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Mara P, Zhou YL, Teske A, Morono Y, Beaudoin D, Edgcomb V. Microbial gene expression in Guaymas Basin subsurface sediments responds to hydrothermal stress and energy limitation. THE ISME JOURNAL 2023; 17:1907-1919. [PMID: 37658181 PMCID: PMC10579382 DOI: 10.1038/s41396-023-01492-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 09/03/2023]
Abstract
Analyses of gene expression of subsurface bacteria and archaea provide insights into their physiological adaptations to in situ subsurface conditions. We examined patterns of expressed genes in hydrothermally heated subseafloor sediments with distinct geochemical and thermal regimes in Guaymas Basin, Gulf of California, Mexico. RNA recovery and cell counts declined with sediment depth, however, we obtained metatranscriptomes from eight sites at depths spanning between 0.8 and 101.9 m below seafloor. We describe the metabolic potential of sediment microorganisms, and discuss expressed genes involved in tRNA, mRNA, and rRNA modifications that enable physiological flexibility of bacteria and archaea in the hydrothermal subsurface. Microbial taxa in hydrothermally influenced settings like Guaymas Basin may particularly depend on these catalytic RNA functions since they modulate the activity of cells under elevated temperatures and steep geochemical gradients. Expressed genes for DNA repair, protein maintenance and circadian rhythm were also identified. The concerted interaction of many of these genes may be crucial for microorganisms to survive and to thrive in the Guaymas Basin subsurface biosphere.
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Affiliation(s)
- Paraskevi Mara
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Ying-Li Zhou
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Andreas Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Yuki Morono
- Kochi Institute for Core Sample Research, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Monobe, Nankoku, Kochi, Japan
| | - David Beaudoin
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Virginia Edgcomb
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
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2
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Kong H, Yang EJ, Jiao N, Lee Y, Jung J, Cho KH, Moon JK, Kim JH, Xu D. RNA outperforms DNA-based metabarcoding in assessing the diversity and response of microeukaryotes to environmental variables in the Arctic Ocean. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 876:162608. [PMID: 36871742 DOI: 10.1016/j.scitotenv.2023.162608] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
The Arctic Ocean (AO) has a harsh environment characterized by low temperatures, extensive ice coverage, and periodic freezing and melting of sea ice, which has provided diverse habitats for microorganisms. Prior studies primarily focused on microeukaryote communities in the upper water or sea ice based on environmental DNA, leaving the composition of active microeukaryotes in the diverse AO environments largely unknown. This study provided a vertical assessment of microeukaryote communities in the AO from snow and ice to sea water at a depth of 1670 m using high-throughput sequencing of co-extracted DNA and RNA. RNA extracts depicted microeukaryote community structure and intergroup correlations more accurately and responded more sensitively to environmental conditions than those derived from DNA. Using RNA:DNA ratios as a proxy for relative activity of major taxonomic groups, the metabolic activities of major microeukaryote groups were determined along depth. Analysis of co-occurrence networks showed that parasitism between Syndiniales and dinoflagellates/ciliates in the deep ocean may be significant. This study increased our knowledge of the diversity of active microeukaryote communities and highlighted the importance of using RNA-based sequencing over DNA-based sequencing to examine the relationship between microeukaryote assemblages and the responses of microeukaryotes to environmental variables in the AO.
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Affiliation(s)
- Hejun Kong
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Eun-Jin Yang
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Youngju Lee
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Jinyoung Jung
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Kyoung-Ho Cho
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Jong-Kuk Moon
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Jee-Hoon Kim
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China; Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China.
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3
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Yu X, Gao X, Shang L, Wang X, Jiao Y, Zhang XH, Shi X. Spatial and temporal change determined co-occurrence networks stability and community assembly processes of epipelagic seawater microbial community in the Nordic Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160321. [PMID: 36414066 DOI: 10.1016/j.scitotenv.2022.160321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/27/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
The Nordic Sea has a vital impact on the global climate change, occupies a significant status in the physical oceanography research, on account of its intersection of complex ocean currents. To explore the influence of seasonal and spatial heterogeneity in its epipelagic seawater on the microbial community structure, a total of 54 seawater samples from 18 stations and 3 water layers (0 m, 50 m, 100 m) were collected in the summer of 2017 and the autumn of 2018 from the Norwegian Sea, the Greenland Sea and the vicinity of Jan Mayen Island in the Nordic Sea. Alpha- and Beta- diversity analysis showed that significant differences were found between characteristic bacterial groups in detached or mixed currents of corresponding seasons, as endemic OTUs with seasonal and ocean current characteristics which revealed the existence of spatiotemporal patterns of microbial communities in the Nordic Sea. Moreover, co-occurrence networks were conducted to show different degree of complexity and stability of microbial community response to spatiotemporal dynamic changes. Furthermore, the flow and collision between ocean currents do have an impact on the community assembly processes by affecting the migration and dispersal of microbial communities. This study reflects the response of microbial communities to the spatiotemporal dynamics and reveals the microbial community assembly mechanisms under complex hydrological condition represented in the Nordic Sea.
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Affiliation(s)
- Xiaowen Yu
- College of Marine Life Science, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, PR China; Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, PR China
| | - Xueyu Gao
- College of Marine Life Science, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, PR China; Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, PR China
| | - Li Shang
- College of Marine Life Science, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, PR China; Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, PR China
| | - Xiaoyu Wang
- Frontier Science Center for Deep Ocean Multispheres and Earth System (FDOMES), Physical Oceanography Laboratory, Ocean University of China, Qingdao 266071, PR China
| | - Yutian Jiao
- Frontier Science Center for Deep Ocean Multispheres and Earth System (FDOMES), Physical Oceanography Laboratory, Ocean University of China, Qingdao 266071, PR China
| | - Xiao-Hua Zhang
- College of Marine Life Science, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, PR China; Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, PR China
| | - Xiaochong Shi
- College of Marine Life Science, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, PR China; Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, PR China.
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Hempel CA, Wright N, Harvie J, Hleap JS, Adamowicz S, Steinke D. Metagenomics versus total RNA sequencing: most accurate data-processing tools, microbial identification accuracy and perspectives for ecological assessments. Nucleic Acids Res 2022; 50:9279-9293. [PMID: 35979944 PMCID: PMC9458450 DOI: 10.1093/nar/gkac689] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/05/2022] [Accepted: 07/29/2022] [Indexed: 12/24/2022] Open
Abstract
Metagenomics and total RNA sequencing (total RNA-Seq) have the potential to improve the taxonomic identification of diverse microbial communities, which could allow for the incorporation of microbes into routine ecological assessments. However, these target-PCR-free techniques require more testing and optimization. In this study, we processed metagenomics and total RNA-Seq data from a commercially available microbial mock community using 672 data-processing workflows, identified the most accurate data-processing tools, and compared their microbial identification accuracy at equal and increasing sequencing depths. The accuracy of data-processing tools substantially varied among replicates. Total RNA-Seq was more accurate than metagenomics at equal sequencing depths and even at sequencing depths almost one order of magnitude lower than those of metagenomics. We show that while data-processing tools require further exploration, total RNA-Seq might be a favorable alternative to metagenomics for target-PCR-free taxonomic identifications of microbial communities and might enable a substantial reduction in sequencing costs while maintaining accuracy. This could be particularly an advantage for routine ecological assessments, which require cost-effective yet accurate methods, and might allow for the incorporation of microbes into ecological assessments.
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Affiliation(s)
- Christopher A Hempel
- To whom correspondence should be addressed. Tel: +1 519 824 4120; Fax: +1 519 824 5703;
| | - Natalie Wright
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Julia Harvie
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Jose S Hleap
- SHARCNET, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Sarah J Adamowicz
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Dirk Steinke
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada,Centre for Biodiversity Genomics, University of Guelph, Guelph, ON N1G 2W1, Canada
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5
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Grattepanche JD, Jeffrey WH, Gast RJ, Sanders RW. Diversity of Microbial Eukaryotes Along the West Antarctic Peninsula in Austral Spring. Front Microbiol 2022; 13:844856. [PMID: 35651490 PMCID: PMC9149413 DOI: 10.3389/fmicb.2022.844856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
During a cruise from October to November 2019, along the West Antarctic Peninsula, between 64.32 and 68.37°S, we assessed the diversity and composition of the active microbial eukaryotic community within three size fractions: micro- (> 20 μm), nano- (20-5 μm), and pico-size fractions (5-0.2 μm). The communities and the environmental parameters displayed latitudinal gradients, and we observed a strong similarity in the microbial eukaryotic communities as well as the environmental parameters between the sub-surface and the deep chlorophyll maximum (DCM) depths. Chlorophyll concentrations were low, and the mixed layer was shallow for most of the 17 stations sampled. The richness of the microplankton was higher in Marguerite Bay (our southernmost stations), compared to more northern stations, while the diversity for the nano- and pico-plankton was relatively stable across latitude. The microplankton communities were dominated by autotrophs, mostly diatoms, while mixotrophs (phototrophs-consuming bacteria and kleptoplastidic ciliates, mostly alveolates, and cryptophytes) were the most abundant and active members of the nano- and picoplankton communities. While phototrophy was the dominant trophic mode, heterotrophy (mixotrophy, phagotrophy, and parasitism) tended to increase southward. The samples from Marguerite Bay showed a distinct community with a high diversity of nanoplankton predators, including spirotrich ciliates, and dinoflagellates, while cryptophytes were observed elsewhere. Some lineages were significantly related-either positively or negatively-to ice coverage (e.g., positive for Pelagophyceae, negative for Spirotrichea) and temperature (e.g., positive for Cryptophyceae, negative for Spirotrichea). This suggests that climate changes will have a strong impact on the microbial eukaryotic community.
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Affiliation(s)
| | - Wade H. Jeffrey
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, Pensacola, FL, United States
| | - Rebecca J. Gast
- Department of Biology, Woods Hole Oceanographic Institution, Pensacola, MA, United States
| | - Robert W. Sanders
- Department of Biology, Temple University, Philadelphia, PA, United States
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6
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Leng H, Zhao W, Xiao X. Cultivation and metabolic insights of an uncultured clade, Bacteroidetes VC2.1 Bac22 (Candidatus Sulfidibacteriales ord. nov.), from deep-sea hydrothermal vents. Environ Microbiol 2022; 24:2484-2501. [PMID: 35165999 DOI: 10.1111/1462-2920.15931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 01/05/2022] [Accepted: 01/31/2022] [Indexed: 01/28/2023]
Abstract
Bacteroidetes VC2.1 Bac22 (referred to as VC2.1) is an uncultured clade that is widely distributed in marine ecosystems, including hydrothermal vents, oxygen-minimum zones and other anoxic, sulfide-rich environments. However, the lack of cultured representatives and sequenced genomes of VC2.1 limit our understanding of its physiology, metabolism and ecological functions. Here, we obtained a stable co-culture of VC2.1 with autotrophic microbes by establishing an autotrophy-based enrichment from a hydrothermal vent chimney sample. We recovered a high-quality metagenome-assembled genome (MAG) that belonged to VC2.1. Phylogenetic analyses of both 16S rRNA genes and conserved protein markers suggested that VC2.1 belongs to a novel order in the Bacteroidetes phylum, which we named Candidatus Sulfidibacteriales. The metabolic reconstruction of this MAG indicated that VC2.1 could utilize polysaccharides, protein polymers and fatty acids as well as flexibly obtain energy via NO/N2 O reduction and polysulfide reduction. Our results reveal the ecological potential of this novel Bacteroidetes for complex organic carbons mineralization and N2 O sinks in deep-sea hydrothermal vents. Furthermore, guided by the genome information, we designed a new culture medium in which starch, ammonium and polysulfide were used as the carbon source, nitrogen source and electron acceptor respectively, to isolate VC2.1 successfully.
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Affiliation(s)
- Hao Leng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, China
| | - Weishu Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
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7
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A Comprehensive Profile of Antibiotic Resistance Genes in the Water Column of a Shallow-Sea Hydrothermal Vent Ecosystem. SUSTAINABILITY 2022. [DOI: 10.3390/su14031776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Antibiotic resistance genes (ARGs) became an emerging contaminant, and were found to accumulate in natural and man-made environments. A comprehensive understanding of the diversity and abundance of ARGs in pristine environments is critical for defining the baseline levels of environmental ARGs. However, there is limited information available on the ARG profiles of pristine environments, especially for shallow-sea hydrothermal vents ecosystems. Here, we combined 16S rRNA gene full-length amplicon sequencing and high-throughput quantitative PCR (HT-qPCR) to study the bacterial communities, and ARG abundance and diversity in the shallow-sea hydrothermal vent ecosystem of the Kueishantao Islet. The results of the 16S rRNA gene amplicon sequencing showed that several sulfur-cycling related bacterial genera, including Thiomicrorhabdus, Thioreductor, Sulfurovum, Sulfurimonas and Lebetimonas, dominated in the water column of the shallow-sea system. Temperature was the significant factor shaping the bacterial communities. The results of HT-qPCR analysis showed that the Kueishantao shallow-sea system harbored the lowest diversity (average 10 ARG subtypes) and abundance (average 1.0 × 10−3 copy per bacterial cell) of ARGs compared with other pristine (i.e., Tibet lake sediments, marine water and sediments) and anthropogenic-disturbed (i.e., drinking water reservoirs, urban ponds and wastewater treatment plants) environments. Procrustes analysis demonstrated a concordant pattern between the compositions of bacterial communities and ARGs in the shallow-sea system, while variation partition analysis revealed that the shared effects of physicochemical and bacterial communities explained >80% of the variation in the composition of ARGs. These results suggest that the vent bacterial communities and local environmental factors played an important role in shaping the distribution of the ARG profiles. Our study provides the first comprehensive overview of the background level of ARGs in a shallow-sea hydrothermal vent ecosystem.
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Barreto MM, Ziegler M, Venn A, Tambutté E, Zoccola D, Tambutté S, Allemand D, Antony CP, Voolstra CR, Aranda M. Effects of Ocean Acidification on Resident and Active Microbial Communities of Stylophora pistillata. Front Microbiol 2021; 12:707674. [PMID: 34899619 PMCID: PMC8656159 DOI: 10.3389/fmicb.2021.707674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/28/2021] [Indexed: 12/12/2022] Open
Abstract
Ocean warming and ocean acidification (OA) are direct consequences of climate change and affect coral reefs worldwide. While the effect of ocean warming manifests itself in increased frequency and severity of coral bleaching, the effects of ocean acidification on corals are less clear. In particular, long-term effects of OA on the bacterial communities associated with corals are largely unknown. In this study, we investigated the effects of ocean acidification on the resident and active microbiome of long-term aquaria-maintained Stylophora pistillata colonies by assessing 16S rRNA gene diversity on the DNA (resident community) and RNA level (active community). Coral colony fragments of S. pistillata were kept in aquaria for 2 years at four different pCO2 levels ranging from current pH conditions to increased acidification scenarios (i.e., pH 7.2, 7.4, 7.8, and 8). We identified 154 bacterial families encompassing 2,047 taxa (OTUs) in the resident and 89 bacterial families including 1,659 OTUs in the active communities. Resident communities were dominated by members of Alteromonadaceae, Flavobacteriaceae, and Colwelliaceae, while active communities were dominated by families Cyclobacteriacea and Amoebophilaceae. Besides the overall differences between resident and active community composition, significant differences were seen between the control (pH 8) and the two lower pH treatments (7.2 and 7.4) in the active community, but only between pH 8 and 7.2 in the resident community. Our analyses revealed profound differences between the resident and active microbial communities, and we found that OA exerted stronger effects on the active community. Further, our results suggest that rDNA- and rRNA-based sequencing should be considered complementary tools to investigate the effects of environmental change on microbial assemblage structure and activity.
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Affiliation(s)
- Marcelle Muniz Barreto
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Maren Ziegler
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany
| | | | | | | | | | | | - Chakkiath Paul Antony
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Manuel Aranda
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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9
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Exploring the Diversity of Active Ureolytic Bacteria in the Rumen by Comparison of cDNA and gDNA. Animals (Basel) 2020; 10:ani10112162. [PMID: 33233592 PMCID: PMC7699693 DOI: 10.3390/ani10112162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/10/2020] [Accepted: 11/15/2020] [Indexed: 11/29/2022] Open
Abstract
Simple Summary Ureolytic bacteria produce urease that hydrolyzes dietary or recycled urea to ammonia, which can then be converted into microbial proteins. The diversity of ruminal ureolytic bacteria benefits N utilization efficiency in ruminants. However, there is no information at the complementary DNA (cDNA) level to reflect the active status of ureolytic bacteria. To reveal the diversity of active ureolytic bacteria in the rumen, we compared ureC amplicons between genomic DNA (gDNA) and cDNA. These results revealed distinct ureolytic bacterial community profiles based on gDNA and cDNA. The dominant ureolytic bacterial had high transcriptional activity, and the differential were mainly distributed in the genus of low abundance. Abstract In this study we revealed the diversity of active ureolytic bacteria in the rumen by compared ureC amplicons between gDNA and cDNA. Rumen fluid was collected from four Holstein dairy cows with rumen fistulas at 0, 2, and 6 h after morning feeding. Total microbial gDNA and RNA were isolated, and the RNA was reverse-transcribed into cDNA. The ureC gene amplicons of gDNA and cDNA were produced and sequenced by MiSeq. These results revealed that the sampling time had no significant difference on the alphssa and beta diversity indices of the ureolytic bacteria. The Shannon diversity of the ureC gene for cDNA was greater than that for gDNA (p < 0.05). There were significant difference in the beta diversity of ureolytic bacteria between gDNA and cDNA (p < 0.01), which indicates a shift in the community of active ureolytic bacteria. Approximately 67% of ureC sequences from cDNA could not be confidently classified at the genus level. The active ureolytic bacteria were mainly from Helicobacter, Herbaspirillum, Clostridium, Paenibacillus, Synechococcus, and Sphingobacterium sp. Changes in the operational taxonomic units revealed that the top abundant ureC genes were mostly consistent between gDNA and cDNA, and most differences occurred in the ureC genes with lower abundances. These results revealed distinct ureolytic bacteria community profiles based on gDNA and cDNA. The dominant ureolytic bacteria had high transcriptional activity, and the differential were mainly distributed in the genus of low abundance.
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10
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Seasonal Dynamics of the Activated Sludge Microbiome in Sequencing Batch Reactors, Assessed Using 16S rRNA Transcript Amplicon Sequencing. Appl Environ Microbiol 2020; 86:AEM.00597-20. [PMID: 32709723 DOI: 10.1128/aem.00597-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/17/2020] [Indexed: 12/29/2022] Open
Abstract
Activated sludge is comprised of diverse microorganisms which remediate wastewater. Previous research has characterized activated sludge using 16S rRNA gene amplicon sequencing, which can help to address questions on the relative abundance of microorganisms. In this study, we used 16S rRNA transcript sequencing in order to characterize "active" populations (via protein synthesis potential) and gain a deeper understanding of microbial activity patterns within activated sludge. Seasonal abundances of individual populations in activated sludge change over time, yet a persistent group of core microorganisms remains throughout the year which are traditionally classified on presence or absence without monitoring of their activity or growth. The goal of this study was to further our understanding of how the activated sludge microbiome changes between seasons with respect to population abundance, activity, and growth. Triplicate sequencing batch reactors were sampled at 10-min intervals throughout reaction cycles during all four seasons. We quantified the gene and transcript copy numbers of 16S rRNA amplicons using real-time PCR and sequenced the products to reveal community abundance and activity changes. We identified 108 operational taxonomic units (OTUs) with stable abundance, activity, and growth throughout the year. Nonproliferating OTUs were commonly human health related, while OTUs that showed seasonal abundance changes have previously been identified as being associated with floc formation and bulking. We observed significant differences in 16S rRNA transcript copy numbers, particularly at lower temperatures in winter and spring. The study provides an analysis of the seasonal dynamics of microbial activity variations in activated sludge based on quantifying and sequencing 16S rRNA transcripts.IMPORTANCE Sequencing batch reactors are a common design for wastewater treatment plants, particularly in smaller municipalities, due to their low footprint and ease of operations. However, like for most treatment plants in temperate/continental climates, the microbial community involved in water treatment is highly seasonal and its biological processes can be sensitive to cold temperatures. The seasonality of these microbial communities has been explored primarily in conventional treatment plants and not in sequencing batch reactors. Furthermore, most studies often only address which organisms are present. However, the activated sludge microbial community is very diverse, and it is often hard to discern which organisms are active and which organisms are simply present. In this study, we applied additional sequencing techniques to also address the issues of which organisms are active and which organisms are growing. By addressing these issues, we gained new insights into seasonal microbial populations dynamics and activity patterns affecting wastewater treatment.
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11
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Xue Y, Lanzén A, Jonassen I. Reconstructing ribosomal genes from large scale total RNA meta-transcriptomic data. Bioinformatics 2020; 36:3365-3371. [PMID: 32167532 PMCID: PMC7267836 DOI: 10.1093/bioinformatics/btaa177] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 02/01/2020] [Accepted: 03/10/2020] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Technological advances in meta-transcriptomics have enabled a deeper understanding of the structure and function of microbial communities. 'Total RNA' meta-transcriptomics, sequencing of total reverse transcribed RNA, provides a unique opportunity to investigate both the structure and function of active microbial communities from all three domains of life simultaneously. A major step of this approach is the reconstruction of full-length taxonomic marker genes such as the small subunit ribosomal RNA. However, current tools for this purpose are mainly targeted towards analysis of amplicon and metagenomic data and thus lack the ability to handle the massive and complex datasets typically resulting from total RNA experiments. RESULTS In this work, we introduce MetaRib, a new tool for reconstructing ribosomal gene sequences from total RNA meta-transcriptomic data. MetaRib is based on the popular rRNA assembly program EMIRGE, together with several improvements. We address the challenge posed by large complex datasets by integrating sub-assembly, dereplication and mapping in an iterative approach, with additional post-processing steps. We applied the method to both simulated and real-world datasets. Our results show that MetaRib can deal with larger datasets and recover more rRNA genes, which achieve around 60 times speedup and higher F1 score compared to EMIRGE in simulated datasets. In the real-world dataset, it shows similar trends but recovers more contigs compared with a previous analysis based on random sub-sampling, while enabling the comparison of individual contig abundances across samples for the first time. AVAILABILITY AND IMPLEMENTATION The source code of MetaRib is freely available at https://github.com/yxxue/MetaRib. CONTACT yaxin.xue@uib.no or Inge.Jonassen@uib.no. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yaxin Xue
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Anders Lanzén
- AZTI-Tecnalia, Herrera Kaia, 20110 Pasaia, Spain.,Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain
| | - Inge Jonassen
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
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12
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Bioinoculants play a significant role in shaping the rhizospheric microbial community: a field study with Cajanus cajan. World J Microbiol Biotechnol 2020; 36:44. [PMID: 32130544 DOI: 10.1007/s11274-020-02818-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 02/22/2020] [Indexed: 12/11/2022]
Abstract
The present study is an attempt to understand the impact of bioinoculants, Azotobacter chroococcum (A), Bacillus megaterium (B), Pseudomonas fluorescens (P), on (a) soil and plant nutrient status, (b) total resident and active bacterial communities, and (c) genes and transcripts involved in nitrogen cycle, during cultivation of Cajanus cajan. In terms of available macro- and micro-nutrients, triple inoculation of the bioinoculants (ABP) competed well with chemical fertilizer (CF). Their 'non-target' effects were assessed in terms of the abundance and activity of the resident bacterial community by employing denaturing gradient gel electrophoresis (DGGE). The resident bacterial community (16S rRNA gene) was stable, while the active fraction (16S rRNA transcripts) was influenced (in terms of abundance) by the treatments. Quantification of the genes and transcripts involved in N cycle by qPCR revealed an increase in the transcripts of nifH in the soil treated with ABP over CF, with an enhancement of 3.36- and 1.57- fold at flowering and maturity stages of plant growth, respectively. The bioinoculants shaped the resident microflora towards a more beneficial community, which helped in increasing soil N turnover and hence, soil fertility as a whole.
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Jang J, Anderson EL, Venterea RT, Sadowsky MJ, Rosen CJ, Feyereisen GW, Ishii S. Denitrifying Bacteria Active in Woodchip Bioreactors at Low-Temperature Conditions. Front Microbiol 2019; 10:635. [PMID: 31001220 PMCID: PMC6454037 DOI: 10.3389/fmicb.2019.00635] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/13/2019] [Indexed: 11/13/2022] Open
Abstract
Woodchip bioreactor technology removes nitrate from agricultural subsurface drainage by using denitrifying microorganisms. Although woodchip bioreactors have demonstrated success in many field locations, low water temperature can significantly limit bioreactor efficiency and performance. To improve bioreactor performance, it is important to identify the microbes responsible for nitrate removal at low temperature conditions. Therefore, in this study, we identified and characterized denitrifiers active at low-temperature conditions by using culture-independent and -dependent approaches. By comparative 16S rRNA (gene) analysis and culture isolation technique, Pseudomonas spp., Polaromonas spp., and Cellulomonas spp. were identified as being important bacteria responsible for denitrification in woodchip bioreactor microcosms at relatively low temperature conditions (15°C). Genome analysis of Cellulomonas sp. strain WB94 confirmed the presence of nitrite reductase gene nirK. Transcription levels of this nirK were significantly higher in the denitrifying microcosms than in the non-denitrifying microcosms. Strain WB94 was also capable of degrading cellulose and other complex polysaccharides. Taken together, our results suggest that Cellulomonas sp. denitrifiers could degrade woodchips to provide carbon source and electron donors to themselves and other denitrifiers in woodchip bioreactors at low-temperature conditions. By inoculating these denitrifiers (i.e., bioaugmentation), it might be possible to increase the nitrate removal rate of woodchip bioreactors at low-temperature conditions.
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Affiliation(s)
- Jeonghwan Jang
- The BioTechnology Institute, University of Minnesota, Saint Paul, MN, United States
| | - Emily L. Anderson
- Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, MN, United States
| | - Rodney T. Venterea
- Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, MN, United States
- Soil and Water Management Research Unit, Agricultural Research Service, United States Department of Agriculture, Saint Paul, MN, United States
| | - Michael J. Sadowsky
- The BioTechnology Institute, University of Minnesota, Saint Paul, MN, United States
- Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, MN, United States
| | - Carl J. Rosen
- Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, MN, United States
| | - Gary W. Feyereisen
- Soil and Water Management Research Unit, Agricultural Research Service, United States Department of Agriculture, Saint Paul, MN, United States
| | - Satoshi Ishii
- The BioTechnology Institute, University of Minnesota, Saint Paul, MN, United States
- Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, MN, United States
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Guevara Campoverde NC, Hassenrück C, Buttigieg PL, Gärdes A. Characterization of bacterioplankton communities and quantification of organic carbon pools off the Galapagos Archipelago under contrasting environmental conditions. PeerJ 2018; 6:e5984. [PMID: 30533298 PMCID: PMC6282939 DOI: 10.7717/peerj.5984] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 10/22/2018] [Indexed: 12/14/2022] Open
Abstract
Bacteria play a crucial role in the marine carbon cycle, contributing to the production and degradation of organic carbon. Here, we investigated organic carbon pools, aggregate formation, and bacterioplankton communities in three contrasting oceanographic settings in the Galapagos Archipelago. We studied a submarine CO2 vent at Roca Redonda (RoR), an upwelling site at Bolivar Channel (BoC) subjected to a weak El Niño event at the time of sampling in October 2014, as well as a site without volcanic or upwelling influence at Cowley Islet (CoI). We recorded physico-chemical parameters, and quantified particulate and dissolved organic carbon, transparent exopolymeric particles, and the potential of the water to form larger marine aggregates. Free-living and particle-attached bacterial communities were assessed via 16S rRNA gene sequencing. Both RoR and BoC exhibited temperatures elevated by 1–1.5 °C compared to CoI. RoR further experienced reduced pH between 6.8 and 7.4. We observed pronounced differences in organic carbon pools at each of the three sites, with highest dissolved organic carbon concentrations at BoC and RoR, and highest particulate organic carbon concentrations and aggregate formation at BoC. Bacterioplankton communities at BoC were dominated by opportunistic copiotrophic taxa, such as Alteromonas and Roseobacter, known to thrive in phytoplankton blooms, as opposed to oligotrophic taxa dominating at CoI, such as members of the SAR11 clade. Therefore, we propose that bacterial communities were mainly influenced by the availability of organic carbon at the investigated sites. Our study provides a comprehensive characterization of organic carbon pools and bacterioplankton communities, highlighting the high heterogeneity of various components of the marine carbon cycle around the Galapagos Archipelago.
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Affiliation(s)
- Nataly Carolina Guevara Campoverde
- Galapagos Science Center, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador.,Tropical Marine Microbiology, Department of Biogeochemistry and Geology, Leibniz-Centre for Tropical Marine Reseach, Bremen, Germany
| | - Christiane Hassenrück
- Tropical Marine Microbiology, Department of Biogeochemistry and Geology, Leibniz-Centre for Tropical Marine Reseach, Bremen, Germany
| | - Pier Luigi Buttigieg
- HGF-MPG Group for Deep Sea Ecology and Technology, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Astrid Gärdes
- Tropical Marine Microbiology, Department of Biogeochemistry and Geology, Leibniz-Centre for Tropical Marine Reseach, Bremen, Germany
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15
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Cerqueira T, Barroso C, Froufe H, Egas C, Bettencourt R. Metagenomic Signatures of Microbial Communities in Deep-Sea Hydrothermal Sediments of Azores Vent Fields. MICROBIAL ECOLOGY 2018; 76:387-403. [PMID: 29354879 DOI: 10.1007/s00248-018-1144-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/02/2018] [Indexed: 05/25/2023]
Abstract
The organisms inhabiting the deep-seafloor are known to play a crucial role in global biogeochemical cycles. Chemolithoautotrophic prokaryotes, which produce biomass from single carbon molecules, constitute the primary source of nutrition for the higher organisms, being critical for the sustainability of food webs and overall life in the deep-sea hydrothermal ecosystems. The present study investigates the metabolic profiles of chemolithoautotrophs inhabiting the sediments of Menez Gwen and Rainbow deep-sea vent fields, in the Mid-Atlantic Ridge. Differences in the microbial community structure might be reflecting the distinct depth, geology, and distance from vent of the studied sediments. A metagenomic sequencing approach was conducted to characterize the microbiome of the deep-sea hydrothermal sediments and the relevant metabolic pathways used by microbes. Both Menez Gwen and Rainbow metagenomes contained a significant number of genes involved in carbon fixation, revealing the largely autotrophic communities thriving in both sites. Carbon fixation at Menez Gwen site was predicted to occur mainly via the reductive tricarboxylic acid cycle, likely reflecting the dominance of sulfur-oxidizing Epsilonproteobacteria at this site, while different autotrophic pathways were identified at Rainbow site, in particular the Calvin-Benson-Bassham cycle. Chemolithotrophy appeared to be primarily driven by the oxidation of reduced sulfur compounds, whether through the SOX-dependent pathway at Menez Gwen site or through reverse sulfate reduction at Rainbow site. Other energy-yielding processes, such as methane, nitrite, or ammonia oxidation, were also detected but presumably contributing less to chemolithoautotrophy. This work furthers our knowledge of the microbial ecology of deep-sea hydrothermal sediments and represents an important repository of novel genes with potential biotechnological interest.
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Affiliation(s)
- Teresa Cerqueira
- Department of Oceanography and Fisheries, University of the Azores, Rua Prof. Dr. Frederico Machado, 9901-862, Horta, Portugal.
- MARE - Marine and Environmental Sciences Centre, 9901-862, Horta, Portugal.
- OKEANOS Research Unit, Faculty of Science and Technology, University of the Azores, 9901-862, Horta, Portugal.
| | - Cristina Barroso
- Next Generation Sequencing Unit - UC-Biotech, Center for Neuroscience and Cell Biology, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal
- Biocant, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal
| | - Hugo Froufe
- Biocant, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal
| | - Conceição Egas
- Next Generation Sequencing Unit - UC-Biotech, Center for Neuroscience and Cell Biology, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal
- Biocant, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal
| | - Raul Bettencourt
- MARE - Marine and Environmental Sciences Centre, 9901-862, Horta, Portugal
- OKEANOS Research Unit, Faculty of Science and Technology, University of the Azores, 9901-862, Horta, Portugal
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Savvichev AS, Rusanov II, Kadnikov VV, Beletskii AV, Ravin NV, Pimenov NV. Microbial Community Composition and Rates of the Methane Cycle Microbial Processes in the Upper Sediments of the Yamal Sector of the Southwestern Kara Sea. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718020121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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17
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Yan YW, Jiang QY, Wang JG, Zhu T, Zou B, Qiu QF, Quan ZX. Microbial Communities and Diversities in Mudflat Sediments Analyzed Using a Modified Metatranscriptomic Method. Front Microbiol 2018; 9:93. [PMID: 29445367 PMCID: PMC5797801 DOI: 10.3389/fmicb.2018.00093] [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] [Received: 09/19/2017] [Accepted: 01/16/2018] [Indexed: 11/17/2022] Open
Abstract
Intertidal mudflats are land–sea interaction areas and play important roles in global nutrient cycles. However, a comprehensive understanding of microbial communities in these mudflats remains elusive. In this study, mudflat sediment samples from the Dongtan wetland of Chongming Island, the largest alluvial island in the world, were collected. Using a modified metatranscriptomic method, the depth-wise distributions of potentially active microbial communities were investigated based on small subunit ribosomal RNA (SSU rRNA) sequences. Multiple environmental factors were also measured and analyzed in conjunction with the prokaryotic composition profiles. A prokaryotic diversity analysis based on the metatranscriptome datasets revealed two or threefold higher diversity indices (associated with potentially active microbes participating in biogeochemical processes in Dongtan) compared with the diversity indices based on 16S rRNA gene amplicons. Bacteria were numerically dominant relative to archaea, and the potentially active prokaryotic taxa were mostly assigned to the bacterial phyla Chloroflexi, Acidobacteria, and Bacteroidetes and the classes Delta- and Gamma-proteobacteria, along with the archaeal lineages phylum Bathyarchaeota and the order Thermoplasmatales. The total nitrogen and carbon content of the sediment samples were environmental factors that significantly affected the depth-wise distributions of both bacterial and archaeal communities. Furthermore, the activity of potentially active taxa (including the prevalent order Desulfobacterales and family Anaerolineaceae) appeared to be significantly underestimated by PCR-based methods, notably at the DNA level, and indicates that using normal PCR amplification of DNA limits the study of potential microbial activity. This is the first study of potentially active microbial communities in depth-wise sediments from Dongtan. The improved knowledge of microbial communities in Dongtan provides a foundation for exploring biogeochemical cycling and microbial functions.
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Affiliation(s)
- Yong-Wei Yan
- Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Qiu-Yue Jiang
- Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Jian-Gong Wang
- Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Ting Zhu
- Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Bin Zou
- Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Qiong-Fen Qiu
- School of Marine Science, Ningbo University, Ningbo, China
| | - Zhe-Xue Quan
- Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
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18
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Li F, Neves ALA, Ghoshal B, Guan LL. Symposium review: Mining metagenomic and metatranscriptomic data for clues about microbial metabolic functions in ruminants. J Dairy Sci 2017; 101:5605-5618. [PMID: 29274958 DOI: 10.3168/jds.2017-13356] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/27/2017] [Indexed: 12/22/2022]
Abstract
Metagenomics and metatranscriptomics can capture the whole genome and transcriptome repertoire of microorganisms through sequencing total DNA/RNA from various environmental samples, providing both taxonomic and functional information with high resolution. The unique and complex rumen microbial ecosystem is receiving great research attention because the rumen microbiota coevolves with the host and equips ruminants with the ability to convert cellulosic plant materials to high-protein products for human consumption. To date, hundreds to thousands of microbial phylotypes have been identified in the rumen using culture-independent molecular-based approaches, and genomic information of rumen microorganisms is rapidly accumulating through the single genome sequencing. However, functional characteristics of the rumen microbiome have not been well described because there are numerous uncultivable microorganisms in the rumen. The advent of metagenomics and metatranscriptomics along with advanced bioinformatics methods can help us better understand mechanisms of the rumen fermentation, which is vital for improving nutrient utilization and animal productivity. Therefore, in this review, we summarize a general workflow to conduct rumen metagenomics and metatranscriptomics and discuss how the data can be interpreted to be useful information. Moreover, we review recent literatures studying associations between the rumen microbiome and host phenotypes (e.g., feed efficiency and methane emissions) using these approaches, aiming to provide a useful guide to include studying the rumen microbiome as one of the research objectives using these 2 approaches.
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Affiliation(s)
- Fuyong Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5
| | - Andre L A Neves
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5
| | - Bibaswan Ghoshal
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5.
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19
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Muto H, Takaki Y, Hirai M, Mino S, Sawayama S, Takai K, Nakagawa S. A Simple and Efficient RNA Extraction Method from Deep-Sea Hydrothermal Vent Chimney Structures. Microbes Environ 2017; 32:330-335. [PMID: 29187693 PMCID: PMC5745017 DOI: 10.1264/jsme2.me17048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
RNA-based microbiological analyses, e.g., transcriptome and reverse transcription-quantitative PCR, require a relatively large amount of high quality RNA. RNA-based analyses on microbial communities in deep-sea hydrothermal environments often encounter methodological difficulties with RNA extraction due to the presence of unique minerals in and the low biomass of samples. In the present study, we assessed RNA extraction methods for deep-sea vent chimneys that had complex mineral compositions. Mineral-RNA adsorption experiments were conducted using mock chimney minerals and Escherichia coli total RNA solution, and showed that detectable RNA significantly decreased possibly due to adsorption onto minerals. This decrease in RNA was prevented by the addition of sodium tripolyphosphate (STPP), deoxynucleotide triphosphates (dNTPs), salmon sperm DNA, and NaOH. The addition of STPP was also effective for RNA extraction from the mixture of E. coli cells and mock chimney minerals when TRIzol reagent and the RNeasy column were used, but not when the RNeasy PowerSoil total RNA kit was used. A combination of STPP, TRIzol reagent, the RNeasy column, and sonication resulted in the highest RNA yield from a natural chimney. This indirect extraction procedure is simple, rapid, inexpensive, and may be used for large-scale RNA extraction.
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Affiliation(s)
- Hisashi Muto
- Laboratory of Marine Environmental Microbiology, Graduate School of Agriculture, Kyoto University
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Miho Hirai
- Research and Development (R&D) Center for Marine Biosciences, Marine Functional Biology Group (MFbio), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University
| | - Shigeki Sawayama
- Laboratory of Marine Environmental Microbiology, Graduate School of Agriculture, Kyoto University
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Graduate School of Agriculture, Kyoto University.,Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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20
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Elekwachi CO, Wang Z, Wu X, Rabee A, Forster RJ. Total rRNA-Seq Analysis Gives Insight into Bacterial, Fungal, Protozoal and Archaeal Communities in the Rumen Using an Optimized RNA Isolation Method. Front Microbiol 2017; 8:1814. [PMID: 28983291 PMCID: PMC5613150 DOI: 10.3389/fmicb.2017.01814] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 09/05/2017] [Indexed: 12/14/2022] Open
Abstract
Advances in high throughput, next generation sequencing technologies have allowed an in-depth examination of biological environments and phenomena, and are particularly useful for culture-independent microbial community studies. Recently the use of RNA for metatranscriptomic studies has been used to elucidate the role of active microbes in the environment. Extraction of RNA of appropriate quality is critical in these experiments and TRIzol reagent is often used for maintaining stability of RNA molecules during extraction. However, for studies using rumen content there is no consensus on (1) the amount of rumen digesta to use or (2) the amount of TRIzol reagent to be used in RNA extraction procedures. This study evaluated the effect of using various quantities of ground rumen digesta and of TRIzol reagent on the yield and quality of extracted RNA. It also investigated the possibility of using lower masses of solid-phase rumen digesta and lower amounts of TRIzol reagent than is used currently, for extraction of RNA for metatranscriptomic studies. We found that high quality RNA could be isolated from 2 g of ground rumen digesta sample, whilst using 0.6 g of ground matter for RNA extraction and using 3 mL (a 5:1 TRIzol : extraction mass ratio) of TRIzol reagent. This represents a significant savings in the cost of RNA isolation. These lower masses and volumes were then applied in the RNA-Seq analysis of solid-phase rumen samples obtained from 6 Angus X Hereford beef heifers which had been fed a high forage diet (comprised of barley straw in a forage-to-concentrate ratio of 70:30) for 102 days. A bioinformatics analysis pipeline was developed in-house that generated relative abundance values of archaea, protozoa, fungi and bacteria in the rumen and also allowed the extraction of individual rRNA variable regions that could be analyzed in downstream molecular ecology programs. The average relative abundances of rRNA transcripts of archaea, bacteria, protozoa and fungi in our samples were 1.4 ± 0.06, 44.16 ± 1.55, 35.38 ± 1.64, and 16.37 ± 0.65% respectively. This represents the first study to define the relative active contributions of these populations to the rumen ecosystem and is especially important in defining the role of the anaerobic fungi and protozoa.
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Affiliation(s)
- Chijioke O Elekwachi
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, LethbridgeAB, Canada
| | - Zuo Wang
- University of Chinese Academy of SciencesBeijing, China.,Key Laboratory for Agro-ecological Processes in Subtropical Region, Hunan Research Center of Livestock and Poultry Sciences, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangsha, China
| | - Xiaofeng Wu
- Institute of Animal Nutrition, Sichuan Agricultural UniversityYa'an, China
| | - Alaa Rabee
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, LethbridgeAB, Canada
| | - Robert J Forster
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, LethbridgeAB, Canada
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21
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Hugerth LW, Andersson AF. Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing. Front Microbiol 2017; 8:1561. [PMID: 28928718 PMCID: PMC5591341 DOI: 10.3389/fmicb.2017.01561] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 08/02/2017] [Indexed: 12/20/2022] Open
Abstract
Microbial ecology as a scientific field is fundamentally driven by technological advance. The past decade's revolution in DNA sequencing cost and throughput has made it possible for most research groups to map microbial community composition in environments of interest. However, the computational and statistical methodology required to analyse this kind of data is often not part of the biologist training. In this review, we give a historical perspective on the use of sequencing data in microbial ecology and restate the current need for this method; but also highlight the major caveats with standard practices for handling these data, from sample collection and library preparation to statistical analysis. Further, we outline the main new analytical tools that have been developed in the past few years to bypass these caveats, as well as highlight the major requirements of common statistical practices and the extent to which they are applicable to microbial data. Besides delving into the meaning of select alpha- and beta-diversity measures, we give special consideration to techniques for finding the main drivers of community dissimilarity and for interaction network construction. While every project design has specific needs, this review should serve as a starting point for considering what options are available.
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Affiliation(s)
- Luisa W Hugerth
- Department of Molecular, Tumour and Cell Biology, Centre for Translational Microbiome Research, Karolinska InstitutetSolna, Sweden.,Division of Gene Technology, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of TechnologySolna, Sweden
| | - Anders F Andersson
- Division of Gene Technology, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of TechnologySolna, Sweden
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22
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Phylogenetic and Functional Diversity of Total (DNA) and Expressed (RNA) Bacterial Communities in Urban Green Infrastructure Bioswale Soils. Appl Environ Microbiol 2017; 83:AEM.00287-17. [PMID: 28576763 DOI: 10.1128/aem.00287-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/26/2017] [Indexed: 01/08/2023] Open
Abstract
New York City (NYC) is pioneering green infrastructure with the use of bioswales and other engineered soil-based habitats to provide stormwater infiltration and other ecosystem functions. In addition to avoiding the environmental and financial costs of expanding traditional built infrastructure, green infrastructure is thought to generate cobenefits in the form of diverse ecological processes performed by its plant and microbial communities. Yet, although plant communities in these habitats are closely managed, we lack basic knowledge about how engineered ecosystems impact the distribution and functioning of soil bacteria. We sequenced amplicons of the 16S ribosomal subunit, as well as seven genes associated with functional pathways, generated from both total (DNA-based) and expressed (RNA) soil communities in the Bronx, NYC, NY, in order to test whether bioswale soils host characteristic bacterial communities with evidence for enriched microbial functioning, compared to nonengineered soils in park lawns and tree pits. Bioswales had distinct, phylogenetically diverse bacterial communities, including taxa associated with nutrient cycling and metabolism of hydrocarbons and other pollutants. Bioswale soils also had a significantly greater diversity of genes involved in several functional pathways, including carbon fixation (cbbL-R [cbbL gene, red-like subunit] and apsA), nitrogen cycling (noxZ and amoA), and contaminant degradation (bphA); conversely, no functional genes were significantly more abundant in nonengineered soils. These results provide preliminary evidence that urban land management can shape the diversity and activity of soil communities, with positive consequences for genetic resources underlying valuable ecological functions, including biogeochemical cycling and degradation of common urban pollutants.IMPORTANCE Management of urban soil biodiversity by favoring taxa associated with decontamination or other microbial metabolic processes is a powerful prospect, but it first requires an understanding of how engineered soil habitats shape patterns of microbial diversity. This research adds to our understanding of urban microbial biogeography by providing data on soil bacteria in bioswales, which had relatively diverse and compositionally distinct communities compared to park and tree pit soils. Bioswales also contained comparatively diverse pools of genes related to carbon sequestration, nitrogen cycling, and contaminant degradation, suggesting that engineered soils may serve as effective reservoirs of functional microbial biodiversity. We also examined both total (DNA-based) and expressed (RNA) communities, revealing that total bacterial communities (the exclusive targets in the vast majority of soil studies) were poor predictors of expressed community diversity, pointing to the value of quantifying RNA, especially when ecological functioning is considered.
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Xu D, Li R, Hu C, Sun P, Jiao N, Warren A. Microbial Eukaryote Diversity and Activity in the Water Column of the South China Sea Based on DNA and RNA High Throughput Sequencing. Front Microbiol 2017; 8:1121. [PMID: 28659910 PMCID: PMC5469884 DOI: 10.3389/fmicb.2017.01121] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 06/01/2017] [Indexed: 12/20/2022] Open
Abstract
To study the diversity and metabolic activity of microbial eukaryotes in the water column of the South China Sea, genomic DNA and RNA were co-extracted from samples collected down to bathyal depth at two sites. V9 regions of both SSU rRNA gene and its transcript (cDNA) were amplified and sequenced using high throughput sequencing. Our study revealed: (1) DNA and RNA datasets showed significant differences in microbial eukaryote community composition, with the variability between the two datasets for the same sample exceeding that between samples within each dataset, indicating that nucleic acid source overrode environmental factors in determining the composition of microeukaryotes; (2) despite the differences in community composition between the two datasets, both DNA and RNA revealed similar depth-related distribution patterns of microbial eukaryotes; (3) using the ratio of RNA: DNA as a proxy of relative metabolic activity, a depth-related pattern was found for the relative metabolic activity of some but not all groups of microbial eukaryotes, with the highest activity for the groups with depth-related pattern usually found in the middle water layers; and (4) the presence of live and active photoautotrophic microbial eukaryotes in the deep ocean was confirmed, indicating that they play an important role in controlling the deep-sea organic carbon pool. Overall, our study sheds light on the diversity and activity of microbial eukaryotes in the water column of a tropical oligotrophic ocean and their potential contributions in the downward transportation of organic material from the surface ocean to the deep via the biological pump.
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Affiliation(s)
- Dapeng Xu
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen UniversityXiamen, China
| | - Ran Li
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen UniversityXiamen, China
| | - Chen Hu
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen UniversityXiamen, China
| | - Ping Sun
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen UniversityXiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen UniversityXiamen, China
| | - Alan Warren
- Department of Life Sciences, Natural History MuseumLondon, United Kingdom
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Li XX, Liu JF, Zhou L, Mbadinga SM, Yang SZ, Gu JD, Mu BZ. Diversity and Composition of Sulfate-Reducing Microbial Communities Based on Genomic DNA and RNA Transcription in Production Water of High Temperature and Corrosive Oil Reservoir. Front Microbiol 2017. [PMID: 28638372 PMCID: PMC5461352 DOI: 10.3389/fmicb.2017.01011] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Deep subsurface petroleum reservoir ecosystems harbor a high diversity of microorganisms, and microbial influenced corrosion is a major problem for the petroleum industry. Here, we used high-throughput sequencing to explore the microbial communities based on genomic 16S rDNA and metabolically active 16S rRNA analyses of production water samples with different extents of corrosion from a high-temperature oil reservoir. Results showed that Desulfotignum and Roseovarius were the most abundant genera in both genomic and active bacterial communities of all the samples. Both genomic and active archaeal communities were mainly composed of Archaeoglobus and Methanolobus. Within both bacteria and archaea, the active and genomic communities were compositionally distinct from one another across the different oil wells (bacteria p = 0.002; archaea p = 0.01). In addition, the sulfate-reducing microorganisms (SRMs) were specifically assessed by Sanger sequencing of functional genes aprA and dsrA encoding the enzymes adenosine-5'-phosphosulfate reductase and dissimilatory sulfite reductase, respectively. Functional gene analysis indicated that potentially active Archaeoglobus, Desulfotignum, Desulfovibrio, and Thermodesulforhabdus were frequently detected, with Archaeoglobus as the most abundant and active sulfate-reducing group. Canonical correspondence analysis revealed that the SRM communities in petroleum reservoir system were closely related to pH of the production water and sulfate concentration. This study highlights the importance of distinguishing the metabolically active microorganisms from the genomic community and extends our knowledge on the active SRM communities in corrosive petroleum reservoirs.
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Affiliation(s)
- Xiao-Xiao Li
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and TechnologyShanghai, China
| | - Jin-Feng Liu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and TechnologyShanghai, China
| | - Lei Zhou
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and TechnologyShanghai, China
| | - Serge M Mbadinga
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and TechnologyShanghai, China.,Shanghai Collaborative Innovation Center for Biomanufacturing TechnologyShanghai, China
| | - Shi-Zhong Yang
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and TechnologyShanghai, China
| | - Ji-Dong Gu
- School of Biological Sciences, The University of Hong KongHong Kong, Hong Kong
| | - Bo-Zhong Mu
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and TechnologyShanghai, China.,Shanghai Collaborative Innovation Center for Biomanufacturing TechnologyShanghai, China
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25
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Matcher GF, Waterworth SC, Walmsley TA, Matsatsa T, Parker‐Nance S, Davies‐Coleman MT, Dorrington RA. Keeping it in the family: Coevolution of latrunculid sponges and their dominant bacterial symbionts. Microbiologyopen 2017; 6:e00417. [PMID: 27781403 PMCID: PMC5387304 DOI: 10.1002/mbo3.417] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/06/2016] [Accepted: 09/14/2016] [Indexed: 01/13/2023] Open
Abstract
The Latrunculiidae are a family of cold water sponges known for their production of bioactive pyrroloiminoquinone alkaloids. Previously it was shown that the bacterial community associated with a Tsitsikamma sponge species comprises unusual bacterial taxa and is dominated by a novel Betaproteobacterium. Here, we have characterized the bacterial communities associated with six latrunculid species representing three genera (Tsitsikamma, Cyclacanthia, and Latrunculia) as well as a Mycale species, collected from Algoa Bay on the South African southeast coast. The bacterial communities of all seven sponge species were dominated by a single Betaproteobacterium operational taxonomic unit (OTU0.03 ), while a second OTU0.03 was dominant in the Mycale sp. The Betaproteobacteria OTUs from the different latrunculid sponges are closely related and their phylogenetic relationship follows that of their hosts. We propose that the latrunculid Betaproteobacteria OTUs are members of a specialized group of sponge symbionts that may have coevolved with their hosts. A single dominant Spirochaetae OTU0.03 was present in the Tsitsikamma and Cyclacanthia sponge species, but absent from the Latrunculia and Mycale sponges. This study sheds new light on the interactions between latrunculid sponges and their bacterial communities and may point to the potential involvement of dominant symbionts in the biosynthesis of the bioactive secondary metabolites.
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Affiliation(s)
- Gwynneth F. Matcher
- Department of Biochemistry and MicrobiologyRhodes UniversityGrahamstownSouth Africa
| | | | - Tara A. Walmsley
- Department of Biochemistry and MicrobiologyRhodes UniversityGrahamstownSouth Africa
- Department of BiotechnologyVaal University of TechnologyVanderbijlparkSouth Africa
| | - Tendayi Matsatsa
- Department of Biochemistry and MicrobiologyRhodes UniversityGrahamstownSouth Africa
| | - Shirley Parker‐Nance
- Department of Biochemistry and MicrobiologyRhodes UniversityGrahamstownSouth Africa
| | - Michael T. Davies‐Coleman
- Department of ChemistryRhodes UniversityGrahamstownSouth Africa
- Faculty of Natural ScienceUniversity of the Western CapeCape TownSouth Africa
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26
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Novel Primer Sets for Next Generation Sequencing-Based Analyses of Water Quality. PLoS One 2017; 12:e0170008. [PMID: 28118368 PMCID: PMC5261608 DOI: 10.1371/journal.pone.0170008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 12/26/2016] [Indexed: 02/01/2023] Open
Abstract
Next generation sequencing (NGS) has rapidly become an invaluable tool for the detection, identification and relative quantification of environmental microorganisms. Here, we demonstrate two new 16S rDNA primer sets, which are compatible with NGS approaches and are primarily for use in water quality studies. Compared to 16S rRNA gene based universal primers, in silico and experimental analyses demonstrated that the new primers showed increased specificity for the Cyanobacteria and Proteobacteria phyla, allowing increased sensitivity for the detection, identification and relative quantification of toxic bloom-forming microalgae, microbial water quality bioindicators and common pathogens. Significantly, Cyanobacterial and Proteobacterial sequences accounted for ca. 95% of all sequences obtained within NGS runs (when compared to ca. 50% with standard universal NGS primers), providing higher sensitivity and greater phylogenetic resolution of key water quality microbial groups. The increased selectivity of the new primers allow the parallel sequencing of more samples through reduced sequence retrieval levels required to detect target groups, potentially reducing NGS costs by 50% but still guaranteeing optimal coverage and species discrimination.
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27
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Hestetun JT, Dahle H, Jørgensen SL, Olsen BR, Rapp HT. The Microbiome and Occurrence of Methanotrophy in Carnivorous Sponges. Front Microbiol 2016; 7:1781. [PMID: 27881974 PMCID: PMC5101230 DOI: 10.3389/fmicb.2016.01781] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 10/24/2016] [Indexed: 12/03/2022] Open
Abstract
As shown by recent studies, filter-feeding sponges are known to host a wide variety of microorganisms. However, the microbial community of the non-filtering carnivorous sponges (Porifera, Cladorhizidae) has been the subject of less scrutiny. Here, we present the results from a comparative study of the methanotrophic carnivorous sponge Cladorhiza methanophila from a mud volcano-rich area at the Barbados Accretionary Prism, and five carnivorous species from the Jan Mayen Vent Field (JMVF) at the Arctic Mid-Ocean Ridge. Results from 16S rRNA microbiome data indicate the presence of a diverse assemblage of associated microorganisms in carnivorous sponges mainly from the Gamma- and Alphaproteobacteria, Flavobacteriaceae, and Thaumarchaeota. While the abundance of particular groups varied throughout the dataset, we found interesting similarities to previous microbiome results from non-carnivorous deep sea sponges, suggesting that the carnivorous sponges share characteristics of a previously hypothesized putative deep-sea sponge microbial community. Chemolithoautotrophic symbiosis was confirmed for C. methanophila through a microbial community with a high abundance of Methylococcales and very light isotopic δ13C and δ15N ratios (-60 to -66‰/3.5 to 5.2‰) compared to the other cladorhizid species (-22 to -24‰/8.5 to 10.5‰). We provide evidence for the presence of putative sulfur-oxidizing Gammaproteobacteria in the arctic cladorhizids; however, δ13C and δ15N signatures did not provide evidence for significant chemoautotrophic symbiosis in this case, and the slightly higher abundance of cladorhizids at the JMVF site compared to the nearby deep sea likely stem from an increased abundance of prey rather than a more direct vent association. The phylogenetic position of C. methanophila in relation to other carnivorous sponges was established using a three-gene phylogenetic analysis, and it was found to be closely related to other non-methanotrophic Cladorhiza species with a similar morphology included in the dataset, suggesting a recent origin for methanotrophy in this species. C. methanophila remains the only known carnivorous sponge with a strong, chemolithoautotrophic symbiont association, and methanotrophic symbiosis does not seem to be a widespread property within the Cladorhizidae.
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Affiliation(s)
- Jon T. Hestetun
- Marine Biodiversity Group, Department of Biology, University of BergenBergen, Norway
- Centre for Geobiology, University of BergenBergen, Norway
| | - Håkon Dahle
- Centre for Geobiology, University of BergenBergen, Norway
| | | | - Bernt R. Olsen
- Marine Biodiversity Group, Department of Biology, University of BergenBergen, Norway
- Centre for Geobiology, University of BergenBergen, Norway
| | - Hans T. Rapp
- Marine Biodiversity Group, Department of Biology, University of BergenBergen, Norway
- Centre for Geobiology, University of BergenBergen, Norway
- Uni Research Environment, Uni Research ASBergen, Norway
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28
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Ivanova AA, Wegner CE, Kim Y, Liesack W, Dedysh SN. Identification of microbial populations driving biopolymer degradation in acidic peatlands by metatranscriptomic analysis. Mol Ecol 2016; 25:4818-35. [DOI: 10.1111/mec.13806] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 06/12/2016] [Accepted: 08/11/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Anastasia A. Ivanova
- Winogradsky Institute of Microbiology; Research Center of Biotechnology of the Russian Academy of Sciences; 33, bld. 2 Leninsky Ave. Moscow 119071 Russia
| | - Carl-Eric Wegner
- Max Planck Institute for Terrestrial Microbiology; D-35043 Marburg Germany
| | - Yongkyu Kim
- Max Planck Institute for Terrestrial Microbiology; D-35043 Marburg Germany
| | - Werner Liesack
- Max Planck Institute for Terrestrial Microbiology; D-35043 Marburg Germany
| | - Svetlana N. Dedysh
- Winogradsky Institute of Microbiology; Research Center of Biotechnology of the Russian Academy of Sciences; 33, bld. 2 Leninsky Ave. Moscow 119071 Russia
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29
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Miranda PJ, McLain NK, Hatzenpichler R, Orphan VJ, Dillon JG. Characterization of Chemosynthetic Microbial Mats Associated with Intertidal Hydrothermal Sulfur Vents in White Point, San Pedro, CA, USA. Front Microbiol 2016; 7:1163. [PMID: 27512390 PMCID: PMC4961709 DOI: 10.3389/fmicb.2016.01163] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 07/12/2016] [Indexed: 11/13/2022] Open
Abstract
The shallow-sea hydrothermal vents at White Point (WP) in Palos Verdes on the southern California coast support microbial mats and provide easily accessed settings in which to study chemolithoautotrophic sulfur cycling. Previous studies have cultured sulfur-oxidizing bacteria from the WP mats; however, almost nothing is known about the in situ diversity and activity of the microorganisms in these habitats. We studied the diversity, micron-scale spatial associations and metabolic activity of the mat community via sequence analysis of 16S rRNA and aprA genes, fluorescence in situ hybridization (FISH) microscopy and sulfate reduction rate (SRR) measurements. Sequence analysis revealed a diverse group of bacteria, dominated by sulfur cycling gamma-, epsilon-, and deltaproteobacterial lineages such as Marithrix, Sulfurovum, and Desulfuromusa. FISH microscopy suggests a close physical association between sulfur-oxidizing and sulfur-reducing genotypes, while radiotracer studies showed low, but detectable, SRR. Comparative 16S rRNA gene sequence analyses indicate the WP sulfur vent microbial mat community is similar, but distinct from other hydrothermal vent communities representing a range of biotopes and lithologic settings. These findings suggest a complete biological sulfur cycle is operating in the WP mat ecosystem mediated by diverse bacterial lineages, with some similarity with deep-sea hydrothermal vent communities.
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Affiliation(s)
- Priscilla J. Miranda
- Department of Geological Sciences, California State University, Long Beach, Long BeachCA, USA
| | - Nathan K. McLain
- Department of Biological Sciences, California State University, Long Beach, Long BeachCA, USA
| | - Roland Hatzenpichler
- Division of Geological and Planetary Sciences, California Institute of Technology, PasadenaCA, USA
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, PasadenaCA, USA
| | - Jesse G. Dillon
- Department of Biological Sciences, California State University, Long Beach, Long BeachCA, USA
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30
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Li F, Henderson G, Sun X, Cox F, Janssen PH, Guan LL. Taxonomic Assessment of Rumen Microbiota Using Total RNA and Targeted Amplicon Sequencing Approaches. Front Microbiol 2016; 7:987. [PMID: 27446027 PMCID: PMC4916217 DOI: 10.3389/fmicb.2016.00987] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 06/08/2016] [Indexed: 12/20/2022] Open
Abstract
Taxonomic characterization of active gastrointestinal microbiota is essential to detect shifts in microbial communities and functions under various conditions. This study aimed to identify and quantify potentially active rumen microbiota using total RNA sequencing and to compare the outcomes of this approach with the widely used targeted RNA/DNA amplicon sequencing technique. Total RNA isolated from rumen digesta samples from five beef steers was subjected to Illumina paired-end sequencing (RNA-seq), and bacterial and archaeal amplicons of partial 16S rRNA/rDNA were subjected to 454 pyrosequencing (RNA/DNA Amplicon-seq). Taxonomic assessments of the RNA-seq, RNA Amplicon-seq, and DNA Amplicon-seq datasets were performed using a pipeline developed in house. The detected major microbial phylotypes were common among the three datasets, with seven bacterial phyla, fifteen bacterial families, and five archaeal taxa commonly identified across all datasets. There were also unique microbial taxa detected in each dataset. Elusimicrobia and Verrucomicrobia phyla; Desulfovibrionaceae, Elusimicrobiaceae, and Sphaerochaetaceae families; and Methanobrevibacter woesei were only detected in the RNA-Seq and RNA Amplicon-seq datasets, whereas Streptococcaceae was only detected in the DNA Amplicon-seq dataset. In addition, the relative abundances of four bacterial phyla, eight bacterial families and one archaeal taxon were different among the three datasets. This is the first study to compare the outcomes of rumen microbiota profiling between RNA-seq and RNA/DNA Amplicon-seq datasets. Our results illustrate the differences between these methods in characterizing microbiota both qualitatively and quantitatively for the same sample, and so caution must be exercised when comparing data.
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Affiliation(s)
- Fuyong Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta Edmonton, AB, Canada
| | - Gemma Henderson
- AgResearch Ltd., Grasslands Research Centre Palmerston North, New Zealand
| | - Xu Sun
- Department of Agricultural, Food and Nutritional Science, University of Alberta Edmonton, AB, Canada
| | - Faith Cox
- AgResearch Ltd., Grasslands Research Centre Palmerston North, New Zealand
| | - Peter H Janssen
- AgResearch Ltd., Grasslands Research Centre Palmerston North, New Zealand
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta Edmonton, AB, Canada
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31
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McDonald JE, Larsen N, Pennington A, Connolly J, Wallis C, Rooks DJ, Hall N, McCarthy AJ, Allison HE. Characterising the Canine Oral Microbiome by Direct Sequencing of Reverse-Transcribed rRNA Molecules. PLoS One 2016; 11:e0157046. [PMID: 27276347 PMCID: PMC4898712 DOI: 10.1371/journal.pone.0157046] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 05/24/2016] [Indexed: 11/18/2022] Open
Abstract
PCR amplification and sequencing of phylogenetic markers, primarily Small Sub-Unit ribosomal RNA (SSU rRNA) genes, has been the paradigm for defining the taxonomic composition of microbiomes. However, ‘universal’ SSU rRNA gene PCR primer sets are likely to miss much of the diversity therein. We sequenced a library comprising purified and reverse-transcribed SSU rRNA (RT-SSU rRNA) molecules from the canine oral microbiome and compared it to a general bacterial 16S rRNA gene PCR amplicon library generated from the same biological sample. In addition, we have developed BIONmeta, a novel, open-source, computer package for the processing and taxonomic classification of the randomly fragmented RT-SSU rRNA reads produced. Direct RT-SSU rRNA sequencing revealed that 16S rRNA molecules belonging to the bacterial phyla Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria and Spirochaetes, were most abundant in the canine oral microbiome (92.5% of total bacterial SSU rRNA). The direct rRNA sequencing approach detected greater taxonomic diversity (1 additional phylum, 2 classes, 1 order, 10 families and 61 genera) when compared with general bacterial 16S rRNA amplicons from the same sample, simultaneously provided SSU rRNA gene inventories of Bacteria, Archaea and Eukarya, and detected significant numbers of sequences not recognised by ‘universal’ primer sets. Proteobacteria and Spirochaetes were found to be under-represented by PCR-based analysis of the microbiome, and this was due to primer mismatches and taxon-specific variations in amplification efficiency, validated by qPCR analysis of 16S rRNA amplicons from a mock community. This demonstrated the veracity of direct RT-SSU rRNA sequencing for molecular microbial ecology.
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Affiliation(s)
- James E. McDonald
- School of Biological Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd, LL57 2UW, United Kingdom
- * E-mail: (JM); (HA)
| | - Niels Larsen
- Danish Genome Institute, Skt. Lucas Kirkeplads 8, 8000, Aarhus C, Denmark
| | - Andrea Pennington
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - John Connolly
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Corrin Wallis
- WALTHAM Centre for Pet Nutrition, Freeby Lane, Waltham-on-the-Wolds, Melton Mowbray, LE14 4RT, United Kingdom
| | - David J. Rooks
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Neil Hall
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Alan J. McCarthy
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Heather E. Allison
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
- * E-mail: (JM); (HA)
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32
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Klein AM, Bohannan BJM, Jaffe DA, Levin DA, Green JL. Molecular Evidence for Metabolically Active Bacteria in the Atmosphere. Front Microbiol 2016; 7:772. [PMID: 27252689 PMCID: PMC4878314 DOI: 10.3389/fmicb.2016.00772] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/09/2016] [Indexed: 01/02/2023] Open
Abstract
Bacterial metabolisms are responsible for critical chemical transformations in nearly all environments, including oceans, freshwater, and soil. Despite the ubiquity of bacteria in the atmosphere, little is known about the metabolic functioning of atmospheric bacterial communities. To gain a better understanding of the metabolism of bacterial communities in the atmosphere, we used a combined empirical and model-based approach to investigate the structure and composition of potentially active bacterial communities in air sampled at a high elevation research station. We found that the composition of the putatively active bacterial community (assayed via rRNA) differed significantly from the total bacterial community (assayed via rDNA). Rare taxa in the total (rDNA) community were disproportionately active relative to abundant taxa, and members of the order Rhodospirillales had the highest potential for activity. We developed theory to explore the effects of random sampling from the rRNA and rDNA communities on observed differences between the communities. We found that random sampling, particularly in cases where active taxa are rare in the rDNA community, will give rise to observed differences in community composition including the occurrence of “phantom taxa”, taxa which are detected in the rRNA community but not the rDNA community. We show that the use of comparative rRNA/rDNA techniques can reveal the structure and composition of the metabolically active portion of bacterial communities. Our observations suggest that metabolically active bacteria exist in the atmosphere and that these communities may be involved in the cycling of organic compounds in the atmosphere.
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Affiliation(s)
- Ann M Klein
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, Eugene, OR USA
| | - Brendan J M Bohannan
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, Eugene, OR USA
| | - Daniel A Jaffe
- Department of Atmospheric Sciences, University of Washington Bothell, Bothell, WA USA
| | - David A Levin
- Department of Mathematics, University of Oregon, Eugene, OR USA
| | - Jessica L Green
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, Eugene, ORUSA; Santa Fe Institute, Santa Fe, NMUSA
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33
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Meier DV, Bach W, Girguis PR, Gruber-Vodicka HR, Reeves EP, Richter M, Vidoudez C, Amann R, Meyerdierks A. HeterotrophicProteobacteriain the vicinity of diffuse hydrothermal venting. Environ Microbiol 2016; 18:4348-4368. [DOI: 10.1111/1462-2920.13304] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/13/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Dimitri V. Meier
- Max Planck Institute for Marine Microbiology; Celsiusstrasse 1 D-28359 Bremen Germany
| | - Wolfgang Bach
- University of Bremen, MARUM - Center for Marine Environmental Sciences, Petrology of the Ocean Crust group; Leobener Str. D-28359 Bremen Germany
| | - Peter R. Girguis
- Harvard University, Department of Organismic & Evolutionary Biology; 16 Divinity Avenue Cambridge MA 02138-2020 USA
| | | | - Eoghan P. Reeves
- University of Bremen, MARUM - Center for Marine Environmental Sciences, Petrology of the Ocean Crust group; Leobener Str. D-28359 Bremen Germany
- University of Bergen, Department of Earth Science and Centre for Geobiology; Postboks 7803 N-5020 Bergen Norway
| | - Michael Richter
- Max Planck Institute for Marine Microbiology; Celsiusstrasse 1 D-28359 Bremen Germany
| | - Charles Vidoudez
- Harvard University, Department of Organismic & Evolutionary Biology; 16 Divinity Avenue Cambridge MA 02138-2020 USA
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology; Celsiusstrasse 1 D-28359 Bremen Germany
| | - Anke Meyerdierks
- Max Planck Institute for Marine Microbiology; Celsiusstrasse 1 D-28359 Bremen Germany
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34
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Zarkasi KZ, Taylor RS, Abell GCJ, Tamplin ML, Glencross BD, Bowman JP. Atlantic Salmon (Salmo salar L.) Gastrointestinal Microbial Community Dynamics in Relation to Digesta Properties and Diet. MICROBIAL ECOLOGY 2016; 71:589-603. [PMID: 26780099 DOI: 10.1007/s00248-015-0728-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/29/2015] [Indexed: 05/11/2023]
Abstract
To better understand salmon GI tract microbial community dynamics in relation to diet, a feeding trial was performed utilising diets with different proportions of fish meal, protein, lipid and energy levels. Salmon gut dysfunction has been associated with the occurrence of casts, or an empty hind gut. A categorical scoring system describing expressed digesta consistency was evaluated in relation to GI tract community structure. Faster growing fish generally had lower faecal scores while the diet cohorts showed minor differences in faecal score though the overall lowest scores were observed with a low protein, low energy diet. The GI tract bacterial communities were highly dynamic over time with the low protein, low energy diet associated with the most divergent community structure. This included transiently increased abundance of anaerobic (Bacteroidia and Clostridia) during January and February, and facultatively anaerobic (lactic acid bacteria) taxa from February onwards. The digesta had enriched populations of these groups in relation to faecal cast samples. The majority of samples (60-86 %) across all diet cohorts were eventually dominated by the genus Aliivibrio. The results suggest that an interaction between time of sampling and diet is most strongly related to community structure. Digesta categorization revealed microbes involved with metabolism of diet components change progressively over time and could be a useful system to assess feeding responses.
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Affiliation(s)
- Kamarul Zaman Zarkasi
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia.
- Tasmanian Institute of Agriculture, Food Safety Centre, University of Tasmania, Hobart, Tasmania, Australia.
| | | | | | - Mark L Tamplin
- Tasmanian Institute of Agriculture, Food Safety Centre, University of Tasmania, Hobart, Tasmania, Australia
| | - Brett D Glencross
- University of Stirling, Institute of Aquaculture, Stirling, Scotland, UK
| | - John P Bowman
- Tasmanian Institute of Agriculture, Food Safety Centre, University of Tasmania, Hobart, Tasmania, Australia
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35
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Moen B, Røssvoll E, Måge I, Møretrø T, Langsrud S. Microbiota formed on attached stainless steel coupons correlates with the natural biofilm of the sink surface in domestic kitchens. Can J Microbiol 2015; 62:148-60. [PMID: 26758935 DOI: 10.1139/cjm-2015-0562] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Stainless steel coupons are frequently used in biofilm studies in the laboratory, as this material is commonly used in the food industry. The coupons are attached to different surfaces to create a "natural" biofilm to be studied further in laboratory trials. However, little has been done to investigate how well the microbiota on such coupons represents the surrounding environment. The microbiota on sink wall surfaces and on new stainless steel coupons attached to the sink wall for 3 months in 8 domestic kitchen sinks was investigated by next-generation sequencing (MiSeq) of the 16S rRNA gene derived from DNA and RNA (cDNA), and by plating and identification of colonies. The mean number of colony-forming units was about 10-fold higher for coupons than sink surfaces, and more variation in bacterial counts between kitchens was seen on sink surfaces than coupons. The microbiota in the majority of biofilms was dominated by Moraxellaceae (genus Moraxella/Enhydrobacter) and Micrococcaceae (genus Kocuria). The results demonstrated that the variation in the microbiota was mainly due to differences between kitchens (38.2%), followed by the different nucleic acid template (DNA vs RNA) (10.8%), and that only 5.1% of the variation was a result of differences between coupons and sink surfaces. The microbiota variation between sink surfaces and coupons was smaller for samples based on their RNA than on their DNA. Overall, our results suggest that new stainless steel coupons are suited to model the dominating part of the natural microbiota of the surrounding environment and, furthermore, are suitable for different downstream studies.
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Affiliation(s)
- Birgitte Moen
- a Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, N-1430 Aas, Norway
| | - Elin Røssvoll
- a Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, N-1430 Aas, Norway.,b Animalia, Norwegian Meat and Poultry Research Center, P.O. Box 396, Økern, 0513 Oslo, Norway
| | - Ingrid Måge
- a Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, N-1430 Aas, Norway
| | - Trond Møretrø
- a Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, N-1430 Aas, Norway
| | - Solveig Langsrud
- a Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, N-1430 Aas, Norway
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Geisen S, Tveit AT, Clark IM, Richter A, Svenning MM, Bonkowski M, Urich T. Metatranscriptomic census of active protists in soils. THE ISME JOURNAL 2015; 9:2178-90. [PMID: 25822483 PMCID: PMC4579471 DOI: 10.1038/ismej.2015.30] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/21/2015] [Accepted: 01/28/2015] [Indexed: 11/08/2022]
Abstract
The high numbers and diversity of protists in soil systems have long been presumed, but their true diversity and community composition have remained largely concealed. Traditional cultivation-based methods miss a majority of taxa, whereas molecular barcoding approaches employing PCR introduce significant biases in reported community composition of soil protists. Here, we applied a metatranscriptomic approach to assess the protist community in 12 mineral and organic soil samples from different vegetation types and climatic zones using small subunit ribosomal RNA transcripts as marker. We detected a broad diversity of soil protists spanning across all known eukaryotic supergroups and revealed a strikingly different community composition than shown before. Protist communities differed strongly between sites, with Rhizaria and Amoebozoa dominating in forest and grassland soils, while Alveolata were most abundant in peat soils. The Amoebozoa were comprised of Tubulinea, followed with decreasing abundance by Discosea, Variosea and Mycetozoa. Transcripts of Oomycetes, Apicomplexa and Ichthyosporea suggest soil as reservoir of parasitic protist taxa. Further, Foraminifera and Choanoflagellida were ubiquitously detected, showing that these typically marine and freshwater protists are autochthonous members of the soil microbiota. To the best of our knowledge, this metatranscriptomic study provides the most comprehensive picture of active protist communities in soils to date, which is essential to target the ecological roles of protists in the complex soil system.
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Affiliation(s)
- Stefan Geisen
- Department of Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
- Department of Terrestrial Ecology, Netherlands Institute for Ecology, (NIOO-KNAW), Wageningen, The Netherlands
| | - Alexander T Tveit
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ian M Clark
- Department of AgroEcology, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Andreas Richter
- Department of Microbiology and Ecosystem Sciences, University of Vienna, Vienna, Austria
| | - Mette M Svenning
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Michael Bonkowski
- Department of Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Tim Urich
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
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İnceoğlu Ö, Llirós M, Crowe SA, García-Armisen T, Morana C, Darchambeau F, Borges AV, Descy JP, Servais P. Vertical Distribution of Functional Potential and Active Microbial Communities in Meromictic Lake Kivu. MICROBIAL ECOLOGY 2015; 70:596-611. [PMID: 25912922 DOI: 10.1007/s00248-015-0612-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/02/2015] [Indexed: 06/04/2023]
Abstract
The microbial community composition in meromictic Lake Kivu, with one of the largest CH4 reservoirs, was studied using 16S rDNA and ribosomal RNA (rRNA) pyrosequencing during the dry and rainy seasons. Highly abundant taxa were shared in a high percentage between bulk (DNA-based) and active (RNA-based) bacterial communities, whereas a high proportion of rare species was detected only in either an active or bulk community, indicating the existence of a potentially active rare biosphere and the possible underestimation of diversity detected when using only one nucleic acid pool. Most taxa identified as generalists were abundant, and those identified as specialists were more likely to be rare in the bulk community. The overall number of environmental parameters that could explain the variation was higher for abundant taxa in comparison to rare taxa. Clustering analysis based on operational taxonomic units (OTUs at 0.03 cutoff) level revealed significant and systematic microbial community composition shifts with depth. In the oxic zone, Actinobacteria were found highly dominant in the bulk community but not in the metabolically active community. In the oxic-anoxic transition zone, highly abundant potentially active Nitrospira and Methylococcales were observed. The co-occurrence of potentially active sulfur-oxidizing and sulfate-reducing bacteria in the anoxic zone may suggest the presence of an active yet cryptic sulfur cycle.
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Affiliation(s)
- Özgul İnceoğlu
- Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Brussel, Belgium.
| | - Marc Llirós
- Laboratory of Freshwater Ecology, Université de Namur, Namur, Belgium
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Sean A Crowe
- Departments of Microbiology and Immunology, and Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
| | | | - Cedric Morana
- Department of Earth and Environmental Sciences, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | | | - Jean-Pierre Descy
- Laboratory of Freshwater Ecology, Université de Namur, Namur, Belgium
| | - Pierre Servais
- Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Brussel, Belgium
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Geisen S, Rosengarten J, Koller R, Mulder C, Urich T, Bonkowski M. Pack hunting by a common soil amoeba on nematodes. Environ Microbiol 2015; 17:4538-46. [DOI: 10.1111/1462-2920.12949] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 06/08/2015] [Accepted: 06/08/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Stefan Geisen
- Department of Terrestrial Ecology; Institute of Zoology; University of Cologne; Cologne Germany
- Department of Terrestrial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); Wageningen The Netherlands
| | - Jamila Rosengarten
- Department of Terrestrial Ecology; Institute of Zoology; University of Cologne; Cologne Germany
| | - Robert Koller
- Department of Terrestrial Ecology; Institute of Zoology; University of Cologne; Cologne Germany
- Forschungszentrum Jülich; IBG-2: Plant Sciences; Jülich Germany
| | - Christian Mulder
- National Institute for Public Health and the Environment (RIVM); Bilthoven The Netherlands
| | - Tim Urich
- Department of Ecogenomics and Systems Biology; University of Vienna; Vienna Austria
- Bacterial Physiology; Institute for Microbiology; Ernst Moritz Arndt University; Greifswald Germany
| | - Michael Bonkowski
- Department of Terrestrial Ecology; Institute of Zoology; University of Cologne; Cologne Germany
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Wang L, Cheung MK, Kwan HS, Hwang JS, Wong CK. Microbial diversity in shallow-water hydrothermal sediments of Kueishan Island, Taiwan as revealed by pyrosequencing. J Basic Microbiol 2015; 55:1308-18. [PMID: 26132902 DOI: 10.1002/jobm.201400811] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 06/14/2015] [Indexed: 01/14/2023]
Abstract
Kueishan Island is a young volcanic island in the southernmost edge of the Okinawa Trough in the northeastern part of Taiwan. A cluster of hydrothermal vents is located off the southeastern tip of the Island at water depths between 10 and 80 m. This paper presents the results of the first study on the microbial communities in bottom sediments collected from the shallow-water hydrothermal vents of Kueishan Island. Small-subunit ribosomal RNA gene-based high-throughput 454 pyrosequencing was used to characterize the assemblages of bacteria, archaea, and small eukaryotes in sediment samples collected at various distances from the hydrothermal vents. Sediment from the vent area contained the highest diversity of archaea and the lowest diversity of bacteria and small eukaryotes. Epsilonproteobacteria were the most abundant group in the vent sediment, but their abundance decreased with increasing distance from the vent area. Most Epsilonproteobacteria belonged to the mesophilic chemolithoautotrophic genera Sulfurovum and Sulfurimonas. Recent reports on these two genera have come from deep-sea hydrothermal vents. Conversely, the relative contribution of Gammaproteobacteria to the bacterial community increased with increasing distance from the vent area. Our study revealed the contrasting effects of venting on the benthic bacterial and archaeal communities, and showed that the sediments of the shallow-waters hydrothermal vents were dominated by chemoautotrophic bacteria. The present work broadens our knowledge on microbial diversity in shallow-water hydrothermal vent habitats.
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Affiliation(s)
- Li Wang
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Man Kit Cheung
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Jiang-Shiou Hwang
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, Taiwan
| | - Chong Kim Wong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
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40
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Epelde L, Lanzén A, Blanco F, Urich T, Garbisu C. Adaptation of soil microbial community structure and function to chronic metal contamination at an abandoned Pb-Zn mine. FEMS Microbiol Ecol 2014; 91:1-11. [PMID: 25764532 DOI: 10.1093/femsec/fiu007] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Toxicity of metals released from mine tailings may cause severe damage to ecosystems. A diversity of microorganisms, however, have successfully adapted to such sites. In this study, our objective was to advance the understanding of the indigenous microbial communities of mining-impacted soils. To this end, a metatranscriptomic approach was used to study a heavily metal-contaminated site along a metal concentration gradient (up to 3220 000 and 97 000 mg kg(-1) of Cd, Pb and Zn, respectively) resulting from previous mining. Metal concentration, soil pH and amount of clay were the most important factors determining the structure of soil microbial communities. Interestingly, evenness of the microbial communities, but not its richness, increased with contamination level. Taxa with high metabolic plasticity like Ktedonobacteria and Chloroflexi were found with higher relative abundance in more contaminated samples. However, several taxa belonging to the phyla Actinobacteria and Acidobacteria followed opposite trends in relation to metal pollution. Besides, functional transcripts related to transposition or transfer of genetic material and membrane transport, potentially involved in metal resistance mechanisms, had a higher expression in more contaminated samples. Our results provide an insight into microbial communities in long-term metal-contaminated environments and how they contrast to nearby sites with lower contamination.
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Affiliation(s)
- Lur Epelde
- NEIKER-Tecnalia, Department of Ecology and Natural Resources, Soil Microbial Ecology Group, c/ Berreaga 1, E-48160 Derio, Spain
| | - Anders Lanzén
- NEIKER-Tecnalia, Department of Ecology and Natural Resources, Soil Microbial Ecology Group, c/ Berreaga 1, E-48160 Derio, Spain
| | - Fernando Blanco
- NEIKER-Tecnalia, Department of Ecology and Natural Resources, Soil Microbial Ecology Group, c/ Berreaga 1, E-48160 Derio, Spain
| | - Tim Urich
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Carlos Garbisu
- NEIKER-Tecnalia, Department of Ecology and Natural Resources, Soil Microbial Ecology Group, c/ Berreaga 1, E-48160 Derio, Spain
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Youssef NH, Couger MB, McCully AL, Criado AEG, Elshahed MS. Assessing the global phylum level diversity within the bacterial domain: A review. J Adv Res 2014; 6:269-82. [PMID: 26257925 PMCID: PMC4522544 DOI: 10.1016/j.jare.2014.10.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/06/2014] [Accepted: 10/23/2014] [Indexed: 12/11/2022] Open
Abstract
Microbial ecology is the study of microbes in the natural environment and their interactions with each other. Investigating the nature of microorganisms residing within a specific habitat is an extremely important component of microbial ecology. Such microbial diversity surveys aim to determine the identity, physiological preferences, metabolic capabilities, and genomic features of microbial taxa within a specific ecosystem. A comprehensive review of various aspects of microbial diversity (phylogenetic, functional, and genomic diversities) in the microbial (bacterial, archaeal, and microeukaryotic) world is clearly a daunting task that could not be aptly summarized in a single review. Here, we focus on one aspect of diversity (phylogenetic diversity) in one microbial domain (the Bacteria). We restrict our analysis to the highest taxonomic rank (phylum) and attempt to investigate the extent of global phylum level diversity within the Bacteria. We present a brief historical perspective on the subject and highlight how the adaptation of molecular biological and phylogenetic approaches has greatly expanded our view of global bacterial diversity. We also summarize recent progress toward the discovery of novel bacterial phyla, present evidences that the scope of phylum level diversity in nature has hardly been exhausted, and propose novel approaches that could greatly facilitate the discovery process of novel bacterial phyla within various ecosystems.
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Affiliation(s)
- Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - M B Couger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Alexandra L McCully
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | | | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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42
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Zarkasi KZ, Abell GCJ, Taylor RS, Neuman C, Hatje E, Tamplin ML, Katouli M, Bowman JP. Pyrosequencing-based characterization of gastrointestinal bacteria of Atlantic salmon (Salmo salar L.) within a commercial mariculture system. J Appl Microbiol 2014; 117:18-27. [PMID: 24698479 DOI: 10.1111/jam.12514] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/19/2014] [Accepted: 03/28/2014] [Indexed: 11/30/2022]
Abstract
AIMS The relationship of Atlantic salmon gastrointestinal (GI) tract bacteria to environmental factors, in particular water temperature within a commercial mariculture system, was investigated. METHODS AND RESULTS Salmon GI tract bacterial communities commercially farmed in south-eastern Tasmania were analysed, over a 13-month period across a standard commercial production farm cycle, using 454 16S rRNA-based pyrosequencing. Faecal bacterial communities were highly dynamic but largely similar between randomly selected fish. In postsmolt, the faecal bacteria population was dominated by Gram-positive fermentative bacteria; however, by midsummer, members of the family Vibrionaceae predominated. As fish progressed towards harvest, a range of different bacterial genera became more prominent corresponding to a decline in Vibrionaceae. The sampled fish were fed two different commercial diet series with slightly different protein, lipid and digestible energy level; however, the effect of these differences was minimal. CONCLUSIONS The overall data demonstrated dynamic hind gut communities in salmon that were related to season and fish growth phases but were less influenced by differences in commercial diets used routinely within the farm system studied. SIGNIFICANCE AND IMPACT OF THE STUDY This study provides understanding of farmed salmon GI bacterial communities and describes the relative impact of diet, environmental and farm factors.
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Affiliation(s)
- K Z Zarkasi
- Tasmanian Institute of Agriculture, Food Safety Centre, University of Tasmania, Hobart, Tas., Australia; School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
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Wilhelm L, Besemer K, Fasching C, Urich T, Singer GA, Quince C, Battin TJ. Rare but active taxa contribute to community dynamics of benthic biofilms in glacier-fed streams. Environ Microbiol 2014; 16:2514-24. [PMID: 24428193 DOI: 10.1111/1462-2920.12392] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 01/01/2014] [Indexed: 01/27/2023]
Abstract
Glaciers harbour diverse microorganisms, which upon ice melt can be released downstream. In glacier-fed streams microorganisms can attach to stones or sediments to form benthic biofilms. We used 454-pyrosequencing to explore the bulk (16S rDNA) and putatively active (16S rRNA) microbial communities of stone and sediment biofilms across 26 glacier-fed streams. We found differences in community composition between bulk and active communities among streams and a stronger congruence between biofilm types. Relative abundances of rRNA and rDNA were positively correlated across different taxa and taxonomic levels, but at lower taxonomic levels, the higher abundance in either the active or the bulk communities became more apparent. Here, environmental variables played a minor role in structuring active communities. However, we found a large number of rare taxa with higher relative abundances in rRNA compared with rDNA. This suggests that rare taxa contribute disproportionately to microbial community dynamics in glacier-fed streams. Our findings propose that high community turnover, where taxa repeatedly enter and leave the 'seed bank', contributes to the maintenance of microbial biodiversity in harsh ecosystems with continuous environmental perturbations, such as glacier-fed streams.
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Affiliation(s)
- Linda Wilhelm
- Department of Limnology and Bio-Oceanography, University of Vienna, Althanstr. 14, A-1090, Vienna, Austria
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Li XR, Lv Y, Meng H, Gu JD, Quan ZX. Analysis of microbial diversity by pyrosequencing the small-subunit ribosomal RNA without PCR amplification. Appl Microbiol Biotechnol 2014; 98:3777-89. [PMID: 24531274 DOI: 10.1007/s00253-014-5583-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/25/2014] [Accepted: 01/28/2014] [Indexed: 12/01/2022]
Abstract
To avoid the biases associated with PCR amplification in analysis of microbial communities, a new method has been tested for direct sequencing of the cDNA of full-length Small-subunit Ribosomal RNA withOut specific PCR amplification (SROP). In silico analysis of the SROP method demonstrated that more than 99 % of the SROP sequences could be correctly annotated. Two environmental samples (activated sludge and anaerobic sludge) with complex microbial communities were used for comparison in this study. The SROP results demonstrated that the families Rhodocyclaceae and Nitrosomonadaceae in activated sludge and the phyla Synergistetes and Spirochaetes in anaerobic sludge were underestimated by PCR-based detection. One third of the 16S ribosomal RNA (rRNA) sequences obtained by the SROP method covered the V3 amplicon region, and they are suitable for phylogenetic and diversity index analyses. The microbial diversity index calculated from the rRNA sequences by the SROP was much higher than that calculated by conventional PCR, particularly for the anaerobic sludge. The metatranscriptome-based SROP method will contribute to our better understanding of the diversity of complex microbial communities.
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Affiliation(s)
- Xiao-Ran Li
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai, 200433, China
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45
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Hadziavdic K, Lekang K, Lanzen A, Jonassen I, Thompson EM, Troedsson C. Characterization of the 18S rRNA gene for designing universal eukaryote specific primers. PLoS One 2014; 9:e87624. [PMID: 24516555 PMCID: PMC3917833 DOI: 10.1371/journal.pone.0087624] [Citation(s) in RCA: 245] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 11/18/2013] [Indexed: 12/03/2022] Open
Abstract
High throughput sequencing technology has great promise for biodiversity studies. However, an underlying assumption is that the primers used in these studies are universal for the prokaryotic or eukaryotic groups of interest. Full primer universality is difficult or impossible to achieve and studies using different primer sets make biodiversity comparisons problematic. The aim of this study was to design and optimize universal eukaryotic primers that could be used as a standard in future biodiversity studies. Using the alignment of all eukaryotic sequences from the publicly available SILVA database, we generated a full characterization of variable versus conserved regions in the 18S rRNA gene. All variable regions within this gene were analyzed and our results suggested that the V2, V4 and V9 regions were best suited for biodiversity assessments. Previously published universal eukaryotic primers as well as a number of self-designed primers were mapped to the alignment. Primer selection will depend on sequencing technology used, and this study focused on the 454 pyrosequencing GS FLX Titanium platform. The results generated a primer pair yielding theoretical matches to 80% of the eukaryotic and 0% of the prokaryotic sequences in the SILVA database. An empirical test of marine sediments using the AmpliconNoise pipeline for analysis of the high throughput sequencing data yielded amplification of sequences for 71% of all eukaryotic phyla with no isolation of prokaryotic sequences. To our knowledge this is the first characterization of the complete 18S rRNA gene using all eukaryotes present in the SILVA database, providing a robust test for universal eukaryotic primers. Since both in silico and empirical tests using high throughput sequencing retained high inclusion of eukaryotic phyla and exclusion of prokaryotes, we conclude that these primers are well suited for assessing eukaryote diversity, and can be used as a standard in biodiversity studies.
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Affiliation(s)
| | - Katrine Lekang
- Department of Biology, University of Bergen, Bergen, Norway
| | - Anders Lanzen
- Department of Biology, University of Bergen, Bergen, Norway
- Uni Computing, Uni Research AS, Bergen, Norway
- Department of Ecology and Natural Resources, NEIKER-Tecnalia, Derio, Spain
| | - Inge Jonassen
- Uni Computing, Uni Research AS, Bergen, Norway
- Department of Informatics, University of Bergen, Bergen, Norway
| | - Eric M. Thompson
- Department of Biology, University of Bergen, Bergen, Norway
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
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Tait K, Laverock B, Shaw J, Somerfield PJ, Widdicombe S. Minor impact of ocean acidification to the composition of the active microbial community in an Arctic sediment. ENVIRONMENTAL MICROBIOLOGY REPORTS 2013; 5:851-860. [PMID: 24249294 DOI: 10.1111/1758-2229.12087] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 07/10/2013] [Indexed: 06/02/2023]
Abstract
Effects of ocean acidification on the composition of the active bacterial and archaeal community within Arctic surface sediment was analysed in detail using 16S rRNA 454 pyrosequencing. Intact sediment cores were collected and exposed to one of five different pCO(2) concentrations [380 (present day), 540, 750, 1120 and 3000 μatm] and RNA extracted after a period of 14 days exposure. Measurements of diversity and multivariate similarity indicated very little difference between pCO(2) treatments. Only when the highest and lowest pCO(2) treatments were compared were significant differences evident, namely increases in the abundance of operational taxonomic units most closely related to the Halobacteria and differences to the presence/absence structure of the Planctomycetes. The relative abundance of members of the classes Planctomycetacia and Nitrospira increased with increasing pCO(2) concentration, indicating that these groups may be able to take advantage of changing pH or pCO(2) conditions. The modest response of the active microbial communities associated with these sediments may be due to the low and fluctuating pore-water pH already experienced by sediment microbes, a result of the pH buffering capacity of marine sediments, or due to currently unknown factors. Further research is required to fully understand the impact of elevated CO(2) on sediment physicochemical parameters, biogeochemistry and microbial community dynamics.
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Affiliation(s)
- Karen Tait
- Plymouth Marine Laboratory, Prospect Place, Plymouth, PL1 3DH, UK
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Urich T, Lanzén A, Stokke R, Pedersen RB, Bayer C, Thorseth IH, Schleper C, Steen IH, Øvreas L. Microbial community structure and functioning in marine sediments associated with diffuse hydrothermal venting assessed by integrated meta-omics. Environ Microbiol 2013; 16:2699-710. [DOI: 10.1111/1462-2920.12283] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 08/23/2013] [Accepted: 09/09/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Tim Urich
- Division of Archaea Biology and Ecogenomics; Department of Ecogenomics and Systems Biology; University of Vienna; 1090 Vienna Austria
- Centre for Geobiology; University of Bergen; 5007 Bergen Norway
| | - Anders Lanzén
- Centre for Geobiology; University of Bergen; 5007 Bergen Norway
- Department of Biology; University of Bergen; 5020 Bergen Norway
| | - Runar Stokke
- Centre for Geobiology; University of Bergen; 5007 Bergen Norway
- Department of Biology; University of Bergen; 5020 Bergen Norway
| | | | - Christoph Bayer
- Division of Archaea Biology and Ecogenomics; Department of Ecogenomics and Systems Biology; University of Vienna; 1090 Vienna Austria
| | - Ingunn H. Thorseth
- Centre for Geobiology; University of Bergen; 5007 Bergen Norway
- Department of Earth Science; University of Bergen; 5020 Bergen Norway
| | - Christa Schleper
- Division of Archaea Biology and Ecogenomics; Department of Ecogenomics and Systems Biology; University of Vienna; 1090 Vienna Austria
- Centre for Geobiology; University of Bergen; 5007 Bergen Norway
| | - Ida H. Steen
- Centre for Geobiology; University of Bergen; 5007 Bergen Norway
- Department of Biology; University of Bergen; 5020 Bergen Norway
| | - Lise Øvreas
- Centre for Geobiology; University of Bergen; 5007 Bergen Norway
- Department of Biology; University of Bergen; 5020 Bergen Norway
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Diversity of Planctomycetes in iron-hydroxide deposits from the Arctic Mid Ocean Ridge (AMOR) and description of Bythopirellula goksoyri gen. nov., sp. nov., a novel Planctomycete from deep sea iron-hydroxide deposits. Antonie van Leeuwenhoek 2013; 104:569-84. [PMID: 24018702 DOI: 10.1007/s10482-013-0019-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 08/24/2013] [Indexed: 10/26/2022]
Abstract
Planctomycetes form a deep branching and distinct phylum of the domain Bacteria, and represent a fascinating group due to their unusual features such as intracellular compartmentalization and lack of peptidoglycan in their cell walls. The phylum Planctomycetes was described already in 1924, but still the diversity of this phylum represents an enigma and unexploited resource. In this study the diversity of the phylum Planctomycetes in low temperature iron-hydroxide deposits at the Mohns Ridge, a part of the Arctic Mid Ocean Ridge (AMOR), was characterised by descriptive analysis of 16S rRNA gene sequences in combination with isolation of planctomycetes strains. The 16S rRNA gene sequences were affiliated with three order within the phylum Planctomycetes namely the (i)Planctomycetales, (ii) "Candidatus Brocadiales" and (iii) Phycisphaerae in addition to sequences affiliating to hitherto unknown Planctomycetes. The majority of the sequences were affiliated with the CCM11a group (Phycisphaerae), and with the Pir4 group (Planctomycetaceae). Two strains from the order Planctomycetales were isolated. One strain (Plm2) showed high similarity to the previously isolated Planctomyces maris (99 % 16S rRNA sequence identity). The other strain (Pr1d) belonged to the Pir4 group, and showed highest identity with Rhodopirellula baltica (86 %), Blastopirellula marina (86 %) and Pirellula staleyi (85 %). Based on its physiological and biochemical properties, strain Pr1d(T) is considered to represent a new genus of the order Planctomycetales. We propose to classify the novel planctomycete in a new genus and species, Bythoypirellula goksoyri gen. nov., sp. nov., the type strain being Pr1d(T).
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Lanzén A, Simachew A, Gessesse A, Chmolowska D, Jonassen I, Øvreås L. Surprising prokaryotic and eukaryotic diversity, community structure and biogeography of Ethiopian soda lakes. PLoS One 2013; 8:e72577. [PMID: 24023625 PMCID: PMC3758324 DOI: 10.1371/journal.pone.0072577] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 07/11/2013] [Indexed: 11/18/2022] Open
Abstract
Soda lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. This makes them valuable model systems for studying the connection between community structure and abiotic parameters such as pH and salinity. For the first time, we apply high-throughput sequencing to accurately estimate phylogenetic richness and composition in five soda lakes, located in the Ethiopian Rift Valley. The lakes were selected for their contrasting pH, salinities and stratification and several depths or spatial positions were covered in each lake. DNA was extracted and analyzed from all lakes at various depths and RNA extracted from two of the lakes, analyzed using both amplicon- and shotgun sequencing. We reveal a surprisingly high biodiversity in all of the studied lakes, similar to that of freshwater lakes. Interestingly, diversity appeared uncorrelated or positively correlated to pH and salinity, with the most “extreme” lakes showing the highest richness. Together, pH, dissolved oxygen, sodium- and potassium concentration explained approximately 30% of the compositional variation between samples. A diversity of prokaryotic and eukaryotic taxa could be identified, including several putatively involved in carbon-, sulfur- or nitrogen cycling. Key processes like methane oxidation, ammonia oxidation and ‘nitrifier denitrification’ were also confirmed by mRNA transcript analyses.
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Affiliation(s)
- Anders Lanzén
- Department of Biology and Centre for Geobiology, University of Bergen, Bergen, Norway
- Computational Biology Unit, Uni Computing, Uni Research AS, Bergen, Norway
- * E-mail:
| | - Addis Simachew
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Amare Gessesse
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Dominika Chmolowska
- Institute of Environmental Sciences, Jagiellonian University, Krakow, Poland
| | - Inge Jonassen
- Computational Biology Unit, Uni Computing, Uni Research AS, Bergen, Norway
- Department of Informatics, University of Bergen, Bergen, Norway
| | - Lise Øvreås
- Department of Biology and Centre for Geobiology, University of Bergen, Bergen, Norway
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Moitinho-Silva L, Bayer K, Cannistraci CV, Giles EC, Ryu T, Seridi L, Ravasi T, Hentschel U. Specificity and transcriptional activity of microbiota associated with low and high microbial abundance sponges from the Red Sea. Mol Ecol 2013; 23:1348-1363. [DOI: 10.1111/mec.12365] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 04/16/2013] [Accepted: 04/18/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Lucas Moitinho-Silva
- Department of Botany II; Julius-von-Sachs Institute for Biological Sciences; University of Wuerzburg; Julius-von-Sachs Platz 3 97082 Wuerzburg Germany
| | - Kristina Bayer
- Department of Botany II; Julius-von-Sachs Institute for Biological Sciences; University of Wuerzburg; Julius-von-Sachs Platz 3 97082 Wuerzburg Germany
| | - Carlo V. Cannistraci
- Division of Biological and Environmental Sciences & Engineering and Division of Applied Mathematics and Computer Science; Computational Biosciences Research Center; King Abdullah University of Science and Technology; Thuwal 23955-6900 Kingdom of Saudi Arabia
| | - Emily C. Giles
- Division of Biological and Environmental Sciences & Engineering and Division of Applied Mathematics and Computer Science; Computational Biosciences Research Center; King Abdullah University of Science and Technology; Thuwal 23955-6900 Kingdom of Saudi Arabia
| | - Taewoo Ryu
- Division of Biological and Environmental Sciences & Engineering and Division of Applied Mathematics and Computer Science; Computational Biosciences Research Center; King Abdullah University of Science and Technology; Thuwal 23955-6900 Kingdom of Saudi Arabia
| | - Loqmane Seridi
- Division of Biological and Environmental Sciences & Engineering and Division of Applied Mathematics and Computer Science; Computational Biosciences Research Center; King Abdullah University of Science and Technology; Thuwal 23955-6900 Kingdom of Saudi Arabia
| | - Timothy Ravasi
- Division of Biological and Environmental Sciences & Engineering and Division of Applied Mathematics and Computer Science; Computational Biosciences Research Center; King Abdullah University of Science and Technology; Thuwal 23955-6900 Kingdom of Saudi Arabia
| | - Ute Hentschel
- Department of Botany II; Julius-von-Sachs Institute for Biological Sciences; University of Wuerzburg; Julius-von-Sachs Platz 3 97082 Wuerzburg Germany
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