in removing fixed N from both engineered and natural ecosystems, broad scale anammox bacterial distributions have not yet been summarized. The objectives of this study were to explore global distributions and diversity of anammox bacteria and to identify factors that influence their biogeography. Over 6000 anammox 16S rRNA gene sequences from the public database were analyzed in this current study. Data ordinations indicated that salinity was an important factor governing anammox bacterial distributions, with distinct populations inhabiting natural and engineered ecosystems. Gene phylogenies and rarefaction analysis demonstrated that freshwater environments and the marine water column harbored the highest and the lowest diversity of anammox bacteria, respectively. Co-occurrence network analysis indicated that Ca. Scalindua strongly connected with other Ca. Scalindua taxa, whereas Ca. Brocadia co-occurred with taxa from both known and unknown anammox genera. Our survey provides a better understanding of ecological factors affecting anammox bacterial distributions and provides a comprehensive baseline for understanding the relationships among anammox communities in global environments.
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Affiliation(s)
| | - Michael W Hall
- Department of Biology, University of Waterloo Waterloo, ON, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo Waterloo, ON, Canada
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45
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Russ L, Speth DR, Jetten MSM, Op den Camp HJM, Kartal B. Interactions between anaerobic ammonium and sulfur-oxidizing bacteria in a laboratory scale model system. Environ Microbiol 2014; 16:3487-98. [DOI: 10.1111/1462-2920.12487] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 04/12/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Lina Russ
- Department of Microbiology; IWWR; Radboud University Nijmegen; Nijmegen The Netherlands
| | - Daan R. Speth
- Department of Microbiology; IWWR; Radboud University Nijmegen; Nijmegen The Netherlands
| | - Mike S. M. Jetten
- Department of Microbiology; IWWR; Radboud University Nijmegen; Nijmegen The Netherlands
| | | | - Boran Kartal
- Department of Microbiology; IWWR; Radboud University Nijmegen; Nijmegen The Netherlands
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46
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Ganesh S, Parris DJ, DeLong EF, Stewart FJ. Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone. THE ISME JOURNAL 2014; 8:187-211. [PMID: 24030599 PMCID: PMC3869020 DOI: 10.1038/ismej.2013.144] [Citation(s) in RCA: 161] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 07/21/2013] [Accepted: 07/22/2013] [Indexed: 01/27/2023]
Abstract
Marine oxygen minimum zones (OMZs) support diverse microbial communities with roles in major elemental cycles. It is unclear how the taxonomic composition and metabolism of OMZ microorganisms vary between particle-associated and free-living size fractions. We used amplicon (16S rRNA gene) and shotgun metagenome sequencing to compare microbial communities from large (>1.6 μm) and small (0.2-1.6 μm) filter size fractions along a depth gradient in the OMZ off Chile. Despite steep vertical redox gradients, size fraction was a significantly stronger predictor of community composition compared to depth. Phylogenetic diversity showed contrasting patterns, decreasing towards the anoxic OMZ core in the small size fraction, but exhibiting maximal values at these depths within the larger size fraction. Fraction-specific distributions were evident for key OMZ taxa, including anammox planctomycetes, whose coding sequences were enriched up to threefold in the 0.2-1.6 μm community. Functional gene composition also differed between fractions, with the >1.6 μm community significantly enriched in genes mediating social interactions, including motility, adhesion, cell-to-cell transfer, antibiotic resistance and mobile element activity. Prokaryotic transposase genes were three to six fold more abundant in this fraction, comprising up to 2% of protein-coding sequences, suggesting that particle surfaces may act as hotbeds for transposition-based genome changes in marine microbes. Genes for nitric and nitrous oxide reduction were also more abundant (three to seven fold) in the larger size fraction, suggesting microniche partitioning of key denitrification steps. These results highlight an important role for surface attachment in shaping community metabolic potential and genome content in OMZ microorganisms.
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Affiliation(s)
- Sangita Ganesh
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
| | - Darren J Parris
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
| | - Edward F DeLong
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Parsons Laboratory 48, Cambridge, MA, USA
- Center for Microbial Ecology: Research and Education, Honolulu, Hawaii, USA
| | - Frank J Stewart
- School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
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Lanzén A, Simachew A, Gessesse A, Chmolowska D, Jonassen I, Øvreås L. Surprising prokaryotic and eukaryotic diversity, community structure and biogeography of Ethiopian soda lakes. PLoS One 2013; 8:e72577. [PMID: 24023625 PMCID: PMC3758324 DOI: 10.1371/journal.pone.0072577] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 07/11/2013] [Indexed: 11/18/2022] Open
Abstract
Soda lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. This makes them valuable model systems for studying the connection between community structure and abiotic parameters such as pH and salinity. For the first time, we apply high-throughput sequencing to accurately estimate phylogenetic richness and composition in five soda lakes, located in the Ethiopian Rift Valley. The lakes were selected for their contrasting pH, salinities and stratification and several depths or spatial positions were covered in each lake. DNA was extracted and analyzed from all lakes at various depths and RNA extracted from two of the lakes, analyzed using both amplicon- and shotgun sequencing. We reveal a surprisingly high biodiversity in all of the studied lakes, similar to that of freshwater lakes. Interestingly, diversity appeared uncorrelated or positively correlated to pH and salinity, with the most “extreme” lakes showing the highest richness. Together, pH, dissolved oxygen, sodium- and potassium concentration explained approximately 30% of the compositional variation between samples. A diversity of prokaryotic and eukaryotic taxa could be identified, including several putatively involved in carbon-, sulfur- or nitrogen cycling. Key processes like methane oxidation, ammonia oxidation and ‘nitrifier denitrification’ were also confirmed by mRNA transcript analyses.
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Affiliation(s)
- Anders Lanzén
- Department of Biology and Centre for Geobiology, University of Bergen, Bergen, Norway
- Computational Biology Unit, Uni Computing, Uni Research AS, Bergen, Norway
- * E-mail:
| | - Addis Simachew
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Amare Gessesse
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Dominika Chmolowska
- Institute of Environmental Sciences, Jagiellonian University, Krakow, Poland
| | - Inge Jonassen
- Computational Biology Unit, Uni Computing, Uni Research AS, Bergen, Norway
- Department of Informatics, University of Bergen, Bergen, Norway
| | - Lise Øvreås
- Department of Biology and Centre for Geobiology, University of Bergen, Bergen, Norway
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Izumi H, Sagulenko E, Webb RI, Fuerst JA. Isolation and diversity of planctomycetes from the sponge Niphates sp., seawater, and sediment of Moreton Bay, Australia. Antonie van Leeuwenhoek 2013; 104:533-46. [DOI: 10.1007/s10482-013-0003-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 08/13/2013] [Indexed: 11/29/2022]
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49
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Ecological characteristics of anaerobic ammonia oxidizing bacteria. Appl Microbiol Biotechnol 2013; 97:1841-9. [DOI: 10.1007/s00253-013-4697-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 12/29/2012] [Accepted: 01/04/2013] [Indexed: 10/27/2022]
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50
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Lage OM, Bondoso J. Bringing Planctomycetes into pure culture. Front Microbiol 2012; 3:405. [PMID: 23335915 PMCID: PMC3538630 DOI: 10.3389/fmicb.2012.00405] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 11/11/2012] [Indexed: 01/09/2023] Open
Abstract
Planctomycetes have been known since the description of Planctomyces bekefii by Gimesi at the beginning of the twentieth century (1924), although the first axenic cultures were only obtained in the 1970s. Since then, 11 genera with 14 species have been validly named and five candidatus genera belonging to the anaerobic ammonium oxidation, anammox bacteria have also been discovered. However, Planctomycetes diversity is much broader than these numbers indicate, as shown by environmental molecular studies. In recent years, the authors have attempted to isolate and cultivate additional strains of Planctomycetes. This paper provides a summary of the isolation work that was carried out to obtain in pure culture Planctomycetes from several environmental sources. The following strains of planctomycetes have been successfully isolated: two freshwater strains from the sediments of an aquarium, which were described as a new genus and species, Aquisphaera giovannonii; several Rhodopirellula strains from the sediments of a water treatment recycling tank of a marine fish farm; and more than 140 planctomycetes from the biofilm community of macroalgae. This collection comprises several novel taxa that are being characterized and described. Improvements in the isolation methodology were made in order to optimize and enlarge the number of Planctomycetes isolated from the macroalgae. The existence of an intimate and an important relationship between planctomycetes and macroalgae reported before by molecular studies is therefore supported by culture-dependent methods.
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Affiliation(s)
- Olga M Lage
- Department of Biology, Faculty of Sciences, University of Porto Porto, Portugal ; CIMAR/CIIMAR - Interdisciplinary Centre for Marine and Environmental Research University of Porto Porto, Portugal
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