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Morales-Rivera MF, Valenzuela-Miranda D, Nuñez-Acuña G, Benavente BP, Gallardo-Escárate C, Valenzuela-Muñoz V. Atlantic Salmon ( Salmo salar) Transfer to Seawater by Gradual Salinity Changes Exhibited an Increase in The Intestinal Microbial Abundance and Richness. Microorganisms 2022; 11:microorganisms11010076. [PMID: 36677368 PMCID: PMC9865641 DOI: 10.3390/microorganisms11010076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/07/2022] [Accepted: 12/20/2022] [Indexed: 12/29/2022] Open
Abstract
The host's physiological history and environment determine the microbiome structure. In that sense, the strategy used for the salmon transfer to seawater after parr-smolt transformation may influence the Atlantic salmon's intestinal microbiota. Therefore, this study aimed to explore the diversity and abundance of the Atlantic salmon intestinal microbiota and metagenome functional prediction during seawater transfer under three treatments. One group was exposed to gradual salinity change (GSC), the other to salinity shock (SS), and the third was fed with a functional diet (FD) before the seawater (SW) transfer. The microbial profile was assessed through full-16S rRNA gene sequencing using the Nanopore platform. In addition, metagenome functional prediction was performed using PICRUSt2. The results showed an influence of salinity changes on Atlantic salmon gut microbiota richness, diversity, and taxonomic composition. The findings reveal that GSC and the FD increased the Atlantic salmon smolt microbiota diversity, suggesting a positive association between the intestinal microbial community and fish health during seawater transfer. The reported knowledge can be applied to surveil the microbiome in smolt fish production, improving the performance of Atlantic salmon to seawater transfer.
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Affiliation(s)
- María F. Morales-Rivera
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
| | - Diego Valenzuela-Miranda
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
- Centro de Biotecnología, Universidad de Concepción, Concepcion 4030000, Chile
| | - Gustavo Nuñez-Acuña
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
| | - Bárbara P. Benavente
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
| | - Cristian Gallardo-Escárate
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
| | - Valentina Valenzuela-Muñoz
- Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepcion 4030000, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, University of Concepción, Concepcion 4030000, Chile
- Centro de Biotecnología, Universidad de Concepción, Concepcion 4030000, Chile
- Correspondence: ; Tel.: +56-41-2204402
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2
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Liu S, Yu S, Lu X, Yang H, Li Y, Xu X, Lu H, Fang Y. Microbial communities associated with thermogenic gas hydrate-bearing marine sediments in Qiongdongnan Basin, South China Sea. Front Microbiol 2022; 13:1032851. [PMID: 36386663 PMCID: PMC9640435 DOI: 10.3389/fmicb.2022.1032851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/10/2022] [Indexed: 11/29/2022] Open
Abstract
Biogenic and thermogenic gas are two major contributors to gas hydrate formation. Methane hydrates from both origins may have critical impacts on the ecological properties of marine sediments. However, research on microbial diversity in thermogenic hydrate-containing sediments is limited. This study examined the prokaryotic diversity and distributions along a sediment core with a vertical distribution of thermogenic gas hydrates with different occurrences obtained from the Qiongdongnan Basin by Illumina sequencing of 16S rRNA genes as well as molecular and geochemical techniques. Here, we show that gas hydrate occurrence has substantial impacts on both microbial diversity and community composition. Compared to the hydrate-free zone, distinct microbiomes with significantly higher abundance and lower diversity were observed within the gas hydrate-containing layers. Gammaproteobacteria and Actinobacterota dominated the bacterial taxa in all collected samples, while archaeal communities shifted sharply along the vertical profile of sediment layers. A notable stratified distribution of anaerobic methanotrophs shaped by both geophysical and geochemical parameters was also determined. In addition, the hydrate-free zone hosted a large number of rare taxa that might perform a fermentative breakdown of proteins in the deep biosphere and probably respond to the hydrate formation.
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Affiliation(s)
- Siwei Liu
- School of Earth and Space Sciences, Peking University, Beijing, China
| | - Shan Yu
- Beijing International Center for Gas Hydrate, School of Earth and Space Sciences, Peking University, Beijing, China
- *Correspondence: Shan Yu,
| | - Xindi Lu
- Beijing International Center for Gas Hydrate, School of Earth and Space Sciences, Peking University, Beijing, China
| | - Hailin Yang
- Beijing International Center for Gas Hydrate, School of Earth and Space Sciences, Peking University, Beijing, China
| | - Yuanyuan Li
- School of Earth and Space Sciences, Peking University, Beijing, China
| | - Xuemin Xu
- School of Earth and Space Sciences, Peking University, Beijing, China
- National Research Center for Geoanalysis, Beijing, China
| | - Hailong Lu
- Beijing International Center for Gas Hydrate, School of Earth and Space Sciences, Peking University, Beijing, China
| | - Yunxin Fang
- Guangzhou Marine Geological Survey, Guangzhou, China
- Yunxin Fang,
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3
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Lin G, Huang J, Luo K, Lin X, Su M, Lu J. Bacterial, archaeal, and fungal community structure and interrelationships of deep-sea shrimp intestine and the surrounding sediment. ENVIRONMENTAL RESEARCH 2022; 205:112461. [PMID: 34863691 DOI: 10.1016/j.envres.2021.112461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/09/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
Invertebrate shrimp are one of the dominant benthic macrofaunae in the deep-sea environment. The microbiota of shrimp intestine can contribute to the adaptation of their host. The impact of surrounding sediment on intestinal microbiota has been observed in cultured shrimp species, but needs to be further investigated in deep-sea shrimp. The characterization of bacterial, archaeal, and fungal community structure and their interrelationships is also limited. In this study, wild-type deep-sea shrimp and the surrounding sediment were sampled. Shrimp individuals incubated in a sediment-absent environment were also used in this study. Microbial community structure of the shrimp intestine and sediment was investigated through amplicon sequencing targeting bacterial 16S rRNA genes, archaeal 16S rRNA genes, and fungal ITS genes. The results demonstrate distinct differences in community structure between shrimp intestine and the surrounding sediment and between surface and deep (5 mbsf) sediment. The composition of the intestinal microbiota in shrimp living without sediment was different from that of wild-type shrimp, indicating that the presence or absence of sediment could influence the shrimp intestinal microbiota. Carbohydrate metabolism, energy metabolism (carbon fixation, methane metabolism, nitrogen metabolism, and sulfur metabolism), amino acid metabolism, and xenobiotic biodegradation were the most commonly predicted microbial functionalities and they interacted closely with one another. Overall, this study provided comprehensive insights into bacterial, archaeal, and fungal community structure of deep-sea shrimp intestine as well as potential ecological interactions with the surrounding sediment. This study could update our understanding of the microbiota characteristics in shrimp and sediment in deep-sea ecosystems.
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Affiliation(s)
- Genmei Lin
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519080, Guangdong, China
| | - Junrou Huang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Kunwen Luo
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Xianbiao Lin
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Ming Su
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519080, Guangdong, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, 510275, Guangdong, China; Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, 519000, Guangdong, China
| | - Jianguo Lu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519080, Guangdong, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, 510275, Guangdong, China; Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, 519000, Guangdong, China.
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Lin G, Lu J, Sun Z, Xie J, Huang J, Su M, Wu N. Characterization of tissue-associated bacterial community of two Bathymodiolus species from the adjacent cold seep and hydrothermal vent environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 796:149046. [PMID: 34328889 DOI: 10.1016/j.scitotenv.2021.149046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/08/2021] [Accepted: 07/10/2021] [Indexed: 06/13/2023]
Abstract
Deep-sea mussels are widely distributed in marine chemosynthetic ecosystems. Bathymodiolus platifrons and B. japonicus, occurring at both cold seeps and hydrothermal vents, have been reported to house exclusively methanotrophic symbionts in the gill. However, the comparison of microbiota associated with different tissues between these two species from two contrasting habitats is still limited. In this study, using B. platifrons and B. japonicus collected from the adjacent cold seep and hydrothermal vent environments, we sampled different tissues (gill, adductor muscle, mantle, foot, and visceral mass including the gut) to decipher the microbial community structure at the tissue scale by employing 16S rRNA gene sequencing strategy. In the gill of both seep mussels and vent mussels, the symbiont gammaproteobacterial Methylomonaceae was the predominant lineage, and methane oxidation was identified as one of the most abundant putative function. In comparison, abundant families in other tissues were Pseudomonadaceae and Enterobacteriaceae in seep mussels and vent mussels, respectively, which may get involved in element cycling. The results revealed high similarity of community structure between two mussel species from the same habitat. The gill showed distinctive bacterial community structure compared with other tissues within the same environment, while the gill communities from two environments were more similar. Remarkably structural variations of adductor muscle, mantle, foot, and visceral mass were observed between two environments. This study can extend the understanding on the characteristics of tissue-associated microbiota of deep-sea mussels from the adjacent cold seep and hydrothermal vent environments.
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Affiliation(s)
- Genmei Lin
- School of Marine Sciences, Sun Yat-sen University, Zhuhai 519082, China
| | - Jianguo Lu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai 519082, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China.
| | - Zhilei Sun
- Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Institute of Marine Geology, China Geological Survey, Qingdao 266071, China; Laboratory for Mineral Resources, Qingdao Pilot National Laboratory for Marine Sciences and Technology, Qingdao 266071, China
| | - Jingui Xie
- School of Marine Sciences, Sun Yat-sen University, Zhuhai 519082, China
| | - Junrou Huang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai 519082, China
| | - Ming Su
- School of Marine Sciences, Sun Yat-sen University, Zhuhai 519082, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China
| | - Nengyou Wu
- Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Institute of Marine Geology, China Geological Survey, Qingdao 266071, China; Laboratory for Mineral Resources, Qingdao Pilot National Laboratory for Marine Sciences and Technology, Qingdao 266071, China.
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5
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C Campbell B, Gong S, Greenfield P, J Midgley D, T Paulsen I, C George S. Aromatic compound-degrading taxa in an anoxic coal seam microbiome from the Surat Basin, Australia. FEMS Microbiol Ecol 2021; 97:6206826. [PMID: 33791788 DOI: 10.1093/femsec/fiab053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
Methane is an important energy resource internationally, and a large proportion of this methane is produced by microbial communities living in coal seams. Despite the value of this resource for human energy security, our understanding of the metabolic roles played by specific taxa during the biodegradation of coal to methane in situ is quite limited. In order to develop a greater understanding of microbial catabolism on coal, a community from a coal seam in the Surat Basin, Australia, was incubated on 10 different aromatic organic compounds: coronene, benzo[a]pyrene, pyrene, phenanthrene, naphthalene, ethylbenzene, phenol, benzoate, vanillate and syringate. Each of these aromatic compounds either occurs in coal or is a possible product of the coal biodegradation process. 16S rRNA sequencing revealed substantial changes to each community in response to each aromatic carbon substrate provided. Abundant taxa from these substrate-specific communities were identified and their probable catabolic roles proposed based on literature searches of related taxa. This study is the first to link specific coal seam taxa to aromatic substrates available in coal seam environments. Two conceptual models of the putative degradation pathways and key taxa responsible are proposed.
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Affiliation(s)
- Bronwyn C Campbell
- Energy Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, NSW 2113, Australia.,Department of Earth and Environmental Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Se Gong
- Energy Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, NSW 2113, Australia
| | - Paul Greenfield
- Energy Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, NSW 2113, Australia
| | - David J Midgley
- Energy Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, NSW 2113, Australia
| | - Ian T Paulsen
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Simon C George
- Department of Earth and Environmental Sciences, Macquarie University, North Ryde, NSW 2109, Australia
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6
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Kerrigan Z, Kirkpatrick JB, D'Hondt S. Influence of 16S rRNA Hypervariable Region on Estimates of Bacterial Diversity and Community Composition in Seawater and Marine Sediment. Front Microbiol 2019; 10:1640. [PMID: 31379788 PMCID: PMC6646839 DOI: 10.3389/fmicb.2019.01640] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/02/2019] [Indexed: 11/13/2022] Open
Abstract
To assess the influence of 16S ribosomal RNA (rRNA) tag choice on estimates of microbial diversity and/or community composition in seawater and marine sediment, we examined bacterial diversity and community composition from a site in the Central North Atlantic and a site in the Equatorial Pacific. For each site, we analyzed samples from four zones in the water column, a seafloor sediment sample, and two subseafloor sediment horizons (with stratigraphic ages of 1.5 and 5.5 million years old). We amplified both the V4 and V6 hypervariable regions of the 16S rRNA gene and clustered the sequences into operational taxonomic units (OTUs) of 97% similarity to analyze for diversity and community composition. OTU richness is much higher with the V6 tag than with the V4 tag, and subsequently OTU-level community composition is quite different between the two tags. Vertical patterns of relative diversity are broadly the same for both tags, with maximum taxonomic richness in seafloor sediment and lowest richness in subseafloor sediment at both geographic locations. Genetic dissimilarity between sample locations is also broadly the same for both tags. Community composition is very similar for both tags at the class level, but very different at the level of 97% similar OTUs. Class-level diversity and community composition of water-column samples are very similar at each water depth between the Atlantic and Pacific. However, sediment communities differ greatly from the Atlantic site to the Pacific site. Finally, for relative patterns of diversity and class-level community composition, deep sequencing and shallow sequencing provide similar results.
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Affiliation(s)
- Zak Kerrigan
- Graduate School of Oceanography, The University of Rhode Island, Narragansett, RI, United States
| | | | - Steven D'Hondt
- Graduate School of Oceanography, The University of Rhode Island, Narragansett, RI, United States
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7
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Kirkpatrick JB, Walsh EA, D'Hondt S. Microbial Selection and Survival in Subseafloor Sediment. Front Microbiol 2019; 10:956. [PMID: 31139156 PMCID: PMC6527604 DOI: 10.3389/fmicb.2019.00956] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 04/16/2019] [Indexed: 01/23/2023] Open
Abstract
Many studies have examined relationships of microorganisms to geochemical zones in subseafloor sediment. However, responses to selective pressure and patterns of community succession with sediment depth have rarely been examined. Here we use 16S rDNA sequencing to examine the succession of microbial communities at sites in the Indian Ocean and the Bering Sea. The sediment ranges in depth from 0.16 to 332 m below seafloor and in age from 660 to 1,300,000 years. The majority of subseafloor taxonomic diversity is present in the shallowest depth sampled. The best predictor of sequence presence or absence in the oldest sediment is relative abundance in the near-seafloor sediment. This relationship suggests that perseverance of specific taxa into deep, old sediment is primarily controlled by the taxonomic abundance that existed when the sediment was near the seafloor. The operational taxonomic units that dominate at depth comprise a subset of the local seafloor community at each site, rather than a grown-in group of geographically widespread subseafloor specialists. At both sites, most taxa classified as abundant decrease in relative frequency with increasing sediment depth and age. Comparison of community composition to cell counts at the Bering Sea site indicates that the rise of the few dominant taxa in the deep subseafloor community does not require net replication, but might simply result from lower mortality relative to competing taxa on the long timescale of community burial.
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Affiliation(s)
- John B Kirkpatrick
- Graduate School of Oceanography, The University of Rhode Island, Narragansett, RI, United States.,The Evergreen State College, Olympia, WA, United States
| | - Emily A Walsh
- Graduate School of Oceanography, The University of Rhode Island, Narragansett, RI, United States
| | - Steven D'Hondt
- Graduate School of Oceanography, The University of Rhode Island, Narragansett, RI, United States
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Pohlner M, Dlugosch L, Wemheuer B, Mills H, Engelen B, Reese BK. The Majority of Active Rhodobacteraceae in Marine Sediments Belong to Uncultured Genera: A Molecular Approach to Link Their Distribution to Environmental Conditions. Front Microbiol 2019; 10:659. [PMID: 31001232 PMCID: PMC6454203 DOI: 10.3389/fmicb.2019.00659] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/15/2019] [Indexed: 12/21/2022] Open
Abstract
General studies on benthic microbial communities focus on fundamental biogeochemical processes or the most abundant constituents. Thereby, minor fractions such as the Rhodobacteraceae are frequently neglected. Even though this family belongs to the most widely distributed bacteria in the marine environment, their proportion on benthic microbial communities is usually within or below the single digit range. Thus, knowledge on these community members is limited, even though their absolute numbers might exceed those from the pelagic zone by orders of magnitudes. To unravel the distribution and diversity of benthic, metabolically active Rhodobacteraceae, we have now analyzed an already existing library of bacterial 16S rRNA transcripts. The dataset originated from 154 individual sediment samples comprising seven oceanic regions and a broad variety of environmental conditions. Across all samples, a total of 0.7% of all 16S rRNA transcripts was annotated as Rhodobacteraceae. Among those, Sulfitobacter, Paracoccus, and Phaeomarinomonas were the most abundant cultured representatives, but the majority (78%) was affiliated to uncultured family members. To define them, the 45 most abundant Rhodobacteraceae-OTUs assigned as “uncultured” were phylogenetically assembled in new clusters. Their next relatives particularly belonged to different subgroups other than the Roseobacter group, reflecting a large part of the hidden diversity within the benthic Rhodobacteraceae with unknown functions. The general composition of active Rhodobacteraceae communities was found to be specific for the geographical location, exhibiting a decreasing richness with sediment depth. One-third of the Rhodobacteraceae-OTUs significantly responded to the prevailing redox regime, suggesting an adaption to anoxic conditions. A possible approach to predict their physiological properties is to identify the metabolic capabilities of their nearest relatives. Those need to be proven by physiological experiments, as soon an isolate is available. Because many uncultured members of these subgroups likely thrive under anoxic conditions, in future research, a molecular-guided cultivation strategy can be pursued to isolate novel Rhodobacteraceae from sediments.
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Affiliation(s)
- Marion Pohlner
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Leon Dlugosch
- Group "Biology of Geological Processes", Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Bernd Wemheuer
- Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, Australia
| | - Heath Mills
- Rhodium Scientific LLC, San Antonio, TX, United States
| | - Bert Engelen
- Paleomicrobiology Group, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Brandi Kiel Reese
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX, United States
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9
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Nazina TN, Shestakova NM, Semenova EM, Korshunova AV, Kostrukova NK, Tourova TP, Min L, Feng Q, Poltaraus AB. Diversity of Metabolically Active Bacteria in Water-Flooded High-Temperature Heavy Oil Reservoir. Front Microbiol 2017; 8:707. [PMID: 28487680 PMCID: PMC5403907 DOI: 10.3389/fmicb.2017.00707] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/05/2017] [Indexed: 11/30/2022] Open
Abstract
The goal of this work was to study the overall genomic diversity of microorganisms of the Dagang high-temperature oilfield (PRC) and to characterize the metabolically active fraction of these populations. At this water-flooded oilfield, the microbial community of formation water from the near-bottom zone of an injection well where the most active microbial processes of oil degradation occur was investigated using molecular, cultural, radiotracer, and physicochemical techniques. The samples of microbial DNA and RNA from back-flushed water were used to obtain the clone libraries for the 16S rRNA gene and cDNA of 16S rRNA, respectively. The DNA-derived clone libraries were found to contain bacterial and archaeal 16S rRNA genes and the alkB genes encoding alkane monooxygenases similar to those encoded by alkB-geo1 and alkB-geo6 of geobacilli. The 16S rRNA genes of methanogens (Methanomethylovorans, Methanoculleus, Methanolinea, Methanothrix, and Methanocalculus) were predominant in the DNA-derived library of Archaea cloned sequences; among the bacterial sequences, the 16S rRNA genes of members of the genus Geobacillus were the most numerous. The RNA-derived library contained only bacterial cDNA of the 16S rRNA sequences belonging to metabolically active aerobic organotrophic bacteria (Tepidimonas, Pseudomonas, Acinetobacter), as well as of denitrifying (Azoarcus, Tepidiphilus, Calditerrivibrio), fermenting (Bellilinea), iron-reducing (Geobacter), and sulfate- and sulfur-reducing bacteria (Desulfomicrobium, Desulfuromonas). The presence of the microorganisms of the main functional groups revealed by molecular techniques was confirmed by the results of cultural, radioisotope, and geochemical research. Functioning of the mesophilic and thermophilic branches was shown for the microbial food chain of the near-bottom zone of the injection well, which included the microorganisms of the carbon, sulfur, iron, and nitrogen cycles.
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Affiliation(s)
- Tamara N. Nazina
- Laboratory of Petroleum Microbiology, Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of SciencesMoscow, Russia
| | - Natalya M. Shestakova
- Laboratory of Petroleum Microbiology, Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of SciencesMoscow, Russia
| | - Ekaterina M. Semenova
- Laboratory of Petroleum Microbiology, Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of SciencesMoscow, Russia
| | - Alena V. Korshunova
- Laboratory of Petroleum Microbiology, Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of SciencesMoscow, Russia
| | - Nadezda K. Kostrukova
- Laboratory of Petroleum Microbiology, Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of SciencesMoscow, Russia
| | - Tatiana P. Tourova
- Laboratory of Petroleum Microbiology, Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of SciencesMoscow, Russia
| | - Liu Min
- Dagang Oil Field Group Ltd.Tianjin, China
| | | | - Andrey B. Poltaraus
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
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10
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Grossmann L, Beisser D, Bock C, Chatzinotas A, Jensen M, Preisfeld A, Psenner R, Rahmann S, Wodniok S, Boenigk J. Trade‐off between taxon diversity and functional diversity in European lake ecosystems. Mol Ecol 2016; 25:5876-5888. [DOI: 10.1111/mec.13878] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 08/13/2016] [Accepted: 08/16/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Lars Grossmann
- Biodiversity Department and Centre for Water and Environmental Research University of Duisburg‐Essen 45141 Essen Germany
| | - Daniela Beisser
- Biodiversity Department and Centre for Water and Environmental Research University of Duisburg‐Essen 45141 Essen Germany
- Genome Informatics Institute of Human Genetics University of Duisburg‐Essen University Hospital Essen 45122 Essen Germany
| | - Christina Bock
- Biodiversity Department and Centre for Water and Environmental Research University of Duisburg‐Essen 45141 Essen Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology Helmholtz Centre for Environmental Research – UFZ Permoserstr. 15 04318 Leipzig Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Deutscher Platz 5e 04103 Leipzig Germany
| | - Manfred Jensen
- Biodiversity Department and Centre for Water and Environmental Research University of Duisburg‐Essen 45141 Essen Germany
| | - Angelika Preisfeld
- Department of Zoology and Didactics of Biology Bergische Universität Wuppertal 42119 Wuppertal Germany
| | - Roland Psenner
- Institute of Ecology University of Innsbruck Technikerstrasse 25 A‐6020 Innsbruck Austria
| | - Sven Rahmann
- Genome Informatics Institute of Human Genetics University of Duisburg‐Essen University Hospital Essen 45122 Essen Germany
| | - Sabina Wodniok
- Biodiversity Department and Centre for Water and Environmental Research University of Duisburg‐Essen 45141 Essen Germany
| | - Jens Boenigk
- Biodiversity Department and Centre for Water and Environmental Research University of Duisburg‐Essen 45141 Essen Germany
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11
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Analysis of Low-Biomass Microbial Communities in the Deep Biosphere. ADVANCES IN APPLIED MICROBIOLOGY 2016; 95:149-78. [PMID: 27261783 DOI: 10.1016/bs.aambs.2016.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Over the past few decades, the subseafloor biosphere has been explored by scientific ocean drilling to depths of about 2.5km below the seafloor. Although organic-rich anaerobic sedimentary habitats in the ocean margins harbor large numbers of microbial cells, microbial populations in ultraoligotrophic aerobic sedimentary habitats in the open ocean gyres are several orders of magnitude less abundant. Despite advances in cultivation-independent molecular ecological techniques, exploring the low-biomass environment remains technologically challenging, especially in the deep subseafloor biosphere. Reviewing the historical background of deep-biosphere analytical methods, the importance of obtaining clean samples and tracing contamination, as well as methods for detecting microbial life, technological aspects of molecular microbiology, and detecting subseafloor metabolic activity will be discussed.
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12
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Nunoura T, Takaki Y, Shimamura S, Kakuta J, Kazama H, Hirai M, Masui N, Tomaru H, Morono Y, Imachi H, Inagaki F, Takai K. Variance and potential niche separation of microbial communities in subseafloor sediments off Shimokita Peninsula, Japan. Environ Microbiol 2015; 18:1889-906. [PMID: 26486095 DOI: 10.1111/1462-2920.13096] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 08/21/2015] [Accepted: 10/05/2015] [Indexed: 01/23/2023]
Abstract
Subseafloor pelagic sediments with high concentrations of organic matter form habitats for diverse microorganisms. Here, we determined depth profiles of genes for SSU rRNA, mcrA, dsrA and amoA from just beneath the seafloor to 363.3 m below the seafloor (mbsf) using core samples obtained from the forearc basin off the Shimokita Peninsula. The molecular profiles were combined with data on lithostratigraphy, depositional age, sedimentation rate and pore-water chemistry. The SSU rRNA gene tag structure and diversity changed at around the sulfate-methane transition zone (SMTZ), whereas the profiles varied further with depth below the SMTZ, probably in connection with the variation in pore-water chemistry. The depth profiles of diversity and abundance of dsrA, a key gene for sulfate reduction, suggested the possible niche separations of sulfate-reducing populations, even below the SMTZ. The diversity and abundance patterns of mcrA, a key gene for methanogenesis/anaerobic methanotrophy, suggested a stratified distribution and separation of anaerobic methanotrophy and hydrogenotrophic or methylotrophic methanogensis below the SMTZ. This study provides novel insights into the relationships between the composition and function of microbial communities and the chemical environment in the nutrient-rich continental margin subseafloor sediments, which may result in niche separation and variability in subseafloor microbial populations.
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Affiliation(s)
- Takuro Nunoura
- Marine Functional Biology Group, Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoshihiro Takaki
- Marine Functional Biology Group, Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.,Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Shigeru Shimamura
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Jungo Kakuta
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Hiromi Kazama
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Miho Hirai
- Marine Functional Biology Group, Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Noriaki Masui
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, Japan
| | - Hitoshi Tomaru
- Department of Earth Sciences, Chiba University, Chiba, Inageku, Japan
| | - Yuki Morono
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, Japan
| | - Hiroyuki Imachi
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, Japan
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
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Torres ME, Cox T, Hong WL, McManus J, Sample JC, Destrigneville C, Gan HM, Gan HY, Moreau JW. Crustal fluid and ash alteration impacts on the biosphere of Shikoku Basin sediments, Nankai Trough, Japan. GEOBIOLOGY 2015; 13:562-580. [PMID: 26081483 DOI: 10.1111/gbi.12146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 05/09/2015] [Indexed: 06/04/2023]
Abstract
We present data from sediment cores collected from IODP Site C0012 in the Shikoku Basin. Our site lies at the Nankai Trough, just prior to subduction of the 19 Ma Philippine Sea plate. Our data indicate that the sedimentary package is undergoing multiple routes of electron transport and that these differing pathways for oxidant supply generate a complex array of metabolic routes and microbial communities involved in carbon cycling. Numerical simulations matched to pore water data document that Ca(2+) and Cl(1-) are largely supplied via diffusion from a high-salinity (44.5 psu) basement fluid, which supports the presence of halophile Archean communities within the deep sedimentary package that are not observed in shallow sediments. Sulfate supply from basement supports anaerobic oxidation of methane (AOM) at a rate of ~0.2 pmol cm(-3) day(-1) at ~400 mbsf. We also note the disappearance of δ-Proteobacteria at 434 mbsf, coincident with the maximum in methane concentration, and their reappearance at 463 mbsf, coinciding with the observed deeper increase in sulfate concentration toward the basement. We did not, however, find ANME representatives in any of the samples analyzed (from 340 to 463 mbsf). The lack of ANME may be due to an overshadowing effect from the more dominant archaeal phylotypes or may indicate involvement of unknown groups of archaea in AOM (i.e., unclassified Euryarchaeota). In addition to the supply of sulfate from a basement aquifer, the deep biosphere at this site is also influenced by an elevated supply of reactive iron (up to 143 μmol g(-1)) and manganese (up to 20 μmol g(-1)). The effect of these metal oxides on the sulfur cycle is inferred from an accompanying sulfur isotope fractionation much smaller than expected from traditional sulfate-reducing pathways. The detection of the manganese- and iron-reducer γ-Proteobacteria Alteromonas at 367 mbsf is consistent with these geochemical inferences.
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Affiliation(s)
- M E Torres
- CEOAS, Oregon State University, Corvallis, OR, USA
| | - T Cox
- School of Earth Sciences, University of Melbourne, Parkville, Vic., Australia
| | - W-L Hong
- CEOAS, Oregon State University, Corvallis, OR, USA
| | - J McManus
- CEOAS, Oregon State University, Corvallis, OR, USA
- Department of Geosciences, University of Akron, Akron, OH, USA
| | - J C Sample
- School of Earth Sciences & Environmental Sustainability, Northern Arizona University, Flagstaff, AZ, USA
| | | | - H M Gan
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia
| | - H Y Gan
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia
| | - J W Moreau
- School of Earth Sciences, University of Melbourne, Parkville, Vic., Australia
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Miyazaki M, Sakai S, Yamanaka Y, Saito Y, Takai K, Imachi H. Spirochaeta psychrophila sp. nov., a psychrophilic spirochaete isolated from subseafloor sediment, and emended description of the genus Spirochaeta. Int J Syst Evol Microbiol 2014; 64:2798-2804. [DOI: 10.1099/ijs.0.062463-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An obligately anaerobic, psychrophilic spirochaete, strain MO-SPC1T, was isolated from a methanogenic microbial community grown in a continuous-flow bioreactor. Originally, this community was obtained from subseafloor sediments off the Shimokita Peninsula of Japan in the north-western Pacific Ocean. The cells were motile, Gram-stain-negative, helical, 0.25–0.55×3.6–15 µm, with a wavelength of approximately 0.5–0.6 µm. Strain MO-SPC1T grew at 0–18 °C (optimally at 15 °C), at pH 6.0–7.5 (optimally at pH 6.8–7.0) and in 20–70 g NaCl l−1 (optimally at 30–40 NaCl l−1). The strain grew chemo-organotrophically with mono-, di- and polysaccharides. The major end products of glucose fermentation were acetate, ethanol, hydrogen and carbon dioxide. The abundant polar lipids of strain MO-SPC1T were diphosphatidylglycerol, phosphatidylglycerol, unknown phospholipids and an unknown lipid. The major cellular fatty acids (>5 % of the total) were C14 : 0, C16 : 0, iso-C13 : 0, iso-C14 : 0, iso-C15 : 0, anteiso-C13 : 0 and anteiso-C15 : 0. To the best of our knowledge, this is the first report of the fatty acids iso-C13 : 0 and anteiso-C13 : 0 from a species of the genus
Spirochaeta
. Isoprenoid quinones were not found. The G+C content of the genomic DNA was 39.8 mol%. 16S rRNA gene sequence-based phylogenetic analysis showed that strain MO-SPC1T was affiliated with the genus
Spirochaeta
, and its closest relatives were
Spirochaeta isovalerica
MA-2T (95.6 % sequence identity) and
Spirochaeta litoralis
R1T (89.4 %). Based on its phenotypic characteristics and phylogenetic traits, strain MO-SPC1T is placed in a separate taxon at the level of a novel species within the genus
Spirochaeta,
for which the name Spirochaeta psychrophila sp. nov. is proposed, reflecting its true psychrophilic physiology. The type strain is MO-SPC1T ( = JCM 17280T = DSM 23951T). To our knowledge, this is the first report of an isolate of the phylum
Spirochaetes
from a deep-sea sedimentary environment, and of an obligately psychrophilic nature.
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Affiliation(s)
- Masayuki Miyazaki
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Sanae Sakai
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Yuko Yamanaka
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Yumi Saito
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Ken Takai
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
| | - Hiroyuki Imachi
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
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15
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Kawai M, Futagami T, Toyoda A, Takaki Y, Nishi S, Hori S, Arai W, Tsubouchi T, Morono Y, Uchiyama I, Ito T, Fujiyama A, Inagaki F, Takami H. High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes. Front Microbiol 2014; 5:80. [PMID: 24624126 PMCID: PMC3939436 DOI: 10.3389/fmicb.2014.00080] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 02/13/2014] [Indexed: 02/01/2023] Open
Abstract
Marine subsurface sediments on the Pacific margin harbor diverse microbial communities even at depths of several hundreds meters below the seafloor (mbsf) or more. Previous PCR-based molecular analysis showed the presence of diverse reductive dehalogenase gene (rdhA) homologs in marine subsurface sediment, suggesting that anaerobic respiration of organohalides is one of the possible energy-yielding pathways in the organic-rich sedimentary habitat. However, primer-independent molecular characterization of rdhA has remained to be demonstrated. Here, we studied the diversity and frequency of rdhA homologs by metagenomic analysis of five different depth horizons (0.8, 5.1, 18.6, 48.5, and 107.0 mbsf) at Site C9001 off the Shimokita Peninsula of Japan. From all metagenomic pools, remarkably diverse rdhA-homologous sequences, some of which are affiliated with novel clusters, were observed with high frequency. As a comparison, we also examined frequency of dissimilatory sulfite reductase genes (dsrAB), key functional genes for microbial sulfate reduction. The dsrAB were also widely observed in the metagenomic pools whereas the frequency of dsrAB genes was generally smaller than that of rdhA-homologous genes. The phylogenetic composition of rdhA-homologous genes was similar among the five depth horizons. Our metagenomic data revealed that subseafloor rdhA homologs are more diverse than previously identified from PCR-based molecular studies. Spatial distribution of similar rdhA homologs across wide depositional ages indicates that the heterotrophic metabolic processes mediated by the genes can be ecologically important, functioning in the organic-rich subseafloor sedimentary biosphere.
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Affiliation(s)
- Mikihiko Kawai
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Nankoku, Japan ; Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan
| | - Taiki Futagami
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Nankoku, Japan ; Department of Bioscience and Biotechnology, Kyushu University Fukuoka, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, Center for Information Biology, National Institute of Genetics Mishima, Japan
| | - Yoshihiro Takaki
- Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan
| | - Shinro Nishi
- Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan
| | - Sayaka Hori
- Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan
| | - Wataru Arai
- Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan
| | - Taishi Tsubouchi
- Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan
| | - Yuki Morono
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Nankoku, Japan ; Geobio-Engineering and Technology Group, Submarine Resources Research Project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Nankoku, Japan
| | - Ikuo Uchiyama
- National Institute for Basic Biology, National Institutes of Natural Sciences Okazaki, Japan ; Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies Okazaki, Japan
| | - Takehiko Ito
- Department of Biological Sciences, Tokyo Institute of Technology Yokohama, Japan
| | - Asao Fujiyama
- Comparative Genomics Laboratory, Center for Information Biology, National Institute of Genetics Mishima, Japan
| | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Nankoku, Japan ; Geobio-Engineering and Technology Group, Submarine Resources Research Project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Nankoku, Japan
| | - Hideto Takami
- Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan
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16
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Hot-alkaline DNA extraction method for deep-subseafloor archaeal communities. Appl Environ Microbiol 2014; 80:1985-94. [PMID: 24441163 DOI: 10.1128/aem.04150-13] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A prerequisite for DNA-based microbial community analysis is even and effective cell disruption for DNA extraction. With a commonly used DNA extraction kit, roughly two-thirds of subseafloor sediment microbial cells remain intact on average (i.e., the cells are not disrupted), indicating that microbial community analyses may be biased at the DNA extraction step, prior to subsequent molecular analyses. To address this issue, we standardized a new DNA extraction method using alkaline treatment and heating. Upon treatment with 1 M NaOH at 98°C for 20 min, over 98% of microbial cells in subseafloor sediment samples collected at different depths were disrupted. However, DNA integrity tests showed that such strong alkaline and heat treatment also cleaved DNA molecules into short fragments that could not be amplified by PCR. Subsequently, we optimized the alkaline and temperature conditions to minimize DNA fragmentation and retain high cell disruption efficiency. The best conditions produced a cell disruption rate of 50 to 80% in subseafloor sediment samples from various depths and retained sufficient DNA integrity for amplification of the complete 16S rRNA gene (i.e., ∼1,500 bp). The optimized method also yielded higher DNA concentrations in all samples tested compared with extractions using a conventional kit-based approach. Comparative molecular analysis using real-time PCR and pyrosequencing of bacterial and archaeal 16S rRNA genes showed that the new method produced an increase in archaeal DNA and its diversity, suggesting that it provides better analytical coverage of subseafloor microbial communities than conventional methods.
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Orcutt BN, Larowe DE, Biddle JF, Colwell FS, Glazer BT, Reese BK, Kirkpatrick JB, Lapham LL, Mills HJ, Sylvan JB, Wankel SD, Wheat CG. Microbial activity in the marine deep biosphere: progress and prospects. Front Microbiol 2013; 4:189. [PMID: 23874326 PMCID: PMC3708129 DOI: 10.3389/fmicb.2013.00189] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Accepted: 06/20/2013] [Indexed: 11/17/2022] Open
Abstract
The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists—all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these “extreme” environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) “theme team” on microbial activity (www.darkenergybiosphere.org).
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Affiliation(s)
- Beth N Orcutt
- Bigelow Laboratory for Ocean Sciences East Boothbay, ME, USA
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Teske A, Biddle JF, Edgcomb VP, Schippers A. Deep subsurface microbiology: a guide to the research topic papers. Front Microbiol 2013; 4:122. [PMID: 23720656 PMCID: PMC3655269 DOI: 10.3389/fmicb.2013.00122] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 04/30/2013] [Indexed: 11/13/2022] Open
Affiliation(s)
- Andreas Teske
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
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Orsi W, Biddle JF, Edgcomb V. Deep sequencing of subseafloor eukaryotic rRNA reveals active Fungi across marine subsurface provinces. PLoS One 2013; 8:e56335. [PMID: 23418556 PMCID: PMC3572030 DOI: 10.1371/journal.pone.0056335] [Citation(s) in RCA: 147] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 01/08/2013] [Indexed: 02/01/2023] Open
Abstract
The deep marine subsurface is a vast habitat for microbial life where cells may live on geologic timescales. Because DNA in sediments may be preserved on long timescales, ribosomal RNA (rRNA) is suggested to be a proxy for the active fraction of a microbial community in the subsurface. During an investigation of eukaryotic 18S rRNA by amplicon pyrosequencing, unique profiles of Fungi were found across a range of marine subsurface provinces including ridge flanks, continental margins, and abyssal plains. Subseafloor fungal populations exhibit statistically significant correlations with total organic carbon (TOC), nitrate, sulfide, and dissolved inorganic carbon (DIC). These correlations are supported by terminal restriction length polymorphism (TRFLP) analyses of fungal rRNA. Geochemical correlations with fungal pyrosequencing and TRFLP data from this geographically broad sample set suggests environmental selection of active Fungi in the marine subsurface. Within the same dataset, ancient rRNA signatures were recovered from plants and diatoms in marine sediments ranging from 0.03 to 2.7 million years old, suggesting that rRNA from some eukaryotic taxa may be much more stable than previously considered in the marine subsurface.
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Affiliation(s)
- William Orsi
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America.
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