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Functional dominance and community compositions of ammonia-oxidizing archaea in extremely acidic soils of natural forests. Appl Microbiol Biotechnol 2019; 103:4229-4240. [PMID: 30923872 DOI: 10.1007/s00253-019-09721-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 02/18/2019] [Accepted: 02/23/2019] [Indexed: 10/27/2022]
Abstract
Extremely acidic soils of natural forests in Nanling National Nature Reserve have been previously investigated and revisited in two successive years to reveal the active ammonia oxidizers. Ammonia-oxidizing archaea (AOA) rather than ammonia-oxidizing bacteria (AOB) were found more functionally important in the extremely acidic soils of the natural forests in Nanling National Nature Reserve. The relative abundances of Nitrosotalea, Nitrososphaera sister group, and Nitrososphaera lineages recovered by ammonia monooxygenase subunit A (amoA) transcripts were reassessed and compared to AOA communities formerly detected by genomic DNA. Nitrosotalea, previously found the most abundant AOA, were the second-most-active lineage after Nitrososphaera sister group. Our field study results, therefore, propose the acidophilic AOA, Nitrosotalea, can better reside in extremely acidic soils while they may not contribute to nitrification proportionately according to their abundances or they are less functionally active. In contrast, the functional importance of Nitrososphaera sister group may be previously underestimated and the functional dominance further extends their ecological distribution as little has been reported. Nitrososphaera gargensis-like AOA, the third abundant lineage, were more active in summer. The analyses of AOA community composition and its correlation with environmental parameters support the previous observations of the potential impact of organic matter on AOA composition. Al3+, however, did not show a strong adverse correlation with the abundances of functional AOA unlike in the DNA-based study. The new data further emphasize the functional dominance of AOA in extremely acidic soils, and unveil the relative contributions of AOA lineages to nitrification and their community transitions under the environmental influences.
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202
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van de Kamp J, Hook SE, Williams A, Tanner JE, Bodrossy L. Baseline characterization of aerobic hydrocarbon degrading microbial communities in deep-sea sediments of the Great Australian Bight, Australia. Environ Microbiol 2019; 21:1782-1797. [PMID: 30761716 DOI: 10.1111/1462-2920.14559] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/28/2019] [Accepted: 02/07/2019] [Indexed: 11/30/2022]
Abstract
Exploratory drilling for deep-sea oil and gas resources is planned for the Great Australian Bight (GAB). There is scant knowledge of the region's benthic ecosystems and no baseline information of the region's indigenous oil degrading bacteria. To address this knowledge gap, we used next generation sequencing (NGS) of three marker genes (alkB, c23o and pmoA) to detect and characterize the microbial communities capable of aerobic hydrocarbon degradation. Unique, highly novel microbial communities capable of degrading hydrocarbons occur in surface sediments at depths between 200 and 2800 m. Clustering at 97% demonstrated differences in community structure with depth, changing most markedly between 400 and 1000 m depth on the continental slope, and identified putative functional 'ecotypes' related to depth. Observed differences in community structure showed strong correlations with temperature, other physicochemical properties of the overlying water column and are further modulated by differences in sediment grain size. This study provides important baseline data on hydrocarbon degrading microbial communities prior to the start of petroleum resource extraction. Our data will inform future ecological monitoring of the GAB deep-sea ecosystem.
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Affiliation(s)
- Jodie van de Kamp
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Sharon E Hook
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Lucas Heights, New South Wales, 2234, Australia
| | - Alan Williams
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
| | - Jason E Tanner
- Aquatic Sciences, South Australian Research and Development Institute, West Beach, South Australia, 5024, Australia
| | - Levente Bodrossy
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Tasmania, 7000, Australia
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203
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Fernández-Baca CP, Omar AEH, Pollard JT, Richardson RE. Microbial communities controlling methane and nutrient cycling in leach field soils. WATER RESEARCH 2019; 151:456-467. [PMID: 30640159 DOI: 10.1016/j.watres.2018.12.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 12/11/2018] [Accepted: 12/13/2018] [Indexed: 06/09/2023]
Abstract
Septic systems inherently rely on microbial communities in the septic tank and leach field to attenuate pollution from household sewage. Operating conditions of septic leach field systems, especially the degree of water saturation, are likely to impact microbial biogeochemical cycling, including carbon (C), nitrogen (N), and phosphorus (P), as well as greenhouse gas (GHG) emissions to the atmosphere. To study the impact of flooding on microbial methane (CH4) and nutrient cycling, two leach field soil columns were constructed. One system was operated as designed and the other was operated in both flooded and well-maintained conditions. CH4 emissions were significantly higher in flooded soils (with means between 0.047 and 0.33 g CH4 m-2 d-1) as compared to well-drained soils (means between -0.0025 and 0.004 g CH4 m-2 d-1). Subsurface CH4 profiles were also elevated under flooded conditions and peaked near the wastewater inlet. Gene abundances of mcrA, a biomarker for methanogens, were also greatest near the wastewater inlet. In contrast, gene abundances of pmoA, a biomarker for methanotrophs, were greatest in surface soils at the interface of CH4 produced subsurface and atmospheric oxygen. 16S rRNA, mcrA, and pmoA amplicon library sequencing revealed microbial community structure in the soil columns differed from that of the original soils and was driven largely by CH4 fluxes and soil VWC. Additionally, active microbial populations differed from those present at the gene level. Flooding did not appear to affect N or P removals in the soil columns (between 75 and 99% removal). COD removal was variable throughout the experiment, and was negatively impacted by flooding. Our study shows septic system leach field soils are dynamic environments where CH4 and nutrients are actively cycled by microbial populations. Our results suggest proper siting, installation, and routine maintenance of leach field systems is key to reducing the overall impact of these systems on water and air quality.
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Affiliation(s)
- Cristina P Fernández-Baca
- Department of Civil and Environmental Engineering, 220 Hollister Hall, Cornell University, Ithaca, NY, USA.
| | - Amir-Eldin H Omar
- Department of Molecular Biology and Genetics, 107 Biotechnology Building, Cornell University, Ithaca, NY, USA
| | - Jesse T Pollard
- Department of Civil and Environmental Engineering, 220 Hollister Hall, Cornell University, Ithaca, NY, USA
| | - Ruth E Richardson
- Department of Civil and Environmental Engineering, 220 Hollister Hall, Cornell University, Ithaca, NY, USA
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204
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Choi J, Rieke EL, Moorman TB, Soupir ML, Allen HK, Smith SD, Howe A. Practical implications of erythromycin resistance gene diversity on surveillance and monitoring of resistance. FEMS Microbiol Ecol 2019; 94:4810543. [PMID: 29346541 PMCID: PMC5939627 DOI: 10.1093/femsec/fiy006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/12/2018] [Indexed: 12/29/2022] Open
Abstract
Use of antibiotics in human and animal medicine has applied selective pressure for the global dissemination of antibiotic-resistant bacteria. Therefore, it is of interest to develop strategies to mitigate the continued amplification and transmission of resistance genes in environmental reservoirs such as farms, hospitals and watersheds. However, the efficacy of mitigation strategies is difficult to evaluate because it is unclear which resistance genes are important to monitor, and which primers to use to detect those genes. Here, we evaluated the diversity of one type of macrolide antibiotic resistance gene (erm) in one type of environment (manure) to determine which primers would be most informative to use in a mitigation study of that environment. We analyzed all known erm genes and assessed the ability of previously published erm primers to detect the diversity. The results showed that all known erm resistance genes group into 66 clusters, and 25 of these clusters (40%) can be targeted with primers found in the literature. These primers can target 74%–85% of the erm gene diversity in the manures analyzed.
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Affiliation(s)
- Jinlyung Choi
- Department of Agricultural and Biosystems Engineering, Iowa State University, 1201 Sukup Hall, Ames, IA 50011, USA
| | - Elizabeth L Rieke
- Department of Agricultural and Biosystems Engineering, Iowa State University, 1201 Sukup Hall, Ames, IA 50011, USA
| | - Thomas B Moorman
- National Laboratory for Agriculture and the Environment, USDA-ARS, 2110 University Blvd, Ames, IA 50011, USA
| | - Michelle L Soupir
- Department of Agricultural and Biosystems Engineering, Iowa State University, 1201 Sukup Hall, Ames, IA 50011, USA
| | - Heather K Allen
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, USDA-ARS, 1920 Dayton Ave, Ames, IA, 50010, USA
| | - Schuyler D Smith
- Department of Bioinformatics and Computational Biology, Iowa State University, 2014 Molecular Biology Building, Ames, IA 50011, USA
| | - Adina Howe
- Department of Agricultural and Biosystems Engineering, Iowa State University, 1201 Sukup Hall, Ames, IA 50011, USA
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205
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Profiling the Clostridia with butyrate-producing potential in the mud of Chinese liquor fermentation cellar. Int J Food Microbiol 2019; 297:41-50. [PMID: 30878841 DOI: 10.1016/j.ijfoodmicro.2019.02.023] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 01/03/2023]
Abstract
Butyrate and its derivates pertain to the key aroma contributors of strong-flavour baijiu, a kind of Chinese liquors, that is produced from grains by solid-state multispecies anaerobic fermentation in a mud cellar. Microbes inhabiting in the fermentation pit mud largely determines baijiu's flavour and quality. In order to shed light on the microbial functional groups driving butyrate production in pit mud, clone library analysis was firstly performed and the results demonstrated that Clostridia (relative abundance: 50%) and Bacilli (37%) were major groups possessing butyrate kinase (buk) pathway and Clostridia (98%) dominated butyryl-CoA:acetate CoA-transferase (but) pathway. According to Clostridial specific-16S rRNA gene sequencing analysis, we found the resilience character of Clostridial community in pit mud. Amongst Clostridial groups, 32.0% of the sequences were grouped into Clostridiales incertae sedis, followed by Heliobacteriaceae (18.3%) and Clostridiaceae 1 (8.4%). Moreover, Hydrogenispora, Sedimentibacter and Clostridium were the top three abundant genera. Relative abundance of Hydrogenispora was higher in the late days of fermentation, while Sedimentibacter exhibited higher proportion in the early days. Different from the previous studies using universal bacterial primer sets, Hydrogenispora was first reported as one dominant genus in pit mud. As for the reported potential butyrate producer Clostridium, nineteen species were obtained and ten of them were first isolated from the pit mud. Amongst them, buk was identified in eleven species by PCR analysis, while but was identified in the other seven, indicating the species-specific butyrate synthesis pathways of Clostridium. This study provides a perspective on targeting and isolating specific functional microbes in baijiu microbiota with the gene sequence-based medium prediction method.
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206
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Sheng R, Li K, Zhang W, Wang H, Liu H, Zhu X, Wu H, Zhang X, Lin Q, Sun X, Tang Y, A L, Wei W. Differentiations of determinants for the community compositions of bacteria, fungi, and nitrogen fixers in various steppes. Ecol Evol 2019; 9:3239-3250. [PMID: 30962889 PMCID: PMC6434564 DOI: 10.1002/ece3.4940] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/01/2019] [Accepted: 01/07/2019] [Indexed: 11/07/2022] Open
Abstract
Different types of steppes could provide heterogeneous habitat environments for underground microorganisms, but much less is known about how soil microbes fit the distinct habitats and what are the underlying mechanisms in shaping their community patterns.We simultaneously examined the community compositions and structures of soil bacteria, fungi, and diazotrophs across desert, typical, and meadow steppes in Inner Mongolia using high-throughput sequencing.The results showed that soil bacteria, fungi, and diazotrophs exhibited different distribution patterns across steppe types. Although different steppes displayed obvious differences in climate conditions, plant traits, and soil properties, most of bacterial species were shared by all the steppes while only a few species were unique, indicating that the soil bacterial compositions were hardly influenced by the steppe types. Nevertheless, the habitat heterogeneity could cause shifts in the relative abundance of some bacterial groups, which resulted in significant changes in the community structure of soil bacteria across steppes. However, the fungal community compositions and structures were similar in typical and meadow steppes but that in desert steppe were significantly different. Whereas, the community compositions and structures of diazotrophs were strongly related to the steppe types. In this study, the similar parent material backgrounds of the steppe soils might be the important factor in shaping the homologous bacterial compositions. However, the variations in soil fertility, soil water repellency, and plant species across steppes would be the major driving forces in regulating the compositions and structures of fungal communities, while the diazotrophic communities would be more closely related to the changes in plant traits and soil fertility among steppes.Our results provided evidence of habitat specificity for different microbial groups and their underlying drivers.
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Affiliation(s)
- Rong Sheng
- Key Laboratory of Agro‐ecological Processes in Subtropical Regions and Taoyuan Agro‐ecosystem Research Station, Soil Molecular Ecology Section, Institute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
| | - Ke Li
- Key Laboratory of Agro‐ecological Processes in Subtropical Regions and Taoyuan Agro‐ecosystem Research Station, Soil Molecular Ecology Section, Institute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
| | - Wenzhao Zhang
- Key Laboratory of Agro‐ecological Processes in Subtropical Regions and Taoyuan Agro‐ecosystem Research Station, Soil Molecular Ecology Section, Institute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
| | - Hai Wang
- Institute of Grassland ScienceChinese Academy of Agricultural SciencesHuhehaoteChina
| | - Honglin Liu
- Institute of Grassland ScienceChinese Academy of Agricultural SciencesHuhehaoteChina
| | - Xiaoya Zhu
- College of Resources and Environmental SciencesChina Agricultural UniversityBeijingChina
| | - Hongxin Wu
- Institute of Grassland ScienceChinese Academy of Agricultural SciencesHuhehaoteChina
| | - Xiaoqing Zhang
- Institute of Grassland ScienceChinese Academy of Agricultural SciencesHuhehaoteChina
| | - Qimei Lin
- College of Resources and Environmental SciencesChina Agricultural UniversityBeijingChina
| | - Xuecheng Sun
- College of Resources and Environmental SciencesHuazhong Agricultural UniversityWuhanChina
| | - Yafang Tang
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and TechnologyHubei Engineering UniversityXiaoganChina
| | - Lamus A
- Institute of Grassland ScienceChinese Academy of Agricultural SciencesHuhehaoteChina
| | - Wenxue Wei
- Key Laboratory of Agro‐ecological Processes in Subtropical Regions and Taoyuan Agro‐ecosystem Research Station, Soil Molecular Ecology Section, Institute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
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207
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RefSoil+: a Reference Database for Genes and Traits of Soil Plasmids. mSystems 2019; 4:mSystems00349-18. [PMID: 30834332 PMCID: PMC6392096 DOI: 10.1128/msystems.00349-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 01/29/2019] [Indexed: 12/01/2022] Open
Abstract
Soil-associated plasmids have the potential to transfer antibiotic resistance genes from environmental to clinical microbial strains, which is a public health concern. A specific resource is needed to aggregate the knowledge of soil plasmid characteristics so that the content, host associations, and dynamics of antibiotic resistance genes can be assessed and then tracked between the environment and the clinic. Here, we present RefSoil+, a database of soil-associated plasmids. RefSoil+ presents a contemporary snapshot of antibiotic resistance genes in soil that can serve as a reference as novel plasmids and transferred antibiotic resistances are discovered. Our study broadens our understanding of plasmids in soil and provides a community resource of important plasmid-associated genes, including antibiotic resistance genes. Plasmids harbor transferable genes that contribute to the functional repertoire of microbial communities, yet their contributions to metagenomes are often overlooked. Environmental plasmids have the potential to spread antibiotic resistance to clinical microbial strains. In soils, high microbiome diversity and high variability in plasmid characteristics present a challenge for studying plasmids. To improve the understanding of soil plasmids, we present RefSoil+, a database containing plasmid sequences from 922 soil microorganisms. Soil plasmids were larger than other described plasmids, which is a trait associated with plasmid mobility. There was a weak relationship between chromosome size and plasmid size and no relationship between chromosome size and plasmid number, suggesting that these genomic traits are independent in soil. We used RefSoil+ to inform the distributions of antibiotic resistance genes among soil microorganisms compared to those among nonsoil microorganisms. Soil-associated plasmids, but not chromosomes, had fewer antibiotic resistance genes than other microorganisms. These data suggest that soils may offer limited opportunity for plasmid-mediated transfer of described antibiotic resistance genes. RefSoil+ can serve as a reference for the diversity, composition, and host associations of plasmid-borne functional genes in soil, a utility that will be enhanced as the database expands. Our study improves the understanding of soil plasmids and provides a resource for assessing the dynamics of the genes that they carry, especially genes conferring antibiotic resistances. IMPORTANCE Soil-associated plasmids have the potential to transfer antibiotic resistance genes from environmental to clinical microbial strains, which is a public health concern. A specific resource is needed to aggregate the knowledge of soil plasmid characteristics so that the content, host associations, and dynamics of antibiotic resistance genes can be assessed and then tracked between the environment and the clinic. Here, we present RefSoil+, a database of soil-associated plasmids. RefSoil+ presents a contemporary snapshot of antibiotic resistance genes in soil that can serve as a reference as novel plasmids and transferred antibiotic resistances are discovered. Our study broadens our understanding of plasmids in soil and provides a community resource of important plasmid-associated genes, including antibiotic resistance genes.
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208
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Hammerl V, Kastl EM, Schloter M, Kublik S, Schmidt H, Welzl G, Jentsch A, Beierkuhnlein C, Gschwendtner S. Influence of rewetting on microbial communities involved in nitrification and denitrification in a grassland soil after a prolonged drought period. Sci Rep 2019; 9:2280. [PMID: 30783152 PMCID: PMC6381133 DOI: 10.1038/s41598-018-38147-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 12/18/2018] [Indexed: 11/11/2022] Open
Abstract
The frequency of extreme drought and heavy rain events during the vegetation period will increase in Central Europe according to future climate change scenarios, which will affect the functioning of terrestrial ecosystems in multiple ways. In this study, we simulated an extreme drought event (40 days) at two different vegetation periods (spring and summer) to investigate season-related effects of drought and subsequent rewetting on nitrifiers and denitrifiers in a grassland soil. Abundance of the microbial groups of interest was assessed by quantification of functional genes (amoA, nirS/nirK and nosZ) via quantitative real-time PCR. Additionally, the diversity of ammonia-oxidizing archaea was determined based on fingerprinting of the archaeal amoA gene. Overall, the different time points of simulated drought and rewetting strongly influenced the obtained response pattern of microbial communities involved in N turnover as well as soil ammonium and nitrate dynamics. In spring, gene abundance of nirS was irreversible reduced after drought whereas nirK and nosZ remained unaffected. Furthermore, community composition of ammonia-oxidizing archaea was altered by subsequent rewetting although amoA gene abundance remained constant. In contrast, no drought/rewetting effects on functional gene abundance or diversity pattern of nitrifying archaea were observed in summer. Our results showed (I) high seasonal dependency of microbial community responses to extreme events, indicating a strong influence of plant-derived factors like vegetation stage and plant community composition and consequently close plant-microbe interactions and (II) remarkable resistance and/or resilience of functional microbial groups involved in nitrogen cycling to extreme weather events what might indicate that microbes in a silty soil are better adapted to stress situations as expected.
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Affiliation(s)
- Verena Hammerl
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
- Chair for Soil Ecology - Technische Universität München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Eva-Maria Kastl
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Holger Schmidt
- Institute of Natural Sciences - Universität Koblenz Landau, Campus Koblenz, Universitätsstraße 1, 56070, Koblenz, Germany
| | - Gerhard Welzl
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Anke Jentsch
- Disturbance Ecology - University of Bayreuth, Universitätsstr. 30, 95447, Bayreuth, Germany
| | - Carl Beierkuhnlein
- Chair of Biogeography - University of Bayreuth, Universitätsstr. 30, 95447, Bayreuth, Germany
| | - Silvia Gschwendtner
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
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209
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Alterations in intestinal microbiota of colorectal cancer patients receiving radical surgery combined with adjuvant CapeOx therapy. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1178-1193. [PMID: 30796721 DOI: 10.1007/s11427-018-9456-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/12/2018] [Indexed: 01/20/2023]
Abstract
An intricate relationship exists and interactions occur between gut microbiota and colorectal cancer (CRC). Radical surgery combined with adjuvant chemotherapy (AC) serves as the mainstream therapeutic scheme for most CRC patients. The current research was conducted to assess the effect of surgery or chemotherapy on gut microbiota. Forty-three CRC patients who received radical surgery and AC were enrolled. Fecal samples were collected preoperatively, postoperatively, and after the first to fifth cycles of postoperative chemotherapy. The microbial community of each sample was analyzed using high throughput 16S rRNA amplicon sequencing. Compared with preoperative samples, fecal samples collected postoperatively exhibited a significant decrease of obligate anaerobes, tumor-related bacteria, and butyric acid-producing bacteria. However, a significant increase of some conditional pathogens was observed. In addition, the AC regimen (CapeOx) was found to alter intestinal microbiota dramatically. In particular, several changes were observed after chemotherapy including an increase of pathogenic bacteria, the "rebound effect" of chemotherapy-adapted bacteria, the shift of lactate-utilizing microbiota from Veillonella to Butyricimonas and Butyricicoccus, as well as the decrease of probiotics. Both radical surgery and CapeOx chemotherapy exert a non-negligible effect on the gut microbiota of CRC patients. Microbiota-based intervention may be beneficial for patients during postoperative clinical management.
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210
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Bellini MI, Kumaresan D, Tarlera S, Murrell JC, Fernández-Scavino A. Identification of active denitrifiers by DNA-stable isotope probing and amplicon sequencing reveals Betaproteobacteria as responsible for attenuation of nitrate contamination in a low impacted aquifer. FEMS Microbiol Ecol 2019; 94:4757058. [PMID: 29267902 DOI: 10.1093/femsec/fix181] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 12/15/2017] [Indexed: 11/13/2022] Open
Abstract
Groundwater reservoirs constitute important freshwater resources. However, these ecosystems are highly vulnerable to contamination and have to rely on the resident microbiota to attenuate the impact of this contamination. Nitrate is one of the main contaminants found in groundwater, and denitrification is the main process that removes the compound. In this study, the response to nutrient load on indigenous microbial communities in groundwater from a low impacted aquifer in Uruguay was evaluated. Denitrification rates were measured in groundwater samples from three different sites with nitrate, acetate and pyrite amendments. Results showed that denitrification is feasible under in situ nitrate and electron donor concentrations, although the lack of readily available organic energy source would limit the attenuation of higher nitrate concentrations. DNA-stable isotope probing, combined with amplicon sequencing of 16S rRNA, nirS and nirK genes, was used to identify the active denitrifiers. Members of the phylum Betaproteobacteria were the dominant denitrifiers in two of three sites, with different families being observed; members of the genus Vogesella (Neisseriaceae) were key denitrifiers at one site, while the genera Dechloromonas (Rhodocyclaceae) and Comamonas (Comamonadaceae) were the main denitrifiers detected at the other sites.
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Affiliation(s)
- M Inés Bellini
- Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, CP 11800, Montevideo, Uruguay
| | - Deepak Kumaresan
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR47TJ, UK.,School of Biological Sciences and Institute for Global Food Security, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Silvana Tarlera
- Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, CP 11800, Montevideo, Uruguay
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR47TJ, UK
| | - Ana Fernández-Scavino
- Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, CP 11800, Montevideo, Uruguay
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211
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Xu H, Sheng R, Xing X, Zhang W, Hou H, Liu Y, Qin H, Chen C, Wei W. Characterization of Fungal nirK-Containing Communities and N 2O Emission From Fungal Denitrification in Arable Soils. Front Microbiol 2019; 10:117. [PMID: 30778342 PMCID: PMC6369356 DOI: 10.3389/fmicb.2019.00117] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 01/18/2019] [Indexed: 11/25/2022] Open
Abstract
Fungal denitrifiers play important roles in soil nitrogen cycling, but we have very limited knowledge about their distribution and functions in ecosystems. In this study, three types of arable soils were collected across different climate zones in China, including quaternary red clay soils, alluvial soils, and black soils. The composition and abundance of fungal nirK-containing denitrifiers was determined by MiSeq high-throughput sequencing and qPCR, respectively. Furthermore, a substrate-induced inhibition approach was used to explore N2O emissions from fungal denitrification. The results showed that the arable soils contained a wide range of nirK-containing fungal denitrifiers, with four orders and eight genera. Additionally, approximately 57.30% of operational taxonomic unit (OTUs) belonged to unclassified nirK-containing fungi. Hypocreales was the most predominant order, with approximately 40.51% of the total number of OTUs, followed by Sordariales, Eurotiales, and Mucorales. It was further indicated that 53% of fungal nirK OTUs were shared by the three types of soils (common), and this group of fungi comprised about 98% of the total relative abundance of the nirK-containing population, indicating that the distribution of fungal nirK-containing denitrifiers was quite homogenous among the soil types. These common OTUs were determined by multiple soil characteristics, while the composition of unique OTUs was manipulated by the specific properties of each soil type. Furthermore, fungal N2O emissions were significantly and positively correlated with fungal nirK abundance in the soils, whereas it was not clearly related to fungal nirK compositions. In conclusion, although the arable soils hosted diverse nirK-containing fungal denitrifiers, fungal nirK compositions were highly homogenous among the soil types, which could be a consequence of enduring agricultural practices. The abundance of fungal nirK-containing denitrifiers, rather than their composition, may play more significant roles in relation to N2O emission from fungal denitrification.
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Affiliation(s)
- Huifang Xu
- Key Laboratory of Agro-Ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China.,College of Resource and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Rong Sheng
- Key Laboratory of Agro-Ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Xiaoyi Xing
- Key Laboratory of Agro-Ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China.,College of Resource and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Wenzhao Zhang
- Key Laboratory of Agro-Ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Haijun Hou
- Key Laboratory of Agro-Ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Yi Liu
- Key Laboratory of Agro-Ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Hongling Qin
- Key Laboratory of Agro-Ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Chunlan Chen
- Key Laboratory of Agro-Ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Wenxue Wei
- Key Laboratory of Agro-Ecological Processes in Subtropical Regions and Taoyuan Station of Agro-Ecology Research, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
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212
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Williams MR, Hashsham SA. Direct or DNA Extraction-Free Amplification and Quantification of Foodborne Pathogens. Methods Mol Biol 2019; 1918:21-33. [PMID: 30580396 DOI: 10.1007/978-1-4939-9000-9_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The use of direct nucleic acid amplification of pathogens from food matrices has the potential to reduce time to results over DNA extraction-based approaches as well as traditional culture-based approaches. Here we describe protocols for assay design and experiments for direct amplification of foodborne pathogens in food sample matrices using loop-mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR). The examples provided include the detection Escherichia coli in milk samples and Salmonella in pork meat samples. This protocol includes relevant reagents and methods including obtaining target sequences, assay design, sample processing, and amplification. These methods, though used for specific example matrices, could be applied to many other foodborne pathogens and sample types.
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Affiliation(s)
- Maggie R Williams
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA. .,Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA.
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213
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Sirová D, Bárta J, Šimek K, Posch T, Pech J, Stone J, Borovec J, Adamec L, Vrba J. Hunters or farmers? Microbiome characteristics help elucidate the diet composition in an aquatic carnivorous plant. MICROBIOME 2018; 6:225. [PMID: 30558682 PMCID: PMC6297986 DOI: 10.1186/s40168-018-0600-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/18/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND Utricularia are rootless aquatic carnivorous plants which have recently attracted the attention of researchers due to the peculiarities of their miniaturized genomes. Here, we focus on a novel aspect of Utricularia ecophysiology-the interactions with and within the complex communities of microorganisms colonizing their traps and external surfaces. RESULTS Bacteria, fungi, algae, and protozoa inhabit the miniature ecosystem of the Utricularia trap lumen and are involved in the regeneration of nutrients from complex organic matter. By combining molecular methods, microscopy, and other approaches to assess the trap-associated microbial community structure, diversity, function, as well as the nutrient turn-over potential of bacterivory, we gained insight into the nutrient acquisition strategies of the Utricularia hosts. CONCLUSIONS We conclude that Utricularia traps can, in terms of their ecophysiological function, be compared to microbial cultivators or farms, which center around complex microbial consortia acting synergistically to convert complex organic matter, often of algal origin, into a source of utilizable nutrients for the plants.
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Affiliation(s)
- Dagmara Sirová
- Biology Centre CAS, Institute of Hydrobiology, Na Sádkách 7, CZ-37005, České Budějovice, Czech Republic.
- Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic.
| | - Jiří Bárta
- Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
| | - Karel Šimek
- Biology Centre CAS, Institute of Hydrobiology, Na Sádkách 7, CZ-37005, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
| | - Thomas Posch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, CH-8802, Kilchberg, Switzerland
| | - Jiří Pech
- Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
| | - James Stone
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK-99775, USA
- Institute of Experimental Botany CAS, Rozvojová 263, CZ-16502, Praha 6-Lysolaje, Czech Republic
| | - Jakub Borovec
- Biology Centre CAS, Institute of Hydrobiology, Na Sádkách 7, CZ-37005, České Budějovice, Czech Republic
| | - Lubomír Adamec
- Institute of Botany CAS, Dukelská 135, CZ-37982, Třeboň, Czech Republic
| | - Jaroslav Vrba
- Biology Centre CAS, Institute of Hydrobiology, Na Sádkách 7, CZ-37005, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 1760, CZ-37005, České Budějovice, Czech Republic
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214
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Xia F, Wang JG, Zhu T, Zou B, Rhee SK, Quan ZX. Ubiquity and Diversity of Complete Ammonia Oxidizers (Comammox). Appl Environ Microbiol 2018; 84:e01390-18. [PMID: 30315079 PMCID: PMC6275355 DOI: 10.1128/aem.01390-18] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/03/2018] [Indexed: 11/20/2022] Open
Abstract
The discovery of complete ammonia oxidizers (comammox) refutes the century-old paradigm that nitrification requires the activity of two types of microbes. Determining the distribution and abundance of comammox in various environments is important for revealing the ecology of microbial nitrification within the global nitrogen cycle. In this study, the ubiquity and diversity of comammox were analyzed for samples from different types of environments, including soil, sediment, sludge, and water. The results of a two-step PCR using highly degenerate primers (THDP-PCR) and quantitative real-time PCR (qPCR) supported the relatively high abundance of comammox in nearly half of all samples tested, sometimes even outnumbering canonical ammonia-oxidizing bacteria (AOB). In addition, a relatively high proportion of comammox in tap and coastal water samples was confirmed via analysis of metagenomic data sets in public databases. The diversity of comammox was estimated by comammox-specific partial nested PCR amplification of the ammonia monooxygenase subunit A (amoA) gene, and phylogenetic analysis of comammox AmoA clearly showed a split of clade A into clades A.1 and A.2, with the proportions of clades A.1, A.2, and B differing among the various environmental samples. Moreover, compared to the amoA genes of AOB and ammonia-oxidizing archaea (AOA), the comammox amoA gene exhibited higher diversity indices. The ubiquitous distribution and high diversity of comammox indicate that they are likely overlooked contributors to nitrification in various ecosystems.IMPORTANCE The discovery of complete ammonia oxidizers (comammox), which oxidize ammonia to nitrate via nitrite, refutes the century-old paradigm that nitrification requires the activity of two types of microbes and redefines a key process in the biogeochemical nitrogen cycle. Understanding the functional relationships between comammox and other nitrifiers is important for ecological studies on the nitrogen cycle. Therefore, the diversity and contribution of comammox should be considered during ecological analyses of nitrifying microorganisms. In this study, a ubiquitous and highly diverse distribution of comammox was observed in various environmental samples, similar to the distribution of canonical ammonia-oxidizing bacteria. The proportion of comammox was relatively high in coastal water and sediment samples, whereas it was nearly undetectable in open-ocean samples. The ubiquitous distribution and high diversity of comammox indicate that these microorganisms might be important contributors to nitrification.
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Affiliation(s)
- Fei Xia
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Jian-Gong Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Ting Zhu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Bin Zou
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju, Republic of Korea
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
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215
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Dang H, Kanitkar YH, Stedtfeld RD, Hatzinger PB, Hashsham SA, Cupples AM. Abundance of Chlorinated Solvent and 1,4-Dioxane Degrading Microorganisms at Five Chlorinated Solvent Contaminated Sites Determined via Shotgun Sequencing. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:13914-13924. [PMID: 30427665 DOI: 10.1021/acs.est.8b04895] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Shotgun sequencing was used for the quantification of taxonomic and functional biomarkers associated with chlorinated solvent bioremediation in 20 groundwater samples (five sites), following bioaugmentation with SDC-9. The analysis determined the abundance of (1) genera associated with chlorinated solvent degradation, (2) reductive dehalogenase (RDases) genes, (3) genes associated with 1,4-dioxane removal, (4) genes associated with aerobic chlorinated solvent degradation, and (5) D. mccartyi genes associated with hydrogen and corrinoid metabolism. The taxonomic analysis revealed numerous genera previously linked to chlorinated solvent degradation, including Dehalococcoides, Desulfitobacterium, and Dehalogenimonas. The functional gene analysis indicated vcrA and tceA from D. mccartyi were the RDases with the highest relative abundance. Reads aligning with both aerobic and anaerobic biomarkers were observed across all sites. Aerobic solvent degradation genes, etnC or etnE, were detected in at least one sample from each site, as were pmoA and mmoX. The most abundant 1,4-dioxane biomarker detected was Methylosinus trichosporium OB3b mmoX. Reads aligning to thmA or Pseudonocardia were not found. The work illustrates the importance of shotgun sequencing to provide a more complete picture of the functional abilities of microbial communities. The approach is advantageous over current methods because an unlimited number of functional genes can be quantified.
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Affiliation(s)
- Hongyu Dang
- Department of Civil and Environmental Engineering , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Yogendra H Kanitkar
- Department of Civil and Environmental Engineering , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Paul B Hatzinger
- APTIM , 17 Princess Road , Lawrenceville , New Jersey 08648 , United States
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering , Michigan State University , East Lansing , Michigan 48824 , United States
- Center for Microbial Ecology , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Alison M Cupples
- Department of Civil and Environmental Engineering , Michigan State University , East Lansing , Michigan 48824 , United States
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216
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Nakagawa T, Tsuchiya Y, Ueda S, Fukui M, Takahashi R. Eelgrass Sediment Microbiome as a Nitrous Oxide Sink in Brackish Lake Akkeshi, Japan. Microbes Environ 2018; 34:13-22. [PMID: 30504642 PMCID: PMC6440730 DOI: 10.1264/jsme2.me18103] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Nitrous oxide (N2O) is a powerful greenhouse gas; however, limited information is currently available on the microbiomes involved in its sink and source in seagrass meadow sediments. Using laboratory incubations, a quantitative PCR (qPCR) analysis of N2O reductase (nosZ) and ammonia monooxygenase subunit A (amoA) genes, and a metagenome analysis based on the nosZ gene, we investigated the abundance of N2O-reducing microorganisms and ammonia-oxidizing prokaryotes as well as the community compositions of N2O-reducing microorganisms in in situ and cultivated sediments in the non-eelgrass and eelgrass zones of Lake Akkeshi, Japan. Laboratory incubations showed that N2O was reduced by eelgrass sediments and emitted by non-eelgrass sediments. qPCR analyses revealed that the abundance of nosZ gene clade II in both sediments before and after the incubation as higher in the eelgrass zone than in the non-eelgrass zone. In contrast, the abundance of ammonia-oxidizing archaeal amoA genes increased after incubations in the non-eelgrass zone only. Metagenome analyses of nosZ genes revealed that the lineages Dechloromonas-Magnetospirillum-Thiocapsa and Bacteroidetes (Flavobacteriia) within nosZ gene clade II were the main populations in the N2O-reducing microbiome in the in situ sediments of eelgrass zones. Sulfur-oxidizing Gammaproteobacteria within nosZ gene clade II dominated in the lineage Dechloromonas-Magnetospirillum-Thiocapsa. Alphaproteobacteria within nosZ gene clade I were predominant in both zones. The proportions of Epsilonproteobacteria within nosZ gene clade II increased after incubations in the eelgrass zone microcosm supplemented with N2O only. Collectively, these results suggest that the N2O-reducing microbiome in eelgrass meadows is largely responsible for coastal N2O mitigation.
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Affiliation(s)
| | | | - Shingo Ueda
- College of Bioresource Sciences, Nihon University
| | - Manabu Fukui
- Institute of Low Temperature Science, Hokkaido University
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217
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Meng H, Zhou Z, Wu R, Wang Y, Gu JD. Diazotrophic microbial community and abundance in acidic subtropical natural and re-vegetated forest soils revealed by high-throughput sequencing of nifH gene. Appl Microbiol Biotechnol 2018; 103:995-1005. [PMID: 30474727 DOI: 10.1007/s00253-018-9466-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 09/17/2018] [Accepted: 10/09/2018] [Indexed: 01/09/2023]
Abstract
Biological nitrogen fixation (BNF) is an important natural biochemical process converting the inert dinitrogen gas (N2) in the atmosphere to ammonia (NH3) in the N cycle. In this study, the nifH gene was chosen to detect the diazotrophic microorganisms with high-throughput sequencing from five acidic forest soils, including three natural forests and two re-vegetated forests. Soil samples were taken in two seasons (summer and winter) at two depth layers (surface and lower depths). A dataset of 179,600 reads obtained from 20 samples were analyzed to provide the microbial community structure, diversity, abundance, and relationship with physiochemical parameters. Both archaea and bacteria were detected in these samples and diazotrophic bacteria were the dominant members contributing to the biological dinitrogen fixation in the acidic forest soils. Cyanobacteria, Firmicutes, Proteobacteria, Spirocheates, and Verrucomicrobia were observed, especially the Proteobacteria as the most abundant phylum. The core genera were Bradyrhizobium and Methylobacterium from α-Proteobacteia, and Desulfovibrio from δ-Proteobacteia in the phylum of Proteobacteia of these samples. The diversity indices and the gene abundances of all samples were higher in the surface layer than the lower layer. Diversity was apparently higher in re-vegetated forests than the natural forests. Significant positive correlation to the organic matter and nitrogen-related parameters was observed, but there was no significant seasonal variation on the community structure and diversity in these samples between the summer and winter. The application of high-throughput sequencing method provides a better understanding and more comprehensive information of diazotrophs in acidic forest soils than conventional and PCR-based ones.
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Affiliation(s)
- Han Meng
- School of Environment, Nanjing Normal University, Nanjing, 210023, China
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China
| | - Zhichao Zhou
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China
| | - Ruonan Wu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China
| | - Yongfeng Wang
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, 233 Guangshan 1st Road, Guangzhou, People's Republic of China
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China.
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218
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Habtewold J, Gordon R, Sokolov V, VanderZaag A, Wagner-Riddle C, Dunfield K. Reduction in Methane Emissions From Acidified Dairy Slurry Is Related to Inhibition of Methanosarcina Species. Front Microbiol 2018; 9:2806. [PMID: 30515146 PMCID: PMC6255968 DOI: 10.3389/fmicb.2018.02806] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 10/31/2018] [Indexed: 12/04/2022] Open
Abstract
Liquid dairy manure treated with sulfuric acid was stored in duplicate pilot-scale storage tanks for 120 days with continuous monitoring of CH4 emissions and concurrent examination of changes in the structure of bacterial and methanogenic communities. Methane emissions were monitored at the site using laser-based Trace Gas Analyzer whereas quantitative real-time polymerase chain reaction and massively parallel sequencing were employed to study bacterial and methanogenic communities using 16S rRNA and methyl-coenzyme M Reductase A (mcrA) genes/transcripts, respectively. When compared with untreated slurries, acidification resulted in 69–84% reductions of cumulative CH4 emissions. The abundance, activity, and proportion of bacterial communities did not vary with manure acidification. However, the abundance and activity of methanogens (as estimated from mcrA gene and transcript copies, respectively) in acidified slurries were reduced by 6 and 20%, respectively. Up to 21% reduction in mcrA transcript/gene ratios were also detected in acidified slurries. Regardless of treatment, Methanocorpusculum predominated archaeal 16S rRNA and mcrA gene and transcript libraries. The proportion of Methanosarcina, which is the most metabolically-diverse methanogen, was the significant discriminant feature between acidified and untreated slurries. In acidified slurries, the relative proportions of Methanosarcina were ≤ 10%, whereas in untreated slurries, it represented up to 24 and 53% of the mcrA gene and transcript libraries, respectively. The low proportions of Methanosarcina in acidified slurries coincided with the reductions in CH4 emissions. The results suggest that reduction of CH4 missions achieved by acidification was due to an inhibition of the growth and activity of Methanosarcina species.
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Affiliation(s)
- Jemaneh Habtewold
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Robert Gordon
- Department of Geography and Environmental Studies, Wilfrid Laurier University, Waterloo, ON, Canada
| | - Vera Sokolov
- Department of Geography and Environmental Studies, Wilfrid Laurier University, Waterloo, ON, Canada
| | | | | | - Kari Dunfield
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
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219
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Zhao S, Wang Q, Zhou J, Yuan D, Zhu G. Linking abundance and community of microbial N 2O-producers and N 2O-reducers with enzymatic N 2O production potential in a riparian zone. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 642:1090-1099. [PMID: 30045490 DOI: 10.1016/j.scitotenv.2018.06.110] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/09/2018] [Accepted: 06/09/2018] [Indexed: 06/08/2023]
Abstract
As aquatic-terrestrial ecotones, riparian zones are hotspots not only for denitrification but also for nitrous oxide (N2O) emission. Due to the potential role of nosZ II in N2O mitigation, emerging studies in terrestrial ecosystems have taken this newly reported N2O-reducer into account. However, our knowledge about the interactions between denitrification activities and both N2O-producers and reducers (especially for nosZ II) in aquatic ecosystems remains limited. In this study, we investigated spatiotemporal distributions of in situ N2O flux, potential N2O production rate, and potential denitrification rate, as well as of the related genes in a riparian zone of Baiyangdian Lake. Real-time quantitative PCR (qPCR) and high-throughput sequencing targeted functional genes were used to analyze the denitrifier communities. Results showed that great differences in microbial activities and abundances were observed between sites and seasons. Waterward sediments (constantly flooded area) had the lowest N2O production potential in both seasons. Not only the environmental factors (moisture content, NH4+ content and TOM) but also the community structure of N2O-producers and N2O-reducers (nirK/nirS and nosZ II/nosZ I ratios) could affect the potential N2O production rate. The abundance of the four functional genes in the winter was higher than in the summer, and the values all peaked at the occasionally flooded area in the winter. The dissimilarity in community composition was mainly driven by moisture content. Altogether, we propose that the N2O production potential was largely regulated by the community structure of N2O-producers and N2O-reducers in riparian zones. Increasing the constantly flooded area and reducing the occasionally flooded area of lake ecosystems may help reduce the level of denitrifier-produced N2O.
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Affiliation(s)
- Siyan Zhao
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiemin Zhou
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Dongdan Yuan
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of Municipal and Environmental Engineering, Jilin Jianzhu University, Changchun 130118, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of Municipal and Environmental Engineering, Jilin Jianzhu University, Changchun 130118, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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220
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Kimble JC, Winter AS, Spilde MN, Sinsabaugh RL, Northup DE. A potential central role of Thaumarchaeota in N-Cycling in a semi-arid environment, Fort Stanton Cave, Snowy River passage, New Mexico, USA. FEMS Microbiol Ecol 2018; 94:5079639. [PMID: 30165514 PMCID: PMC6669814 DOI: 10.1093/femsec/fiy173] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/23/2018] [Indexed: 01/03/2023] Open
Abstract
Low biomass and productivity of arid-land caves with limited availability of nitrogen (N) raises the question of how microbes acquire and cycle this essential element. Caves are ideal environments for investigating microbial functional capabilities, as they lack phototrophic activity and have near constant temperatures and high relative humidity. From the walls of Fort Stanton Cave (FSC), multicolored secondary mineral deposits of soil-like material low in fixed N, known as ferromanganese deposits (FMD), were collected. We hypothesized that within FMD samples we would find the presence of microbial N cycling genes and taxonomy related to N cycling microorganisms. Community DNA were sequenced using Illumina shotgun metagenomics and 16S rRNA gene sequencing. Results suggest a diverse N cycle encompassing several energetic pathways including nitrification, dissimilatory nitrate reduction and denitrification. N cycling genes associated with assimilatory nitrate reduction were also identified. Functional gene sequences and taxonomic findings suggest several bacterial and archaeal phyla potentially play a role in nitrification pathways in FSC and FMD. Thaumarchaeota, a deep-branching archaeal division, likely play an essential and possibly dominant role in the oxidation of ammonia. Our results provide genomic evidence for understanding how microbes are potentially able to acquire and cycle N in a low-nutrient subterranean environment.
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Affiliation(s)
- Jason C Kimble
- Department of Biology, MSC03-2020, University of New Mexico, Albuquerque, NM 87131, USA
| | - Ara S Winter
- Department of Biology, MSC03-2020, University of New Mexico, Albuquerque, NM 87131, USA
| | - Michael N Spilde
- Institute of Meteoritics, MSC03-2050, University of New Mexico, Albuquerque, NM 87131, USA
| | - Robert L Sinsabaugh
- Department of Biology, MSC03-2020, University of New Mexico, Albuquerque, NM 87131, USA
| | - Diana E Northup
- Department of Biology, MSC03-2020, University of New Mexico, Albuquerque, NM 87131, USA
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221
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Zhang X, Xu W, Liu Y, Cai M, Luo Z, Li M. Metagenomics Reveals Microbial Diversity and Metabolic Potentials of Seawater and Surface Sediment From a Hadal Biosphere at the Yap Trench. Front Microbiol 2018; 9:2402. [PMID: 30369913 PMCID: PMC6194347 DOI: 10.3389/fmicb.2018.02402] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/19/2018] [Indexed: 11/13/2022] Open
Abstract
Hadal biosphere represents the deepest part of the ocean with water depth >6,000 m. Accumulating evidence suggests the existence of unique microbial communities dominated by heterotrophic processes in this environment. However, investigations of the microbial diversity and their metabolic potentials are limited because of technical constraints for sample collection. Here, we provide a detailed metagenomic analysis of three seawater samples at water depths 5,000-6,000 m below sea level (mbsl) and three surface sediment samples at water depths 4,435-6,578 mbsl at the Yap Trench of the western Pacific. Distinct microbial community compositions were observed with the dominance of Gammaproteobacteria in seawater and Thaumarchaeota in surface sediment. Comparative analysis of the genes involved in carbon, nitrogen and sulfur metabolisms revealed that heterotrophic processes (i.e., degradation of carbohydrates, hydrocarbons, and aromatics) are the most common microbial metabolisms in the seawater, while chemolithoautotrophic metabolisms such as ammonia oxidation with the HP/HB cycle for CO2 fixation probably dominated the surface sediment communities of the Yap Trench. Furthermore, abundant genes involved in stress response and metal resistance were both detected in the seawater and sediments, thus the enrichment of metal resistance genes is further hypothesized to be characteristic of the hadal microbial communities. Overall, this study sheds light on the metabolic versatility of microorganisms in the Yap Trench, their roles in carbon, nitrogen, and sulfur biogeochemical cycles, and how they have adapted to this unique hadal environment.
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Affiliation(s)
- Xinxu Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China
| | - Yang Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Mingwei Cai
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Zhuhua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
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222
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Long-Term Biogas Production from Glycolate by Diverse and Highly Dynamic Communities. Microorganisms 2018; 6:microorganisms6040103. [PMID: 30287755 PMCID: PMC6313629 DOI: 10.3390/microorganisms6040103] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/25/2018] [Accepted: 09/29/2018] [Indexed: 12/19/2022] Open
Abstract
Generating chemical energy carriers and bulk chemicals from solar energy by microbial metabolic capacities is a promising technology. In this long-term study of over 500 days, methane was produced by a microbial community that was fed by the mono-substrate glycolate, which was derived from engineered algae. The microbial community structure was measured on the single cell level using flow cytometry. Abiotic and operational reactor parameters were analyzed in parallel. The R-based tool flowCyBar facilitated visualization of community dynamics and indicated sub-communities involved in glycolate fermentation and methanogenesis. Cell sorting and amplicon sequencing of 16S rRNA and mcrA genes were used to identify the key organisms involved in the anaerobic conversion process. The microbial community allowed a constant fermentation, although it was sensitive to high glycolate concentrations in the feed. A linear correlation between glycolate loading rate and biogas amount was observed (R2 = 0.99) for glycolate loading rates up to 1.81 g L−1 day−1 with a maximum in biogas amount of 3635 mL day−1 encompassing 45% methane. The cytometric diversity remained high during the whole cultivation period. The dominating bacterial genera were Syntrophobotulus, Clostridia genus B55_F, Aminobacterium, and Petrimonas. Methanogenesis was almost exclusively performed by the hydrogenotrophic genus Methanobacterium.
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223
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Shade A, Dunn RR, Blowes SA, Keil P, Bohannan BJ, Herrmann M, Küsel K, Lennon JT, Sanders NJ, Storch D, Chase J. Macroecology to Unite All Life, Large and Small. Trends Ecol Evol 2018; 33:731-744. [DOI: 10.1016/j.tree.2018.08.005] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/29/2018] [Accepted: 08/15/2018] [Indexed: 12/13/2022]
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224
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Rath S, Rud T, Karch A, Pieper DH, Vital M. Pathogenic functions of host microbiota. MICROBIOME 2018; 6:174. [PMID: 30266099 PMCID: PMC6162913 DOI: 10.1186/s40168-018-0542-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/29/2018] [Indexed: 05/11/2023]
Abstract
BACKGROUND It is becoming evident that certain features of human microbiota, encoded by distinct autochthonous taxa, promote disease. As a result, borders between the so-called opportunistic pathogens, pathobionts, and commensals are increasingly blurred, and specific targets for manipulating microbiota to improve host health are becoming elusive. RESULTS In this study, we focus on the functions of host bacterial communities that have the potential to cause disease, proposing the term "pathogenic function (pathofunction)". The concept is presented via three distinct examples, namely, the formation of (i) trimethylamine, (ii) secondary bile acids, and (iii) hydrogen sulfide, which represent metabolites of the gut microbiota linked to the development of non-communicable diseases. Using publicly available metagenomic and metatranscriptomic data (n = 2975), we quantified those pathofunctions in health and disease and exposed the key players. Pathofunctions were ubiquitously present with increased abundances in patient groups. Overall, the three pathofunctions were detected at low mean concentrations (< 1% of total bacteria carried respective genes) and encompassed various taxa, including uncultured members. CONCLUSIONS We outline how this function-centric approach, where all members of a community exhibiting a particular pathofunction are redundant, can contribute to risk assessment and the development of precision treatment directing gut microbiota to increase host health.
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Affiliation(s)
- Silke Rath
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Tatjana Rud
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - André Karch
- Epidemiological and Statistical Methods Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Dietmar Helmut Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Marius Vital
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
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225
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Aalto SL, Saarenheimo J, Mikkonen A, Rissanen AJ, Tiirola M. Resistant ammonia-oxidizing archaea endure, but adapting ammonia-oxidizing bacteria thrive in boreal lake sediments receiving nutrient-rich effluents. Environ Microbiol 2018; 20:3616-3628. [PMID: 30003649 PMCID: PMC6221106 DOI: 10.1111/1462-2920.14354] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/31/2018] [Accepted: 06/04/2018] [Indexed: 11/28/2022]
Abstract
Climate change along with anthropogenic activities changes biogeochemical conditions in lake ecosystems, modifying the sediment microbial communities. Wastewater effluents introduce nutrients and organic material but also novel microbes to lake ecosystems, simulating forthcoming increases in catchment loadings. In this work, we first used 16s rRNA gene sequencing to study how the overall sediment microbial community responds to wastewater in six boreal lakes. To examine forthcoming changes in the lake biogeochemistry, we focused on the ammonia‐oxidizing archaea (AOA) and bacteria (AOB), and examined their functional and compositional community response to wastewater. Although we found the least diverse and least resistant prokaryotic communities from the most wastewater‐influenced sediments, the community changed fast toward the natural composition with the diminishing influence of wastewater. Each lake hosted a unique resistant AOA community, while AOB communities were adapting, responding to environmental conditions as well as receiving new members from WWTPs. In general, AOB dominated in numbers in wastewater‐influenced sediments, while the ratio between AOA and AOB increased when moving toward pristine conditions. Our results suggest that although future climate‐change‐driven increases in nutrient loading and microbial migration might significantly disrupt lake sediment microbiomes, they can promote nitrification through adapting and abundant AOB communities.
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Affiliation(s)
- Sanni L Aalto
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland.,Department of Environmental and Biological Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Jatta Saarenheimo
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Anu Mikkonen
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Antti J Rissanen
- Laboratory of Chemistry and Bioengineering, Tampere University of Technology, 33101, Tampere, Finland
| | - Marja Tiirola
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland.,Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, 40014, Jyväskylä, Finland
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226
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Cryptic CH 4 cycling in the sulfate-methane transition of marine sediments apparently mediated by ANME-1 archaea. ISME JOURNAL 2018; 13:250-262. [PMID: 30194429 DOI: 10.1038/s41396-018-0273-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 08/10/2018] [Accepted: 08/17/2018] [Indexed: 11/09/2022]
Abstract
Methane in the seabed is mostly oxidized to CO2 with sulfate as the oxidant before it reaches the overlying water column. This microbial oxidation takes place within the sulfate-methane transition (SMT), a sediment horizon where the downward diffusive flux of sulfate encounters an upward flux of methane. Across multiple sites in the Baltic Sea, we identified a systematic discrepancy between the opposing fluxes, such that more sulfate was consumed than expected from the 1:1 stoichiometry of methane oxidation with sulfate. The flux discrepancy was consistent with an oxidation of buried organic matter within the SMT, as corroborated by stable carbon isotope budgets. Detailed radiotracer experiments showed that up to 60% of the organic matter oxidation within the SMT first produced methane, which was concurrently oxidized to CO2 by sulfate reduction. This previously unrecognized "cryptic" methane cycling in the SMT is not discernible from geochemical profiles due to overall net methane consumption. Sedimentary gene pools suggested that nearly all potential methanogens within and beneath the SMT belonged to ANME-1 archaea, which are typically associated with anaerobic methane oxidation. Analysis of a metagenome-assembled genome suggests that predominant ANME-1 do indeed have the enzymatic potential to catalyze both methane production and consumption.
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227
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Higgins SA, Schadt CW, Matheny PB, Löffler FE. Phylogenomics Reveal the Dynamic Evolution of Fungal Nitric Oxide Reductases and Their Relationship to Secondary Metabolism. Genome Biol Evol 2018; 10:2474-2489. [PMID: 30165640 PMCID: PMC6161760 DOI: 10.1093/gbe/evy187] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2018] [Indexed: 12/16/2022] Open
Abstract
Fungi expressing P450nor, an unconventional nitric oxide (NO) reducing cytochrome P450, are considered significant contributors to environmental nitrous oxide (N2O) emissions. Despite extensive efforts, fungal contributions to N2O emissions remain uncertain. For example, the majority of N2O emitted from antibiotic-amended soil microcosms is attributed to fungal activity, yet axenic fungal cultures do not couple N-oxyanion respiration to growth and these fungi produce only minor quantities of N2O. To assist in reconciling these conflicting observations and produce a benchmark genomic analysis of fungal denitrifiers, genes underlying denitrification were examined in >700 fungal genomes. Of 167 p450nor—containing genomes identified, 0, 30, and 48 also harbored the denitrification genes narG, napA, or nirK, respectively. Compared with napA and nirK, p450nor was twice as abundant and exhibited 2–5-fold more gene duplications, losses, and transfers, indicating a disconnect between p450nor presence and denitrification potential. Furthermore, cooccurrence of p450nor with genes encoding NO-detoxifying flavohemoglobins (Spearman r = 0.87, p = 1.6e−10) confounds hypotheses regarding P450nor’s primary role in NO detoxification. Instead, ancestral state reconstruction united P450nor with actinobacterial cytochrome P450s (CYP105) involved in secondary metabolism (SM) and 19 (11%) p450nor-containing genomic regions were predicted to be SM clusters. Another 40 (24%) genomes harbored genes nearby p450nor predicted to encode hallmark SM functions, providing additional contextual evidence linking p450nor to SM. These findings underscore the potential physiological implications of widespread p450nor gene transfer, support the undiscovered affiliation of p450nor with fungal SM, and challenge the hypothesis of p450nor’s primary role in denitrification.
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Affiliation(s)
- Steven A Higgins
- Department of Microbiology, University of Tennessee, Knoxville.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge
| | - Christopher W Schadt
- Department of Microbiology, University of Tennessee, Knoxville.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge.,University of Tennessee and Oak Ridge National Laboratory (UT-ORNL), Joint Institute for Biological Sciences (JIBS), Oak Ridge
| | - Patrick B Matheny
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville
| | - Frank E Löffler
- Department of Microbiology, University of Tennessee, Knoxville.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge.,University of Tennessee and Oak Ridge National Laboratory (UT-ORNL), Joint Institute for Biological Sciences (JIBS), Oak Ridge.,Department of Civil and Environmental Engineering, University of Tennessee, Knoxville.,Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville.,Center for Environmental Biotechnology, University of Tennessee, Knoxville
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228
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Wilhelm RC, Hanson BT, Chandra S, Madsen E. Community dynamics and functional characteristics of naphthalene-degrading populations in contaminated surface sediments and hypoxic/anoxic groundwater. Environ Microbiol 2018; 20:3543-3559. [PMID: 30051558 DOI: 10.1111/1462-2920.14309] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/07/2018] [Indexed: 12/19/2022]
Abstract
Earlier research on the biogeochemical factors affecting natural attenuation in coal-tar contaminated groundwater, at South Glens Falls, NY, revealed the importance of anaerobic metabolism and trophic interactions between degrader and bacterivore populations. Field-based characterizations of both phenomena have proven challenging, but advances in stable isotope probing (SIP), single-cell imaging and shotgun metagenomics now provide cultivation-independent tools for their study. We tracked carbon from 13 C-labelled naphthalene through microbial populations in contaminated surface sediments over 6 days using respiration assays, secondary ion mass spectrometry imaging and shotgun metagenomics to disentangle the contaminant-based trophic web. Contaminant-exposed communities in hypoxic/anoxic groundwater were contrasted with those from oxic surface sediments to identify putative features of anaerobic catabolism of naphthalene. In total, six bacteria were responsible for naphthalene degradation. Cupriavidus, Ralstonia and Sphingomonas predominated at the earliest stages of SIP incubations and were succeeded in later stages by Stenotrophomonas and Rhodococcus. Metagenome-assembled genomes provided evidence for the ecological and functional characteristics underlying these temporal shifts. Identical species of Stenotrophomonas and Rhodococcus were abundant in the most contaminated, anoxic groundwater. Apparent increases in bacterivorous protozoa were observed following exposure to naphthalene, though insignificant amounts of carbon were transferred between bacterial degraders and populations of secondary feeders.
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Affiliation(s)
- Roland C Wilhelm
- Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Buck T Hanson
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Subhash Chandra
- Cornell SIMS Laboratory, Department of Earth and Atmospheric Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Eugene Madsen
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
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229
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Mackelprang R, Grube AM, Lamendella R, Jesus EDC, Copeland A, Liang C, Jackson RD, Rice CW, Kapucija S, Parsa B, Tringe SG, Tiedje JM, Jansson JK. Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States. Front Microbiol 2018; 9:1775. [PMID: 30158906 PMCID: PMC6104126 DOI: 10.3389/fmicb.2018.01775] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/16/2018] [Indexed: 11/19/2022] Open
Abstract
The North American prairie covered about 3.6 million-km2 of the continent prior to European contact. Only 1-2% of the original prairie remains, but the soils that developed under these prairies are some of the most productive and fertile in the world, containing over 35% of the soil carbon in the continental United States. Cultivation may alter microbial diversity and composition, influencing the metabolism of carbon, nitrogen, and other elements. Here, we explored the structure and functional potential of the soil microbiome in paired cultivated-corn (at the time of sampling) and never-cultivated native prairie soils across a three-states transect (Wisconsin, Iowa, and Kansas) using metagenomic and 16S rRNA gene sequencing and lipid analysis. At the Wisconsin site, we also sampled adjacent restored prairie and switchgrass plots. We found that agricultural practices drove differences in community composition and diversity across the transect. Microbial biomass in prairie samples was twice that of cultivated soils, but alpha diversity was higher with cultivation. Metagenome analyses revealed denitrification and starch degradation genes were abundant across all soils, as were core genes involved in response to osmotic stress, resource transport, and environmental sensing. Together, these data indicate that cultivation shifted the microbiome in consistent ways across different regions of the prairie, but also suggest that many functions are resilient to changes caused by land management practices - perhaps reflecting adaptations to conditions common to tallgrass prairie soils in the region (e.g., soil type, parent material, development under grasses, temperature and rainfall patterns, and annual freeze-thaw cycles). These findings are important for understanding the long-term consequences of land management practices to prairie soil microbial communities and their genetic potential to carry out key functions.
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Affiliation(s)
- Rachel Mackelprang
- Department of Biology, California State University, Northridge, Northridge, CA, United States
| | - Alyssa M. Grube
- Department of Biology, Juniata College, Huntingdon, PA, United States
| | - Regina Lamendella
- Department of Biology, Juniata College, Huntingdon, PA, United States
| | - Ederson da C. Jesus
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States
- Great Lakes Bioenergy Research Center, U.S. Department of Energy, University of Wisconsin–Madison, Madison, WI, United States
| | - Alex Copeland
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Chao Liang
- Great Lakes Bioenergy Research Center, U.S. Department of Energy, University of Wisconsin–Madison, Madison, WI, United States
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Randall D. Jackson
- Great Lakes Bioenergy Research Center, U.S. Department of Energy, University of Wisconsin–Madison, Madison, WI, United States
- Department of Agronomy, University of Wisconsin–Madison, Madison, WI, United States
| | - Charles W. Rice
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Stefanie Kapucija
- Department of Biology, California State University, Northridge, Northridge, CA, United States
| | - Bayan Parsa
- Department of Biology, California State University, Northridge, Northridge, CA, United States
| | - Susannah G. Tringe
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - James M. Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, United States
- Great Lakes Bioenergy Research Center, U.S. Department of Energy, University of Wisconsin–Madison, Madison, WI, United States
| | - Janet K. Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
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230
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Heller P, Casaletto J, Ruiz G, Geller J. A database of metazoan cytochrome c oxidase subunit I gene sequences derived from GenBank with CO-ARBitrator. Sci Data 2018; 5:180156. [PMID: 30084847 PMCID: PMC6080493 DOI: 10.1038/sdata.2018.156] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 05/30/2018] [Indexed: 11/30/2022] Open
Abstract
The Cytochrome C Oxidase subunit I gene ("COI") is the de facto standard for animal DNA barcoding. Organism identification based on COI requires an accurate and extensive annotated database of COI sequences. Such a database can also be of value in reconstructing evolutionary history and in diversity studies. Two COI databases are currently available: BOLD and Midori. BOLD's submissions conform to stringent sequence and metadata requirements; BOLD is specific to COI but makes no attempt to be comprehensive. Midori, derived from GenBank, has more sequences but less stringent standards than BOLD, resulting in higher error rates. To address the need for a comprehensive and accurate COI database, we adapted the ARBitrator algorithm, which classifies based only on sequence properties and has successfully auto-curated bacterial genes mined from GenBank. The adapted algorithm, which we call CO-ARBitrator, built a database of over a million metazoan COI sequences. Sensitivity and specificity are significantly higher than Midori. Specificity is comparable to what BOLD achieves with data quality prerequisites. Results and software are publicly available.
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Affiliation(s)
- Philip Heller
- Moss Landing Marine Laboratories, Moss Landing, California 94039, USA
- San Jose State University, San Jose, California 95192, USA
| | | | - Gregory Ruiz
- Smithsonian Environmental Research Center, Edgewater, Maryland 21037, USA
| | - Jonathan Geller
- Moss Landing Marine Laboratories, Moss Landing, California 94039, USA
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231
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Wang H, Gilbert JA, Zhu Y, Yang X. Salinity is a key factor driving the nitrogen cycling in the mangrove sediment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 631-632:1342-1349. [PMID: 29727958 DOI: 10.1016/j.scitotenv.2018.03.102] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 03/05/2018] [Accepted: 03/09/2018] [Indexed: 06/08/2023]
Abstract
Coastal ecosystems are hotspots for nitrogen cycling, and specifically for nitrogen removal from water and sediment through the coupled nitrification-denitrification process. Salinity is globally important in structuring bacterial and archaeal communities, but the association between salinity and microbially-mediated nitrification and denitrification remains unclear. The denitrification activity and composition and structure of microbial nitrifiers and denitrifiers were characterized across a gradient of manipulated salinity (0, 10, 20 and 30ppt) in a mangrove sediment. Salinity negatively correlated with both denitrifying activity and the abundance of nirK and nosZ denitrifying genes. Ammonia-oxidizing bacteria (AOB), which dominated nitrification, had significantly greater abundance at intermediate salinity (10 and 20ppt). However, a positive correlation between ammonia concentration and salinity suggested that nitrifying activity might also be inhibited at higher salinity. The community structure of ammonia-oxidizing archaea (AOA) and bacteria (AOB), as well as nirK, nirS and nosZ denitrifying communities, were all significantly correlated with salinity. These changes were also associated with structural shifts in phylogeny. These findings provide a strong evidence that salinity is a key factor that influences the nitrogen transformations in coastal wetlands, indicating that salinity intrusion caused by climate change might have a broader impact on the coastal biospheres.
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Affiliation(s)
- Haitao Wang
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian Province 361024, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, China; School of Life Sciences, Xiamen University, Xiamen, Fujian Province 361102, China; The Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL 60637, USA
| | - Jack A Gilbert
- The Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL 60637, USA
| | - Yongguan Zhu
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian Province 361024, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, China
| | - Xiaoru Yang
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian Province 361024, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, China.
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232
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Zhang Y, Cui M, Duan J, Zhuang X, Zhuang G, Ma A. Abundance, rather than composition, of methane-cycling microbes mainly affects methane emissions from different vegetation soils in the Zoige alpine wetland. Microbiologyopen 2018; 8:e00699. [PMID: 30047238 PMCID: PMC6460274 DOI: 10.1002/mbo3.699] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/09/2018] [Accepted: 06/25/2018] [Indexed: 11/10/2022] Open
Abstract
Methane fluxes, which are controlled by methanogens and methanotrophs, vary among wetland vegetation species. In this study, we investigated belowground methanogens and methanotrophs in two soils under two different dominant vegetation species with different methane fluxes in the Zoige wetland, which was slightly but significantly (p ≤ 0.05) higher in soils covered by Carex muliensis than that in soils covered by Eleocharis valleculosa. Real‐time quantitative PCR and Illumina MiSeq sequencing methods were used to elucidate the microbial communities based on the key genes involved in methane production and oxidation. The absolute abundances of methanogens and methanotrophs of samples from C. muliensis were 1.80 ± 0.07 × 106 and 4.03 ± 0.28 × 106 copies g‐soil−1, respectively, and which from E. valleculosa were 3.99 ± 0.19 × 105 and 2.53 ± 0.22 × 106 copies g‐soil−1 , respectively. The t‐test result showed that both the abundance of methanogens and methanotrophs from C. muliensis were significantly higher (p ≤ 0.05) than that of samples from E. valleculosa. However, the diversities and compositions of both methanogens and methanotrophs showed no significant differences (p ≥ 0.05) between vegetation species. The path analysis showed that the microbial abundance had a greater effect than the microbial diversity on methane production potentials and the regression analysis also showed that the methane emissions significantly (p ≤ 0.05) varied with the abundance of methane‐cycling microbes. These findings imply that abundance rather than diversity and composition of a methane‐cycling microbial community is the major contributor to the variations in methane emissions between vegetation types in the Zoige wetland.
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Affiliation(s)
- Yanfen Zhang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mengmeng Cui
- University of Chinese Academy of Sciences, Beijing, China.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jingbo Duan
- University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Environmental Optics & Technology, Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Hefei, China
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guoqiang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Anzhou Ma
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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233
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Delmont TO, Quince C, Shaiber A, Esen ÖC, Lee ST, Rappé MS, McLellan SL, Lücker S, Eren AM. Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. Nat Microbiol 2018; 3:804-813. [PMID: 29891866 PMCID: PMC6792437 DOI: 10.1038/s41564-018-0176-9] [Citation(s) in RCA: 246] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 05/15/2018] [Indexed: 01/28/2023]
Abstract
Nitrogen fixation in the surface ocean impacts global marine nitrogen bioavailability and thus microbial primary productivity. Until now, cyanobacterial populations have been viewed as the main suppliers of bioavailable nitrogen in this habitat. Although PCR amplicon surveys targeting the nitrogenase reductase gene have revealed the existence of diverse non-cyanobacterial diazotrophic populations, subsequent quantitative PCR surveys suggest that they generally occur in low abundance. Here, we use state-of-the-art metagenomic assembly and binning strategies to recover nearly one thousand non-redundant microbial population genomes from the TARA Oceans metagenomes. Among these, we provide the first genomic evidence for non-cyanobacterial diazotrophs inhabiting surface waters of the open ocean, which correspond to lineages within the Proteobacteria and, most strikingly, the Planctomycetes. Members of the latter phylum are prevalent in aquatic systems, but have never been linked to nitrogen fixation previously. Moreover, using genome-wide quantitative read recruitment, we demonstrate that the discovered diazotrophs were not only widespread but also remarkably abundant (up to 0.3% of metagenomic reads for a single population) in both the Pacific Ocean and the Atlantic Ocean northwest. Our results extend decades of PCR-based gene surveys, and substantiate the importance of heterotrophic bacteria in the fixation of nitrogen in the surface ocean.
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Affiliation(s)
- Tom O Delmont
- Department of Medicine, University of Chicago, Chicago, IL, USA.
| | | | - Alon Shaiber
- Graduate Program in the Biophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Özcan C Esen
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sonny Tm Lee
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Michael S Rappé
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, HI, USA
| | - Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Sebastian Lücker
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA. .,Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA. .,Committee on Microbiology, University of Chicago, Chicago, IL, USA.
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234
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Rathnayake RMLD, Oshiki M, Ishii S, Segawa T, Satoh H, Okabe S. Experimental Evidence for in Situ Nitric Oxide Production in Anaerobic Ammonia-Oxidizing Bacterial Granules. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:5744-5752. [PMID: 29678110 DOI: 10.1021/acs.est.8b00876] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Although nitric oxide (NO) emissions from anaerobic ammonium oxidation (anammox)-based processes were reported previously, the NO production pathways are poorly understood. Here, we investigated the NO production pathways in anammox granules in detail by combining 15N-stable isotope tracer experiments with various inhibitors, microsensor measurements, and transcriptome analysis for key genes of NO2- reduction. NO was emitted from the anammox granules, which account for 0.07% of the N2 emission. 15N-stable isotope-tracer experiments indicated that most of the N2 was produced by anammox bacteria, whereas NO was produced from NO2- reduction by anammox and denitrifying bacteria. The NO emission rate was highest at pH 8.0 and accelerated by increasing NH4+ and NO2- concentrations in the culture media. The microsensor analyses showed the in situ NO production rate was highest in the outer layer of the anammox granule where anammox activity was also highest. The detected in situ NO concentrations of up to 2.7 μM were significantly above physiological thresholds known to affect a wide range of microorganisms present in wastewater. Hence, NO likely plays pivotal roles in the microbial interactions in anammox granules, which needs to be further investigated.
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Affiliation(s)
- Rathnayake M L D Rathnayake
- Department of Civil Engineering, Faculty of Engineering , University of Peradeniya , Peradeniya 20400 , Sri Lanka
- Division of Environmental Engineering, Graduate School of Engineering , Hokkaido University , North-13, West-8 , Sapporo 060-8628 , Japan
| | - Mamoru Oshiki
- Division of Environmental Engineering, Graduate School of Engineering , Hokkaido University , North-13, West-8 , Sapporo 060-8628 , Japan
- Department of Civil Engineering , National Institute of Technology, Nagaoka College , 888 Nishikatakaimachi , Nagaoka , Niigata 940-8532 , Japan
| | - Satoshi Ishii
- Division of Environmental Engineering, Graduate School of Engineering , Hokkaido University , North-13, West-8 , Sapporo 060-8628 , Japan
- Department of Soil, Water and Climate , University of Minnesota , 439 Borlaug Hall, 1991 Upper Buford Circle , St. Paul , Minnesota 55108 , United States
- BioTechnology Institute , University of Minnesota , 140 Gortner Laboratory, 1479 Gortner Avenue , St. Paul , Minnesota 55108 , United States
| | - Takahiro Segawa
- Center for Life Science Research , University of Yamanashi , 1110, Shimokato , Chuo , Yamanashi 409-3898 , Japan
- Transdisciplinary Research Integration Center , National Institute of Polar Research , 10-3 Midori-cho , Tachikawa , Tokyo 190-8518 , Japan
| | - Hisashi Satoh
- Division of Environmental Engineering, Graduate School of Engineering , Hokkaido University , North-13, West-8 , Sapporo 060-8628 , Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Graduate School of Engineering , Hokkaido University , North-13, West-8 , Sapporo 060-8628 , Japan
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235
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Anthropogenic N Deposition Alters the Composition of Expressed Class II Fungal Peroxidases. Appl Environ Microbiol 2018; 84:AEM.02816-17. [PMID: 29453258 DOI: 10.1128/aem.02816-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/09/2018] [Indexed: 01/13/2023] Open
Abstract
Here, we present evidence that ca. 20 years of experimental N deposition altered the composition of lignin-decaying class II peroxidases expressed by forest floor fungi, a response which has occurred concurrently with reductions in plant litter decomposition and a rapid accumulation of soil organic matter. This finding suggests that anthropogenic N deposition has induced changes in the biological mediation of lignin decay, the rate limiting step in plant litter decomposition. Thus, an altered composition of transcripts for a critical gene that is associated with terrestrial C cycling may explain the increased soil C storage under long-term increases in anthropogenic N deposition.IMPORTANCE Fungal class II peroxidases are enzymes that mediate the rate-limiting step in the decomposition of plant material, which involves the oxidation of lignin and other polyphenols. In field experiments, anthropogenic N deposition has increased soil C storage in forests, a result which could potentially arise from anthropogenic N-induced changes in the composition of class II peroxidases expressed by the fungal community. In this study, we have gained unique insight into how anthropogenic N deposition, a widespread agent of global change, affects the expression of a functional gene encoding an enzyme that plays a critical role in a biologically mediated ecosystem process.
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236
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Angel R, Nepel M, Panhölzl C, Schmidt H, Herbold CW, Eichorst SA, Woebken D. Evaluation of Primers Targeting the Diazotroph Functional Gene and Development of NifMAP - A Bioinformatics Pipeline for Analyzing nifH Amplicon Data. Front Microbiol 2018; 9:703. [PMID: 29760683 PMCID: PMC5936773 DOI: 10.3389/fmicb.2018.00703] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 03/27/2018] [Indexed: 11/13/2022] Open
Abstract
Diazotrophic microorganisms introduce biologically available nitrogen (N) to the global N cycle through the activity of the nitrogenase enzyme. The genetically conserved dinitrogenase reductase (nifH) gene is phylogenetically distributed across four clusters (I-IV) and is widely used as a marker gene for N2 fixation, permitting investigators to study the genetic diversity of diazotrophs in nature and target potential participants in N2 fixation. To date there have been limited, standardized pipelines for analyzing the nifH functional gene, which is in stark contrast to the 16S rRNA gene. Here we present a bioinformatics pipeline for processing nifH amplicon datasets - NifMAP ("NifH MiSeq Illumina Amplicon Analysis Pipeline"), which as a novel aspect uses Hidden-Markov Models to filter out homologous genes to nifH. By using this pipeline, we evaluated the broadly inclusive primer pairs (Ueda19F-R6, IGK3-DVV, and F2-R6) that target the nifH gene. To evaluate any systematic biases, the nifH gene was amplified with the aforementioned primer pairs in a diverse collection of environmental samples (soils, rhizosphere and roots samples, biological soil crusts and estuarine samples), in addition to a nifH mock community consisting of six phylogenetically diverse members. We noted that all primer pairs co-amplified nifH homologs to varying degrees; up to 90% of the amplicons were nifH homologs with IGK3-DVV in some samples (rhizosphere and roots from tall oat-grass). In regards to specificity, we observed some degree of bias across the primer pairs. For example, primer pair F2-R6 discriminated against cyanobacteria (amongst others), yet captured many sequences from subclusters IIIE and IIIL-N. These aforementioned subclusters were largely missing by the primer pair IGK3-DVV, which also tended to discriminate against Alphaproteobacteria, but amplified sequences within clusters IIIC (affiliated with Clostridia) and clusters IVB and IVC. Primer pair Ueda19F-R6 exhibited the least bias and successfully captured diazotrophs in cluster I and subclusters IIIE, IIIL, IIIM, and IIIN, but tended to discriminate against Firmicutes and subcluster IIIC. Taken together, our newly established bioinformatics pipeline, NifMAP, along with our systematic evaluations of nifH primer pairs permit more robust, high-throughput investigations of diazotrophs in diverse environments.
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Affiliation(s)
- Roey Angel
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of Vienna, Vienna, Austria
| | | | | | | | | | | | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of Vienna, Vienna, Austria
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237
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Li YY, Chen XH, Xie ZX, Li DX, Wu PF, Kong LF, Lin L, Kao SJ, Wang DZ. Bacterial Diversity and Nitrogen Utilization Strategies in the Upper Layer of the Northwestern Pacific Ocean. Front Microbiol 2018; 9:797. [PMID: 29922238 PMCID: PMC5996900 DOI: 10.3389/fmicb.2018.00797] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 04/10/2018] [Indexed: 11/13/2022] Open
Abstract
Nitrogen (N) is a primary limiting nutrient for bacterial growth and productivity in the ocean. To better understand bacterial community and their N utilization strategy in different N regimes of the ocean, we examined bacterial diversity, diazotrophic diversity, and N utilization gene expressions in the northwestern Pacific Ocean (NWPO) using a combination of high-throughput sequencing and real-time qPCR methods. 521 and 204 different operational taxonomic units (OTUs) were identified in the 16s rRNA and nifH libraries from nine surface samples. Of the 16s rRNA gene OTUs, 11.9% were observed in all samples while 3.5 and 15.9% were detected only in N-sufficient and N-deficient samples. Proteobacteria, Cyanobacteria and Bacteroidetes dominated the bacterial community. Prochlorococcus and Pseudoalteromonas were the most abundant at the genus level in N-deficient regimes, while SAR86, Synechococcus and SAR92 were predominant in the Kuroshio-Oyashio confluence region. The distribution of the nifH gene presented great divergence among sampling stations: Cyanobacterium_UCYN-A dominated the N-deficient stations, while clusters related to the Alpha-, Beta-, and Gamma-Proteobacteria were abundant in other stations. Temperature was the main factor that determined bacterial community structure and diversity while concentration of NOX-N was significantly correlated with structure and distribution of N2-fixing microorganisms. Expression of the ammonium transporter was much higher than that of urea transporter subunit A (urtA) and ferredoxin-nitrate reductase, while urtA had an increased expression in N-deficient surface water. The predicted ammonium transporter and ammonium assimilation enzymes were most abundant in surface samples while urease and nitrogenase were more abundant in the N-deficient regions. These findings underscore the fact that marine bacteria have evolved diverse N utilization strategies to adapt to different N habitats, and that urea metabolism is of vital ecological importance in N-deficient regimes.
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Affiliation(s)
- Yuan-Yuan Li
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Xiao-Huang Chen
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Zhang-Xian Xie
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Dong-Xu Li
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Peng-Fei Wu
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Ling-Fen Kong
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
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238
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Effects of reforestation on ammonia-oxidizing microbial community composition and abundance in subtropical acidic forest soils. Appl Microbiol Biotechnol 2018; 102:5309-5322. [DOI: 10.1007/s00253-018-8873-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 02/03/2018] [Accepted: 02/10/2018] [Indexed: 01/01/2023]
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239
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Nitrogen Cycle Evaluation (NiCE) Chip for Simultaneous Analysis of Multiple N Cycle-Associated Genes. Appl Environ Microbiol 2018. [PMID: 29427421 DOI: 10.1128/aem.02615‐17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Various microorganisms play key roles in the nitrogen (N) cycle. Quantitative PCR (qPCR) and PCR amplicon sequencing of N cycle functional genes allow us to analyze the abundance and diversity of microbes responsible for N-transforming reactions in various environmental samples. However, analysis of multiple target genes can be cumbersome and expensive. PCR-independent analysis, such as metagenomics and metatranscriptomics, is useful but expensive, especially when we analyze multiple samples and try to detect N cycle functional genes present at a relatively low abundance. Here, we present the application of microfluidic qPCR chip technology to simultaneously quantify and prepare amplicon sequence libraries for multiple N cycle functional genes as well as taxon-specific 16S rRNA gene markers for many samples. This approach, named the nitrogen cycle evaluation (NiCE) chip, was evaluated by using DNA from pure and artificially mixed bacterial cultures and by comparing the results with those obtained by conventional qPCR and amplicon sequencing methods. Quantitative results obtained by the NiCE chip were comparable to those obtained by conventional qPCR. In addition, the NiCE chip was successfully applied to examine the abundance and diversity of N cycle functional genes in wastewater samples. Although nonspecific amplification was detected on the NiCE chip, this can be overcome by optimizing the primer sequences in the future. As the NiCE chip can provide a high-throughput format to quantify and prepare sequence libraries for multiple N cycle functional genes, this tool should advance our ability to explore N cycling in various samples.IMPORTANCE We report a novel approach, namely, the nitrogen cycle evaluation (NiCE) chip, by using microfluidic qPCR chip technology. By sequencing the amplicons recovered from the NiCE chip, we can assess the diversities of N cycle functional genes. The NiCE chip technology is applicable to analysis of the temporal dynamics of N cycle gene transcription in wastewater treatment bioreactors. The NiCE chip can provide a high-throughput format to quantify and prepare sequence libraries for multiple N cycle functional genes. While there is room for future improvement, this tool should significantly advance our ability to explore the N cycle in various environmental samples.
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240
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Lourenço KS, Cassman NA, Pijl AS, van Veen JA, Cantarella H, Kuramae EE. Nitrosospira sp. Govern Nitrous Oxide Emissions in a Tropical Soil Amended With Residues of Bioenergy Crop. Front Microbiol 2018; 9:674. [PMID: 29692763 PMCID: PMC5902487 DOI: 10.3389/fmicb.2018.00674] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 03/22/2018] [Indexed: 11/13/2022] Open
Abstract
Organic vinasse, a residue produced during bioethanol production, increases nitrous oxide (N2O) emissions when applied with inorganic nitrogen (N) fertilizer in soil. The present study investigated the role of the ammonia-oxidizing bacteria (AOB) community on the N2O emissions in soils amended with organic vinasse (CV: concentrated and V: non-concentrated) plus inorganic N fertilizer. Soil samples and N2O emissions were evaluated at 11, 19, and 45 days after fertilizer application, and the bacterial and archaea gene (amoA) encoding the ammonia monooxygenase enzyme, bacterial denitrifier (nirK, nirS, and nosZ) genes and total bacteria were quantified by real time PCR. We also employed a deep amoA amplicon sequencing approach to evaluate the effect of treatment on the community structure and diversity of the soil AOB community. Both vinasse types applied with inorganic N application increased the total N2O emissions and the abundance of AOB. Nitrosospira sp. was the dominant AOB in the soil and was correlated with N2O emissions. However, the diversity and the community structure of AOB did not change with vinasse and inorganic N fertilizer amendment. The results highlight the importance of residues and fertilizer management in sustainable agriculture and can be used as a reference and an input tool to determine good management practices for organic fertilization.
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Affiliation(s)
- Késia S Lourenço
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands.,Soils and Environmental Resources Center, Agronomic Institute of Campinas, Campinas, Brazil.,Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Noriko A Cassman
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Agata S Pijl
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Heitor Cantarella
- Soils and Environmental Resources Center, Agronomic Institute of Campinas, Campinas, Brazil
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
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241
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Nitrogen Cycle Evaluation (NiCE) Chip for Simultaneous Analysis of Multiple N Cycle-Associated Genes. Appl Environ Microbiol 2018; 84:AEM.02615-17. [PMID: 29427421 DOI: 10.1128/aem.02615-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 01/28/2018] [Indexed: 01/20/2023] Open
Abstract
Various microorganisms play key roles in the nitrogen (N) cycle. Quantitative PCR (qPCR) and PCR amplicon sequencing of N cycle functional genes allow us to analyze the abundance and diversity of microbes responsible for N-transforming reactions in various environmental samples. However, analysis of multiple target genes can be cumbersome and expensive. PCR-independent analysis, such as metagenomics and metatranscriptomics, is useful but expensive, especially when we analyze multiple samples and try to detect N cycle functional genes present at a relatively low abundance. Here, we present the application of microfluidic qPCR chip technology to simultaneously quantify and prepare amplicon sequence libraries for multiple N cycle functional genes as well as taxon-specific 16S rRNA gene markers for many samples. This approach, named the nitrogen cycle evaluation (NiCE) chip, was evaluated by using DNA from pure and artificially mixed bacterial cultures and by comparing the results with those obtained by conventional qPCR and amplicon sequencing methods. Quantitative results obtained by the NiCE chip were comparable to those obtained by conventional qPCR. In addition, the NiCE chip was successfully applied to examine the abundance and diversity of N cycle functional genes in wastewater samples. Although nonspecific amplification was detected on the NiCE chip, this can be overcome by optimizing the primer sequences in the future. As the NiCE chip can provide a high-throughput format to quantify and prepare sequence libraries for multiple N cycle functional genes, this tool should advance our ability to explore N cycling in various samples.IMPORTANCE We report a novel approach, namely, the nitrogen cycle evaluation (NiCE) chip, by using microfluidic qPCR chip technology. By sequencing the amplicons recovered from the NiCE chip, we can assess the diversities of N cycle functional genes. The NiCE chip technology is applicable to analysis of the temporal dynamics of N cycle gene transcription in wastewater treatment bioreactors. The NiCE chip can provide a high-throughput format to quantify and prepare sequence libraries for multiple N cycle functional genes. While there is room for future improvement, this tool should significantly advance our ability to explore the N cycle in various environmental samples.
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242
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Wu B, Liu F, Weiser MD, Ning D, Okie JG, Shen L, Li J, Chai B, Deng Y, Feng K, Wu L, Chen S, Zhou J, He Z. Temperature determines the diversity and structure of N
2
O‐reducing microbial assemblages. Funct Ecol 2018. [DOI: 10.1111/1365-2435.13091] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Bo Wu
- Environmental Microbiomics Research Center and Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology School of Environmental Science and Engineering Sun Yat‐sen University Guangzhou China
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology University of Oklahoma Norman OK USA
- State Key Laboratory of Agricultural Microbiology Huazhong Agricultural University Wuhan China
| | - Feifei Liu
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology University of Oklahoma Norman OK USA
- Guangdong Provincial Key Lab of Microbial Culture Collection and Application Guangdong Institute of Microbiology and State Key Laboratory of Applied Microbiology Southern China Guangzhou China
| | | | - Daliang Ning
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology University of Oklahoma Norman OK USA
| | - Jordan G. Okie
- School of Earth and Space Exploration Arizona State University Tempe AZ USA
- School of Life Sciences Arizona State University Tempe AZ USA
| | - Lina Shen
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology University of Oklahoma Norman OK USA
| | - Juan Li
- College of Agriculture Hunan Agricultural University Changsha Hunan China
| | - Benli Chai
- Center for Microbial Ecology Michigan State University East Lansing MI USA
| | - Ye Deng
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology University of Oklahoma Norman OK USA
- CAS Key Laboratory of Environmental Biotechnology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
| | - Kai Feng
- CAS Key Laboratory of Environmental Biotechnology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Liyou Wu
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology University of Oklahoma Norman OK USA
| | - Shouwen Chen
- State Key Laboratory of Agricultural Microbiology Huazhong Agricultural University Wuhan China
- Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources College of Life Sciences Hubei University Wuhan China
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology University of Oklahoma Norman OK USA
- Earth Sciences Division Lawrence Berkeley National Laboratory Berkeley CA USA
- School of Environment Tsinghua University Beijing China
| | - Zhili He
- Environmental Microbiomics Research Center and Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology School of Environmental Science and Engineering Sun Yat‐sen University Guangzhou China
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology University of Oklahoma Norman OK USA
- State Key Laboratory of Agricultural Microbiology Huazhong Agricultural University Wuhan China
- College of Agriculture Hunan Agricultural University Changsha Hunan China
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243
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Wintsche B, Jehmlich N, Popp D, Harms H, Kleinsteuber S. Metabolic Adaptation of Methanogens in Anaerobic Digesters Upon Trace Element Limitation. Front Microbiol 2018; 9:405. [PMID: 29593674 PMCID: PMC5859356 DOI: 10.3389/fmicb.2018.00405] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/21/2018] [Indexed: 11/13/2022] Open
Abstract
Anaerobic digestion (AD) is a complex multi-stage process relying on the activity of highly diverse microbial communities including hydrolytic, acidogenic and syntrophic acetogenic bacteria as well as methanogenic archaea. The lower diversity of methanogenic archaea compared to the bacterial groups involved in AD and the corresponding lack of functional redundancy cause a stronger susceptibility of methanogenesis to unfavorable process conditions such as trace element (TE) deprivation, thus controlling the stability of the overall process. Here, we investigated the effects of a slowly increasing TE deficit on the methanogenic community function in a semi-continuous biogas process. The aim of the study was to understand how methanogens in digester communities cope with TE limitation and sustain their growth and metabolic activity. Two lab-scale biogas reactors fed with distillers grains and supplemented with TEs were operated in parallel for 76 weeks before one of the reactors was subjected to TE deprivation, leading to a decline of cobalt and molybdenum concentrations from 0.9 to 0.2 mg/L, nickel concentrations from 2.9 to 0.8 mg/L, manganese concentrations from 38 to 18 mg/L, and tungsten concentrations from 1.4 to 0.2 mg/L. Amplicon sequencing of mcrA genes revealed Methanosarcina (72%) and Methanoculleus (23%) as the predominant methanogens in the undisturbed reactors. With increasing TE limitation, the relative abundance of Methanosarcina dropped to 67% and a slight decrease of acetoclastic methanogenic activity was observed in batch tests with 13C-methyl-labeled acetate, suggesting a shift toward syntrophic acetate oxidation coupled to hydrogenotrophic methanogenesis. Metaproteome analysis revealed abundance shifts of the enzymes involved in methanogenic pathways. Proteins involved in methylotrophic and acetoclastic methanogenesis decreased in abundance while formylmethanofuran dehydrogenase from Methanosarcinaceae increased, confirming our hypothesis of a shift from acetoclastic to hydrogenotrophic methanogenesis by Methanosarcina. Both Methanosarcina and Methanoculleus increased the abundance of N5-methyltetrahydromethanopterin-coenzyme M methyltransferase and methyl-coenzyme M reductase. However, these efforts to preserve the ion motive force for energy conservation were seemingly more successful in Methanoculleus. We conclude that both methanogenic genera use different strategies to stabilize their energy balance under TE limitation. Methanosarcina switched from TE expensive pathways (methylotrophic and acetoclastic methanogenesis) to hydrogenotrophic methanogenesis. Methanoculleus showed a higher robustness and was favored over the more fastidious Methanosarcina, thus stabilizing reactor performance under TE limitation.
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Affiliation(s)
- Babett Wintsche
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-Helmholtz-Zentrum für Umweltforschung (UFZ), Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-Helmholtz-Zentrum für Umweltforschung (UFZ), Leipzig, Germany
| | - Denny Popp
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-Helmholtz-Zentrum für Umweltforschung (UFZ), Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-Helmholtz-Zentrum für Umweltforschung (UFZ), Leipzig, Germany
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-Helmholtz-Zentrum für Umweltforschung (UFZ), Leipzig, Germany
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244
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Dang C, Liu W, Lin Y, Zheng M, Jiang H, Chen Q, Ni J. Dominant role of ammonia-oxidizing bacteria in nitrification due to ammonia accumulation in sediments of Danjiangkou reservoir, China. Appl Microbiol Biotechnol 2018; 102:3399-3410. [PMID: 29497800 DOI: 10.1007/s00253-018-8865-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/31/2018] [Accepted: 02/12/2018] [Indexed: 11/29/2022]
Abstract
Surface sediments are the inner source of contaminations in aquatic systems and usually maintain aerobic conditions. As the key participators of nitrification process, little is known about the activities and contributions of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the surface sediments. In this study, we determined the net and potential nitrification rates and used 1-octyne as an AOB specific inhibitor to detect the contributions of AOA and AOB to nitrification in surface sediments of Danjiangkou reservoir, which is the water source area of the middle route of South-to-North Water Diversion Project in China. Quantitative PCR and Illumina high-throughput sequencing were used to evaluate the abundance and diversity of the amoA gene. The net and potential nitrification rates ranged from 0.42 to 1.93 and 2.06 to 8.79 mg N kg-1 dry sediments d-1, respectively. AOB dominated in both net and potential nitrification, whose contribution accounted for 52.7-78.6% and 59.9-88.1%, respectively. The cell-specific ammonia oxidation rate calculation also revealed the cell-specific rates of AOB were higher than that of AOA. The Spearman's rank correlation analysis suggested that ammonia accumulation led to the AOB predominant role in net nitrification activity, and AOB abundance played the key role in potential nitrification activity. Furthermore, phylogenetic analysis suggested AOB were predominantly characterized by the Nitrosospira cluster, while AOA by the Nitrososphaera and Nitrososphaera sister clusters. This study will help us to better understand the contributions and characteristics of AOA and AOB in aquatic sediments and provide improved strategies for nitrogen control in large reservoirs.
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Affiliation(s)
- Chenyuan Dang
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, 100871, People's Republic of China
| | - Wen Liu
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, 100871, People's Republic of China.,School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Yaxuan Lin
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, 100871, People's Republic of China
| | - Maosheng Zheng
- MOE Key Laboratory of Regional Energy Systems Optimization, Sino-Canada Resources and Environmental Research Academy, North China Electric Power University, Beijing, 102206, People's Republic of China
| | - Huan Jiang
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, 100871, People's Republic of China
| | - Qian Chen
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, 100871, People's Republic of China
| | - Jinren Ni
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Peking University, Beijing, 100871, People's Republic of China.
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Dunivin TK, Shade A. Community structure explains antibiotic resistance gene dynamics over a temperature gradient in soil. FEMS Microbiol Ecol 2018; 94:4834000. [PMID: 29401285 PMCID: PMC6018995 DOI: 10.1093/femsec/fiy016] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/30/2018] [Indexed: 12/16/2022] Open
Abstract
Soils are reservoirs of antibiotic resistance genes (ARGs), but environmental dynamics of ARGs are largely unknown. Long-term disturbances offer opportunities to examine microbiome responses at scales relevant for both ecological and evolutionary processes and can be insightful for studying ARGs. We examined ARGs in soils overlying the underground coal seam fire in Centralia, PA, which has been burning since 1962. As the fire progresses, previously hot soils can recover to ambient temperatures, which creates a gradient of fire impact. We examined metagenomes from surface soils along this gradient to examine ARGs using a gene-targeted assembler. We targeted 35 clinically relevant ARGs and two horizontal gene transfer-related genes (intI and repA). We detected 17 ARGs in Centralia: AAC6-Ia, adeB, bla_A, bla_B, bla_C, cmlA, dfra12, intI, sul2, tetA, tetW, tetX, tolC, vanA, vanH, vanX and vanZ. The diversity and abundance of bla_A, bla_B, dfra12 and tolC decreased with soil temperature, and changes in ARGs were largely explained by changes in community structure. We observed sequence-specific biogeography along the temperature gradient and observed compositional shifts in bla_A, dfra12 and intI. These results suggest that increased temperatures can reduce soil ARGs but that this is largely due to a concomitant reduction in community-level diversity.
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Affiliation(s)
- T K Dunivin
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
- Environmental and Integrative Toxicological Sciences Doctoral Program, Michigan State University, East Lansing, MI 48824, USA
| | - A Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
- Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI 48824, USA
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
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246
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Curson ARJ, Williams BT, Pinchbeck BJ, Sims LP, Martínez AB, Rivera PPL, Kumaresan D, Mercadé E, Spurgin LG, Carrión O, Moxon S, Cattolico RA, Kuzhiumparambil U, Guagliardo P, Clode PL, Raina JB, Todd JD. DSYB catalyses the key step of dimethylsulfoniopropionate biosynthesis in many phytoplankton. Nat Microbiol 2018; 3:430-439. [PMID: 29483657 DOI: 10.1038/s41564-018-0119-5] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 01/29/2018] [Indexed: 01/08/2023]
Abstract
Dimethylsulfoniopropionate (DMSP) is a globally important organosulfur molecule and the major precursor for dimethyl sulfide. These compounds are important info-chemicals, key nutrients for marine microorganisms, and are involved in global sulfur cycling, atmospheric chemistry and cloud formation1-3. DMSP production was thought to be confined to eukaryotes, but heterotrophic bacteria can also produce DMSP through the pathway used by most phytoplankton 4 , and the DsyB enzyme catalysing the key step of this pathway in bacteria was recently identified 5 . However, eukaryotic phytoplankton probably produce most of Earth's DMSP, yet no DMSP biosynthesis genes have been identified in any such organisms. Here we identify functional dsyB homologues, termed DSYB, in many phytoplankton and corals. DSYB is a methylthiohydroxybutryate methyltransferase enzyme localized in the chloroplasts and mitochondria of the haptophyte Prymnesium parvum, and stable isotope tracking experiments support these organelles as sites of DMSP synthesis. DSYB transcription levels increased with DMSP concentrations in different phytoplankton and were indicative of intracellular DMSP. Identification of the eukaryotic DSYB sequences, along with bacterial dsyB, provides the first molecular tools to predict the relative contributions of eukaryotes and prokaryotes to global DMSP production. Furthermore, evolutionary analysis suggests that eukaryotic DSYB originated in bacteria and was passed to eukaryotes early in their evolution.
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Affiliation(s)
- Andrew R J Curson
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Beth T Williams
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | | | - Leanne P Sims
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | | | | | - Deepak Kumaresan
- School of Biological Sciences and Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - Elena Mercadé
- Laboratory of Microbiology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Ornella Carrión
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Simon Moxon
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | | | | | - Paul Guagliardo
- The Centre for Microscopy Characterisation and Analysis, University of Western Australia, Crawley, Australia
| | - Peta L Clode
- The Centre for Microscopy Characterisation and Analysis, University of Western Australia, Crawley, Australia.,Oceans Institute, University of Western Australia, Crawley, Australia
| | - Jean-Baptiste Raina
- Climate Change Cluster (C3), Faculty of Science, University of Technology, Sydney, New South Wales, Australia
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich, UK.
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247
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Yang S, Winkel M, Wagner D, Liebner S. Community structure of rare methanogenic archaea: insight from a single functional group. FEMS Microbiol Ecol 2018; 93:4331631. [PMID: 29029047 PMCID: PMC5812523 DOI: 10.1093/femsec/fix126] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/29/2017] [Indexed: 11/24/2022] Open
Abstract
The rare biosphere, the low abundant microbial populations, is suggested to be a conserved way of microbial life. Here we conducted a molecular survey of rare methanogenic archaea in the environment targeting the mcrA gene in order to test if general concepts associated with the structure of the rare bacterial biosphere also apply to single functional groups. Similar to what is known about rare bacterial communities, the contribution of rare methanogens to the alpha diversity is much larger than to Bray-Curtis measures. Moreover, a similar core group of methanogens harbored by the abundant and rare communities suggests similar sources and environmental controls of both groups. Among the communities of different levels of rarity, the conditionally rare methanogenic taxa largely account for the overall community dynamics of the rare biosphere and likely enter the dominant community under favorable environmental conditions. In addition, we observed a positive correlation between the alpha diversity and the production of methane when the rare taxa were taken into account. This supports the concept that increasing microbial biodiversity enhances ecological function. The composition and environmental associations of the rare methanogenic biosphere allow us to conclude that rarity is a conserved way also for single functional groups.
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Affiliation(s)
- Sizhong Yang
- GFZ German Research Center for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473 Potsdam, Germany.,State Key Laboratory of Frozen Soil Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, 730000 Lanzhou, China
| | - Matthias Winkel
- GFZ German Research Center for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473 Potsdam, Germany
| | - Dirk Wagner
- GFZ German Research Center for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473 Potsdam, Germany
| | - Susanne Liebner
- GFZ German Research Center for Geosciences, Helmholtz Centre Potsdam, Section 5.3 Geomicrobiology, 14473 Potsdam, Germany
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248
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Cardenas E, Orellana LH, Konstantinidis KT, Mohn WW. Effects of timber harvesting on the genetic potential for carbon and nitrogen cycling in five North American forest ecozones. Sci Rep 2018; 8:3142. [PMID: 29453368 PMCID: PMC5816661 DOI: 10.1038/s41598-018-21197-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 01/31/2018] [Indexed: 01/23/2023] Open
Abstract
Forest ecosystems are critical to global biogeochemical cycles but under pressure from harvesting and climate change. We investigated the effects of organic matter (OM) removal during forest harvesting on the genetic potential of soil communities for biomass decomposition and nitrogen cycling in five ecozones across North America. We analyzed 107 samples, representing four treatments with varied levels of OM removal, at Long-Term Soil Productivity Study sites. Samples were collected more than ten years after harvesting and replanting and were analyzed via shotgun metagenomics. High-quality short reads totaling 1.2 Tbp were compared to the Carbohydrate Active Enzyme (CAZy) database and a custom database of nitrogen cycle genes. Gene profile variation was mostly explained by ecozone and soil layer. Eleven CAZy and nine nitrogen cycle gene families were associated with particular soil layers across all ecozones. Treatment effects on gene profiles were mainly due to harvesting, and only rarely to the extent of OM removal. Harvesting generally decreased the relative abundance of CAZy genes while increasing that of nitrogen cycle genes, although these effects varied among ecozones. Our results suggest that ecozone-specific nutrient availability modulates the sensitivity of the carbon and nitrogen cycles to harvesting with possible consequences for long-term forest sustainability.
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Affiliation(s)
- Erick Cardenas
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Luis H Orellana
- Georgia Institute of Technology, School of Civil and Environmental Engineering, Atlanta, GA, 30332, USA
| | | | - William W Mohn
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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249
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Gaby JC, Rishishwar L, Valderrama-Aguirre LC, Green SJ, Valderrama-Aguirre A, Jordan IK, Kostka JE. Diazotroph Community Characterization via a High-Throughput nifH Amplicon Sequencing and Analysis Pipeline. Appl Environ Microbiol 2018; 84:e01512-17. [PMID: 29180374 PMCID: PMC5795091 DOI: 10.1128/aem.01512-17] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/21/2017] [Indexed: 11/20/2022] Open
Abstract
The dinitrogenase reductase gene (nifH) is the most widely established molecular marker for the study of nitrogen-fixing prokaryotes in nature. A large number of PCR primer sets have been developed for nifH amplification, and the effective deployment of these approaches should be guided by a rapid, easy-to-use analysis protocol. Bioinformatic analysis of marker gene sequences also requires considerable expertise. In this study, we advance the state of the art for nifH analysis by evaluating nifH primer set performance, developing an improved amplicon sequencing workflow, and implementing a user-friendly bioinformatics pipeline. The developed amplicon sequencing workflow is a three-stage PCR-based approach that uses established technologies for incorporating sample-specific barcode sequences and sequencing adapters. Based on our primer evaluation, we recommend the Ando primer set be used with a modified annealing temperature of 58°C, as this approach captured the largest diversity of nifH templates, including paralog cluster IV/V sequences. To improve nifH sequence analysis, we developed a computational pipeline which infers taxonomy and optionally filters out paralog sequences. In addition, we employed an empirical model to derive optimal operational taxonomic unit (OTU) cutoffs for the nifH gene at the species, genus, and family levels. A comprehensive workflow script named TaxADivA (TAXonomy Assignment and DIVersity Assessment) is provided to ease processing and analysis of nifH amplicons. Our approach is then validated through characterization of diazotroph communities across environmental gradients in beach sands impacted by the Deepwater Horizon oil spill in the Gulf of Mexico, in a peat moss-dominated wetland, and in various plant compartments of a sugarcane field.IMPORTANCE Nitrogen availability often limits ecosystem productivity, and nitrogen fixation, exclusive to prokaryotes, comprises a major source of nitrogen input that sustains food webs. The nifH gene, which codes for the iron protein of the nitrogenase enzyme, is the most widely established molecular marker for the study of nitrogen-fixing microorganisms (diazotrophs) in nature. In this study, a flexible sequencing/analysis pipeline, named TaxADivA, was developed for nifH amplicons produced by Illumina paired-end sequencing, and it enables an inference of taxonomy, performs clustering, and produces output in formats that may be used by programs that facilitate data exploration and analysis. Diazotroph diversity and community composition are linked to ecosystem functioning, and our results advance the phylogenetic characterization of diazotroph communities by providing empirically derived nifH similarity cutoffs for species, genus, and family levels. The utility of our pipeline is validated for diazotroph communities in a variety of ecosystems, including contaminated beach sands, peatland ecosystems, living plant tissues, and rhizosphere soil.
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Affiliation(s)
- John Christian Gaby
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Lavanya Rishishwar
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
- Applied Bioinformatics Laboratory, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Lina C Valderrama-Aguirre
- Laboratory of Microorganismal Production (Bioinoculums), Department of Field Research in Sugarcane, Incauca S.A.S, Cali, Valle del Cauca, Colombia
- School of Natural Resources and Environmental Engineering, PhD Program in Sanitary and Environmental Engineering, Universidad del Valle, Cali, Valle del Cauca, Colombia
| | - Stefan J Green
- DNA Services Facility, Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Augusto Valderrama-Aguirre
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
- Biomedical Research Institute, Universidad Libre, Cali, Valle del Cauca, Colombia
- Regenerar, Center of Excellence for Regenerative and Personalized Medicine, Valle del Cauca, Colombia
| | - I King Jordan
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
- Applied Bioinformatics Laboratory, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
| | - Joel E Kostka
- School of Biology, The Georgia Institute of Technology, Atlanta, Georgia, USA
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
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250
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Conthe M, Wittorf L, Kuenen JG, Kleerebezem R, van Loosdrecht MCM, Hallin S. Life on N 2O: deciphering the ecophysiology of N 2O respiring bacterial communities in a continuous culture. ISME JOURNAL 2018; 12:1142-1153. [PMID: 29416125 PMCID: PMC5864245 DOI: 10.1038/s41396-018-0063-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 12/19/2017] [Accepted: 12/29/2017] [Indexed: 01/04/2023]
Abstract
Reduction of the greenhouse gas N2O to N2 is a trait among denitrifying and non-denitrifying microorganisms having an N2O reductase, encoded by nosZ. The nosZ phylogeny has two major clades, I and II, and physiological differences among organisms within the clades may affect N2O emissions from ecosystems. To increase our understanding of the ecophysiology of N2O reducers, we determined the thermodynamic growth efficiency of N2O reduction and the selection of N2O reducers under N2O- or acetate-limiting conditions in a continuous culture enriched from a natural community with N2O as electron acceptor and acetate as electron donor. The biomass yields were higher during N2O limitation, irrespective of dilution rate and community composition. The former was corroborated in a continuous culture of Pseudomonas stutzeri and was potentially due to cytotoxic effects of surplus N2O. Denitrifiers were favored over non-denitrifying N2O reducers under all conditions and Proteobacteria harboring clade I nosZ dominated. The abundance of nosZ clade II increased when allowing for lower growth rates, but bacteria with nosZ clade I had a higher affinity for N2O, as defined by μmax/Ks. Thus, the specific growth rate is likely a key factor determining the composition of communities living on N2O respiration under growth-limited conditions.
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Affiliation(s)
- Monica Conthe
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Lea Wittorf
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - J Gijs Kuenen
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Robbert Kleerebezem
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | | | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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