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Liu H, Cai X, Luo K, Chen S, Su M, Lu J. Microbial Diversity, Community Turnover, and Putative Functions in Submarine Canyon Sediments under the Action of Sedimentary Geology. Microbiol Spectr 2023; 11:e0421022. [PMID: 36802161 PMCID: PMC10100816 DOI: 10.1128/spectrum.04210-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 01/31/2023] [Indexed: 02/23/2023] Open
Abstract
Sampling challenges in deep-sea ecosystems lead to a lack of knowledge about the distribution of microbes in different submarine canyons. To study microbial diversity and community turnover under different ecological processes, we performed 16S/18S rRNA gene amplicon sequencing for sediment samples from a submarine canyon in the South China Sea. Bacteria, archaea, and eukaryotes made up 57.94% (62 phyla), 41.04% (12 phyla), and 1.02% (4 phyla) of the sequences, respectively. Thaumarchaeota, Planctomycetota, Proteobacteria, Nanoarchaeota, and Patescibacteria are the five most abundant phyla. Heterogeneous community composition was mainly observed in vertical profiles rather than horizontal geographic locations, and microbial diversity in the surface layer was much lower than that in deep layers. According to the null model tests, homogeneous selection dominated community assembly within each sediment layer, whereas heterogeneous selection and dispersal limitation dominated community assembly between distant layers. Different sedimentation processes of sediments, i.e., rapid deposition caused by turbidity currents or slow sedimentation, seem to be primarily responsible for these vertical variations. Finally, functional annotation through shotgun-metagenomic sequencing found that glycosyl transferases and glycoside hydrolases are the most abundant carbohydrate-active enzyme categories. The most likely expressed sulfur cycling pathways include assimilatory sulfate reduction, the link between inorganic and organic sulfur transformation, and organic sulfur transformation, while the potentially activated methane cycling pathways include aceticlastic methanogenesis and aerobic and anaerobic oxidation of methane. Overall, our study revealed high levels of microbial diversity and putative functions in canyon sediments and the important influence of sedimentary geology on microbial community turnover between vertical sediment layers. IMPORTANCE Deep-sea microbes have received growing attention due to their contribution to biogeochemical cycles and climate change. However, related research lags due to the difficulty of collecting samples. Based on our previous study, which revealed the formation of sediments under the dual action of turbidity currents and seafloor obstacles in a submarine canyon in the South China Sea, this interdisciplinary research provides new insights into how sedimentary geology influences microbial community assembly in sediments. We proposed some uncommon or new findings, including the following: (i) microbial diversity was much lower on the surface than in deeper layers (ii) archaea and bacteria dominated the surface and deep layers, respectively; (iii) sedimentary geology played key roles in vertical community turnover; and (iv) the microbes have great potential to catalyze sulfur, carbon, and methane cycling. This study may lead to extensive discussion of the assembly and function of deep-sea microbial communities in the context of geology.
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Affiliation(s)
- Hualin Liu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Xueyu Cai
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Kunwen Luo
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Sihan Chen
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Ming Su
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou Guangdong, China
| | - Jianguo Lu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou Guangdong, China
- Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, China
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2
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Fan S, Wang M, Ding W, Li YX, Zhang YZ, Zhang W. Scientific and technological progress in the microbial exploration of the hadal zone. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:127-137. [PMID: 37073349 PMCID: PMC10077178 DOI: 10.1007/s42995-021-00110-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 05/11/2021] [Indexed: 05/03/2023]
Abstract
The hadal zone is the deepest point in the ocean with a depth that exceeds 6000 m. Exploration of the biological communities in hadal zone began in the 1950s (the first wave of hadal exploration) and substantial advances have been made since the turn of the twenty-first century (the second wave of hadal exploration), resulting in a focus on the hadal sphere as a research hotspot because of its unique physical and chemical conditions. A variety of prokaryotes are found in the hadal zone. The mechanisms used by these prokaryotes to manage the high hydrostatic pressures and acquire energy from the environment are of substantial interest. Moreover, the symbioses between microbes and hadal animals have barely been studied. In addition, equipment has been developed that can now mimic hadal environments in the laboratory and allow cultivation of microbes under simulated in situ pressure. This review provides a brief summary of recent progress in the mechanisms by which microbes adapt to high hydrostatic pressures, manage limited energy resources and coexist with animals in the hadal zone, as well as technical developments in the exploration of hadal microbial life.
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Affiliation(s)
- Shen Fan
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Meng Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Wei Ding
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Yong-Xin Li
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237 China
| | - Weipeng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
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3
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Xue CX, Lin H, Zhu XY, Liu J, Zhang Y, Rowley G, Todd JD, Li M, Zhang XH. DiTing: A Pipeline to Infer and Compare Biogeochemical Pathways From Metagenomic and Metatranscriptomic Data. Front Microbiol 2021; 12:698286. [PMID: 34408730 PMCID: PMC8367434 DOI: 10.3389/fmicb.2021.698286] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/05/2021] [Indexed: 12/15/2022] Open
Abstract
Metagenomics and metatranscriptomics are powerful methods to uncover key micro-organisms and processes driving biogeochemical cycling in natural ecosystems. Databases dedicated to depicting biogeochemical pathways (for example, metabolism of dimethylsulfoniopropionate (DMSP), which is an abundant organosulfur compound) from metagenomic/metatranscriptomic data are rarely seen. Additionally, a recognized normalization model to estimate the relative abundance and environmental importance of pathways from metagenomic and metatranscriptomic data has not been organized to date. These limitations impact the ability to accurately relate key microbial-driven biogeochemical processes to differences in environmental conditions. Thus, an easy-to-use, specialized tool that infers and visually compares the potential for biogeochemical processes, including DMSP cycling, is urgently required. To solve these issues, we developed DiTing, a tool wrapper to infer and compare biogeochemical pathways among a set of given metagenomic or metatranscriptomic reads in one step, based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) and a manually created DMSP cycling gene database. Accurate and specific formulae for over 100 pathways were developed to calculate their relative abundance. Output reports detail the relative abundance of biogeochemical pathways in both text and graphical format. DiTing was applied to simulated metagenomic data and resulted in consistent genetic features of simulated benchmark genomic data. Subsequently, when applied to natural metagenomic and metatranscriptomic data from hydrothermal vents and the Tara Ocean project, the functional profiles predicted by DiTing were correlated with environmental condition changes. DiTing can now be confidently applied to wider metagenomic and metatranscriptomic datasets, and it is available at https://github.com/xuechunxu/DiTing.
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Affiliation(s)
- Chun-Xu Xue
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Heyu Lin
- School of Earth Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Xiao-Yu Zhu
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Jiwen Liu
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yunhui Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Gary Rowley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Jonathan D. Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
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4
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Peoples LM, Kyaw TS, Ugalde JA, Mullane KK, Chastain RA, Yayanos AA, Kusube M, Methé BA, Bartlett DH. Distinctive gene and protein characteristics of extremely piezophilic Colwellia. BMC Genomics 2020; 21:692. [PMID: 33023469 PMCID: PMC7542103 DOI: 10.1186/s12864-020-07102-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 09/24/2020] [Indexed: 01/05/2023] Open
Abstract
Background The deep ocean is characterized by low temperatures, high hydrostatic pressures, and low concentrations of organic matter. While these conditions likely select for distinct genomic characteristics within prokaryotes, the attributes facilitating adaptation to the deep ocean are relatively unexplored. In this study, we compared the genomes of seven strains within the genus Colwellia, including some of the most piezophilic microbes known, to identify genomic features that enable life in the deep sea. Results Significant differences were found to exist between piezophilic and non-piezophilic strains of Colwellia. Piezophilic Colwellia have a more basic and hydrophobic proteome. The piezophilic abyssal and hadal isolates have more genes involved in replication/recombination/repair, cell wall/membrane biogenesis, and cell motility. The characteristics of respiration, pilus generation, and membrane fluidity adjustment vary between the strains, with operons for a nuo dehydrogenase and a tad pilus only present in the piezophiles. In contrast, the piezosensitive members are unique in having the capacity for dissimilatory nitrite and TMAO reduction. A number of genes exist only within deep-sea adapted species, such as those encoding d-alanine-d-alanine ligase for peptidoglycan formation, alanine dehydrogenase for NADH/NAD+ homeostasis, and a SAM methyltransferase for tRNA modification. Many of these piezophile-specific genes are in variable regions of the genome near genomic islands, transposases, and toxin-antitoxin systems. Conclusions We identified a number of adaptations that may facilitate deep-sea radiation in members of the genus Colwellia, as well as in other piezophilic bacteria. An enrichment in more basic and hydrophobic amino acids could help piezophiles stabilize and limit water intrusion into proteins as a result of high pressure. Variations in genes associated with the membrane, including those involved in unsaturated fatty acid production and respiration, indicate that membrane-based adaptations are critical for coping with high pressure. The presence of many piezophile-specific genes near genomic islands highlights that adaptation to the deep ocean may be facilitated by horizontal gene transfer through transposases or other mobile elements. Some of these genes are amenable to further study in genetically tractable piezophilic and piezotolerant deep-sea microorganisms.
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Affiliation(s)
- Logan M Peoples
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093-0202, USA.,Flathead Lake Biological Station, University of Montana, Polson, MT, 59860, USA
| | - Than S Kyaw
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093-0202, USA
| | - Juan A Ugalde
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Kelli K Mullane
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093-0202, USA
| | - Roger A Chastain
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093-0202, USA
| | - A Aristides Yayanos
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093-0202, USA
| | - Masataka Kusube
- Department of Material Science, National Institute of Technology, Wakayama College, 77 Noshima, Nada-cho, Gobo, Wakayama, 644-0023, Japan
| | - Barbara A Methé
- Center for Microbiome and Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Douglas H Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093-0202, USA.
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5
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Chen M, Song Y, Feng X, Tang K, Jiao N, Tian J, Zhang Y. Genomic Characteristics and Potential Metabolic Adaptations of Hadal Trench Roseobacter and Alteromonas Bacteria Based on Single-Cell Genomics Analyses. Front Microbiol 2020; 11:1739. [PMID: 32793171 PMCID: PMC7393951 DOI: 10.3389/fmicb.2020.01739] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 07/03/2020] [Indexed: 11/30/2022] Open
Abstract
Heterotrophic bacteria such as those from the Roseobacter group and genus Alteromonas dominate the hadal zones of oceans; however, we know little about the genomic characteristics and potential metabolic adaptations of hadal trench-dwelling bacteria. Here, we report multiple single amplified genomes (SAGs) belonging to Roseobacter and Alteromonas, recovered from the hadal zone of the Mariana Trench. While phylogenetic analyses show that these hadal SAGs cluster with their surface relatives, an analysis of genomic recruitment indicates that they have higher relative abundances in the hadal zone of the Mariana Trench. Comparative genomic analyses between the hadal SAGs and reference genomes of closely related shallow-water relatives indicate that genes involved in the mobilome (prophages and transposons) are overrepresented among the unique genes of the hadal Roseobacter and Alteromonas SAGs; the functional proteins encoded by this category of genes also shows higher amino acid sequence variation than those encoded by other gene sets within the Roseobacter SAGs. We also found that genes involved in cell wall/membrane/envelope biogenesis, transcriptional regulation, and metal transport may be important for the adaptation of hadal Roseobacter and Alteromonas lineages. These results imply that the modification of cell surface-related proteins and transporters is the major direction of genomic evolution in Roseobacter and Alteromonas bacteria adapting to the hadal environment, and that prophages and transposons may be the key factors driving this process.
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Affiliation(s)
- Mingming Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Yu Song
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Xiaoyuan Feng
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Jiwei Tian
- Physical Oceanography Laboratory, Ocean University of China, Qingdao, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
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6
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Xaxiri NA, Nikouli E, Berillis P, Kormas KA. Bacterial biofilm development during experimental degradation of Melicertus kerathurus exoskeleton in seawater. AIMS Microbiol 2019; 4:397-412. [PMID: 31294223 PMCID: PMC6604942 DOI: 10.3934/microbiol.2018.3.397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 05/29/2018] [Indexed: 11/28/2022] Open
Abstract
Chitinolytic bacteria are widespread in marine and terrestrial environment, and this is rather a reflection of their principle growth substrate's ubiquity, chitin, in our planet. In this paper, we investigated the development of naturally occurring bacterial biofilms on the exoskeleton of the shrimp Melicertus kerathurus during its degradation in sea water. During a 12-day experiment with exoskeleton fragments in batch cultures containing only sea water as the growth medium at 18 °C in darkness, we analysed the formation and succession of biofilms by scanning electron microscopy and 16S rRNA gene diversity by next generation sequencing. Bacteria belonging to the γ- and α-Proteobacteria and Bacteroidetes showed marked (less or more than 10%) changes in their relative abundance from the beginning of the experiment. These bacterial taxa related to known chitinolytic bacteria were the Pseudolateromonas porphyrae, Halomonasaquamarina, Reinekea aestuarii, Colwellia asteriadis and Vibrio crassostreae. These bacteria could be considered as appropriate candidates for the degradation of chitinous crustacean waste from the seafood industry as they dominated in the biofilms developed on the shrimp's exoskeleton in natural sea water with no added substrates and the degradation of the shrimp exoskeleton was also evidenced.
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Affiliation(s)
- Nikolina-Alexandra Xaxiri
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
| | - Eleni Nikouli
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
| | - Panagiotis Berillis
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
| | - Konstantinos Ar Kormas
- Department of Ichthyology & Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
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7
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Zhang X, Xu W, Liu Y, Cai M, Luo Z, Li M. Metagenomics Reveals Microbial Diversity and Metabolic Potentials of Seawater and Surface Sediment From a Hadal Biosphere at the Yap Trench. Front Microbiol 2018; 9:2402. [PMID: 30369913 PMCID: PMC6194347 DOI: 10.3389/fmicb.2018.02402] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/19/2018] [Indexed: 11/13/2022] Open
Abstract
Hadal biosphere represents the deepest part of the ocean with water depth >6,000 m. Accumulating evidence suggests the existence of unique microbial communities dominated by heterotrophic processes in this environment. However, investigations of the microbial diversity and their metabolic potentials are limited because of technical constraints for sample collection. Here, we provide a detailed metagenomic analysis of three seawater samples at water depths 5,000-6,000 m below sea level (mbsl) and three surface sediment samples at water depths 4,435-6,578 mbsl at the Yap Trench of the western Pacific. Distinct microbial community compositions were observed with the dominance of Gammaproteobacteria in seawater and Thaumarchaeota in surface sediment. Comparative analysis of the genes involved in carbon, nitrogen and sulfur metabolisms revealed that heterotrophic processes (i.e., degradation of carbohydrates, hydrocarbons, and aromatics) are the most common microbial metabolisms in the seawater, while chemolithoautotrophic metabolisms such as ammonia oxidation with the HP/HB cycle for CO2 fixation probably dominated the surface sediment communities of the Yap Trench. Furthermore, abundant genes involved in stress response and metal resistance were both detected in the seawater and sediments, thus the enrichment of metal resistance genes is further hypothesized to be characteristic of the hadal microbial communities. Overall, this study sheds light on the metabolic versatility of microorganisms in the Yap Trench, their roles in carbon, nitrogen, and sulfur biogeochemical cycles, and how they have adapted to this unique hadal environment.
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Affiliation(s)
- Xinxu Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China
| | - Yang Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Mingwei Cai
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Zhuhua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
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Xu Z, Wang M, Wu W, Li Y, Liu Q, Han Y, Jiang Y, Shao H, McMinn A, Liu H. Vertical Distribution of Microbial Eukaryotes From Surface to the Hadal Zone of the Mariana Trench. Front Microbiol 2018; 9:2023. [PMID: 30210485 PMCID: PMC6120995 DOI: 10.3389/fmicb.2018.02023] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 08/09/2018] [Indexed: 12/20/2022] Open
Abstract
Marine microbial eukaryotes are ubiquitous, comprised of phylogenetically diverse groups and play key roles in microbial food webs and global biogeochemical cycling. However, their vertical distribution in the deep sea has received little attention. In this study, we investigated the composition and diversity of the eukaryotes of both 0.2–3 μm and >3 μm size fractions from the surface to the hadal zone (8727 m) of the Mariana Trench using Illumina MiSeq sequencing for the 18S rDNA. The microbial eukaryotic community structure differed substantially across size fractions and depths. Operational taxonomic unit (OTU) richness in the >3 μm fraction was higher than that in the 0.2–3 μm fraction at the same depth. For the 0.2–3 μm fraction, sequences of Retaria (Rhizaria) were most abundant in the surface water (53.5%). Chrysophyceae (Stramenopiles) sequences dominated mostly in the samples from water depths below 1795 m. For the >3 μm fraction, sequences of Dinophyceae (Alveolata) were most abundant in surface waters (49.3%) and remained a significant proportion of total sequences at greater depths (9.8%, on average). Retaria sequences were abundant in samples of depths ≥1000 m. Amoebozoa and Apusozoa sequences were enriched in the hadal sample, comprising 38 and 20.4% of total sequences, respectively. Fungi (Opisthokonta) sequences were most abundant at 1759 m in both size fractions. Strong positive associations were found between Syndiniales (mainly MALV-I and MALV-II) and Retaria while negative associations were shown between MALV-II and Fungi in a co-occurrence analysis. This study compared the community structure of microbial eukaryotes in different zones in the deep sea and identified a distinct hadal community in the larger size fraction, suggesting the uniqueness of the eukaryotes in the biosphere in the Mariana Trench.
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Affiliation(s)
- Zhimeng Xu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Min Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Wenxue Wu
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Yifan Li
- Institute for Geophysics and Meteorology, University of Cologne, Cologne, Germany
| | - Qian Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuye Han
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yong Jiang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Hongbing Shao
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Andrew McMinn
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Hongbin Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
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9
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Peoples LM, Donaldson S, Osuntokun O, Xia Q, Nelson A, Blanton J, Allen EE, Church MJ, Bartlett DH. Vertically distinct microbial communities in the Mariana and Kermadec trenches. PLoS One 2018; 13:e0195102. [PMID: 29621268 PMCID: PMC5886532 DOI: 10.1371/journal.pone.0195102] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/17/2018] [Indexed: 01/13/2023] Open
Abstract
Hadal trenches, oceanic locations deeper than 6,000 m, are thought to have distinct microbial communities compared to those at shallower depths due to high hydrostatic pressures, topographical funneling of organic matter, and biogeographical isolation. Here we evaluate the hypothesis that hadal trenches contain unique microbial biodiversity through analyses of the communities present in the bottom waters of the Kermadec and Mariana trenches. Estimates of microbial protein production indicate active populations under in situ hydrostatic pressures and increasing adaptation to pressure with depth. Depth, trench of collection, and size fraction are important drivers of microbial community structure. Many putative hadal bathytypes, such as members related to the Marinimicrobia, Rhodobacteraceae, Rhodospirilliceae, and Aquibacter, are similar to members identified in other trenches. Most of the differences between the two trench microbiomes consists of taxa belonging to the Gammaproteobacteria whose distributions extend throughout the water column. Growth and survival estimates of representative isolates of these taxa under deep-sea conditions suggest that some members may descend from shallower depths and exist as a potentially inactive fraction of the hadal zone. We conclude that the distinct pelagic communities residing in these two trenches, and perhaps by extension other trenches, reflect both cosmopolitan hadal bathytypes and ubiquitous genera found throughout the water column.
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Affiliation(s)
- Logan M. Peoples
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of America
| | - Sierra Donaldson
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of America
| | - Oladayo Osuntokun
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of America
| | - Qing Xia
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of America
- Department of Soil Science, North Carolina State University, Raleigh, NC, United States of America
| | - Alex Nelson
- Center for Microbial Oceanography: Research and Education, C-MORE Hale, University of Hawaiʻi at Mānoa, Honolulu, HI, United States of America
| | - Jessica Blanton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of America
| | - Eric E. Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of America
| | - Matthew J. Church
- Center for Microbial Oceanography: Research and Education, C-MORE Hale, University of Hawaiʻi at Mānoa, Honolulu, HI, United States of America
- Flathead Lake Biological Station, University of Montana, Polson, MT, United States of America
| | - Douglas H. Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of America
- * E-mail:
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10
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Li Y, Jing H, Xia X, Cheung S, Suzuki K, Liu H. Metagenomic Insights Into the Microbial Community and Nutrient Cycling in the Western Subarctic Pacific Ocean. Front Microbiol 2018; 9:623. [PMID: 29670596 PMCID: PMC5894113 DOI: 10.3389/fmicb.2018.00623] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 03/19/2018] [Indexed: 01/05/2023] Open
Abstract
The composition and metabolic functions of prokaryotic communities in the western subarctic Pacific (WSP), where strong mixing of waters from the Sea of Okhotsk and the East Kamchatka Current result in transfer to the Oyashio Current, were investigated using a shotgun metagenome sequencing approach. Functional metabolic genes related to nutrient cycling of nitrogen, sulfur, carbohydrates, iron and amino acids were differently distributed between the surface and deep waters of the WSP. Genes related to nitrogen metabolism were mainly found in deep waters, where Thaumarchaeaota, Sphingomonadales, and Pseudomonadales were closely associated and performing important roles in ammonia oxidation, assimilatory nitrate reduction, and dissimilatory nitrate reduction processes, respectively. In addition, orders affiliated to Spingobacteria and Alphaproteobacteria were crucial for sulfate reduction and abundant at 3000 m, whereas orders affiliated to Gammaproteobacteria, which harbored the most sulfate reduction genes, were abundant at 1000 m. Additionally, when compared with the East Kamchatka Current, the prokaryotes in the Oyashio Current were likely to consume more energy for synthesizing cellular components. Also, genes encoding iron transport and siderophore biosynthesis proteins were in low abundance, indicating that the iron was not a limiting factor in the Oyashio current. In contrast, in the East Kamchatka Current, prokaryotes were more likely to directly utilize the amino acids and absorb iron from the environment. Overall, our data indicated that the transformation from the East Kamchatka Current to the Oyashio Current reshapes not only the composition of microbial community, but also the function of the metabolic processes. These results extended our knowledge of the microbial composition and potential metabolism in the WSP.
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Affiliation(s)
- Yingdong Li
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study Under Deep-Sea Extreme Conditions, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Xiaomin Xia
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Shunyan Cheung
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Koji Suzuki
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan
| | - Hongbin Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
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11
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La Cono V, Ruggeri G, Azzaro M, Crisafi F, Decembrini F, Denaro R, La Spada G, Maimone G, Monticelli LS, Smedile F, Giuliano L, Yakimov MM. Contribution of Bicarbonate Assimilation to Carbon Pool Dynamics in the Deep Mediterranean Sea and Cultivation of Actively Nitrifying and CO 2-Fixing Bathypelagic Prokaryotic Consortia. Front Microbiol 2018; 9:3. [PMID: 29403458 PMCID: PMC5780414 DOI: 10.3389/fmicb.2018.00003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/03/2018] [Indexed: 11/16/2022] Open
Abstract
Covering two-thirds of our planet, the global deep ocean plays a central role in supporting life on Earth. Among other processes, this biggest ecosystem buffers the rise of atmospheric CO2. Despite carbon sequestration in the deep ocean has been known for a long time, microbial activity in the meso- and bathypelagic realm via the "assimilation of bicarbonate in the dark" (ABD) has only recently been described in more details. Based on recent findings, this process seems primarily the result of chemosynthetic and anaplerotic reactions driven by different groups of deep-sea prokaryoplankton. We quantified bicarbonate assimilation in relation to total prokaryotic abundance, prokaryotic heterotrophic production and respiration in the meso- and bathypelagic Mediterranean Sea. The measured ABD values, ranging from 133 to 370 μg C m-3 d-1, were among the highest ones reported worldwide for similar depths, likely due to the elevated temperature of the deep Mediterranean Sea (13-14°C also at abyssal depths). Integrated over the dark water column (≥200 m depth), bicarbonate assimilation in the deep-sea ranged from 396 to 873 mg C m-2 d-1. This quantity of produced de novo organic carbon amounts to about 85-424% of the phytoplankton primary production and covers up to 62% of deep-sea prokaryotic total carbon demand. Hence, the ABD process in the meso- and bathypelagic Mediterranean Sea might substantially contribute to the inorganic and organic pool and significantly sustain the deep-sea microbial food web. To elucidate the ABD key-players, we established three actively nitrifying and CO2-fixing prokaryotic enrichments. Consortia were characterized by the co-occurrence of chemolithoautotrophic Thaumarchaeota and chemoheterotrophic proteobacteria. One of the enrichments, originated from Ionian bathypelagic waters (3,000 m depth) and supplemented with low concentrations of ammonia, was dominated by the Thaumarchaeota "low-ammonia-concentration" deep-sea ecotype, an enigmatic and ecologically important group of organisms, uncultured until this study.
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Affiliation(s)
- Violetta La Cono
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Gioachino Ruggeri
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Maurizio Azzaro
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Francesca Crisafi
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Franco Decembrini
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Renata Denaro
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Gina La Spada
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Giovanna Maimone
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Luis S. Monticelli
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Francesco Smedile
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, United States
| | - Laura Giuliano
- Mediterranean Science Commission (CIESM), Monaco, Monaco
| | - Michail M. Yakimov
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
- Institute of Living Systems, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
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12
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Guerrero-Feijóo E, Sintes E, Herndl GJ, Varela MM. High dark inorganic carbon fixation rates by specific microbial groups in the Atlantic off the Galician coast (NW Iberian margin). Environ Microbiol 2017; 20:602-611. [DOI: 10.1111/1462-2920.13984] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 10/30/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Elisa Guerrero-Feijóo
- IEO, Instituto Español de Oceanografía, Centro Oceanográfico de A Coruña, Apdo 130; 15080 A Coruña Spain
| | - Eva Sintes
- Department of Limnology and Bio-Oceanography; University of Vienna, Center of Ecology; Austria
| | - Gerhard J. Herndl
- Department of Limnology and Bio-Oceanography; University of Vienna, Center of Ecology; Austria
- Department of Marine Microbiology and Biogeochemistry; NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, PO Box 59, 1790 AB Den Burg; The Netherlands
| | - Marta M. Varela
- IEO, Instituto Español de Oceanografía, Centro Oceanográfico de A Coruña, Apdo 130; 15080 A Coruña Spain
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13
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Danovaro R, Rastelli E, Corinaldesi C, Tangherlini M, Dell'Anno A. Marine archaea and archaeal viruses under global change. F1000Res 2017; 6:1241. [PMID: 29034077 PMCID: PMC5532796 DOI: 10.12688/f1000research.11404.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/26/2017] [Indexed: 01/08/2023] Open
Abstract
Global change is altering oceanic temperature, salinity, pH, and oxygen concentration, directly and indirectly influencing marine microbial food web structure and function. As microbes represent >90% of the ocean’s biomass and are major drivers of biogeochemical cycles, understanding their responses to such changes is fundamental for predicting the consequences of global change on ecosystem functioning. Recent findings indicate that marine archaea and archaeal viruses are active and relevant components of marine microbial assemblages, far more abundant and diverse than was previously thought. Further research is urgently needed to better understand the impacts of global change on virus–archaea dynamics and how archaea and their viruses can interactively influence the ocean’s feedbacks on global change.
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Affiliation(s)
- Roberto Danovaro
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy.,Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Eugenio Rastelli
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy.,Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Cinzia Corinaldesi
- Department of Sciences and Engineering of Materials, Environment and Urbanistics, Polytechnic University of Marche, Ancona, Italy
| | - Michael Tangherlini
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Antonio Dell'Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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14
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Haro-Moreno JM, Rodriguez-Valera F, López-García P, Moreira D, Martin-Cuadrado AB. New insights into marine group III Euryarchaeota, from dark to light. ISME JOURNAL 2017; 11:1102-1117. [PMID: 28085158 DOI: 10.1038/ismej.2016.188] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 11/25/2016] [Accepted: 12/05/2016] [Indexed: 01/29/2023]
Abstract
Marine Euryarchaeota remain among the least understood major components of marine microbial communities. Marine group II Euryarchaeota (MG-II) are more abundant in surface waters (4-20% of the total prokaryotic community), whereas marine group III Euryarchaeota (MG-III) are generally considered low-abundance members of deep mesopelagic and bathypelagic communities. Using genome assembly from direct metagenome reads and metagenomic fosmid clones, we have identified six novel MG-III genome sequence bins from the photic zone (Epi1-6) and two novel bins from deep-sea samples (Bathy1-2). Genome completeness in those genome bins varies from 44% to 85%. Photic-zone MG-III bins corresponded to novel groups with no similarity, and significantly lower GC content, when compared with previously described deep-MG-III genome bins. As found in many other epipelagic microorganisms, photic-zone MG-III bins contained numerous photolyase and rhodopsin genes, as well as genes for peptide and lipid uptake and degradation, suggesting a photoheterotrophic lifestyle. Phylogenetic analysis of these photolyases and rhodopsins as well as their genomic context suggests that these genes are of bacterial origin, supporting the hypothesis of an MG-III ancestor that lived in the dark ocean. Epipelagic MG-III occur sporadically and in relatively small proportions in marine plankton, representing only up to 0.6% of the total microbial community reads in metagenomes. None of the reconstructed epipelagic MG-III genomes were present in metagenomes from aphotic zone depths or from high latitude regions. Most low-GC bins were highly enriched at the deep chlorophyll maximum zones, with the exception of Epi1, which appeared evenly distributed throughout the photic zone worldwide.
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Affiliation(s)
- Jose M Haro-Moreno
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Purificación López-García
- Unité d'Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Orsay Cedex, France
| | - David Moreira
- Unité d'Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Orsay Cedex, France
| | - Ana-Belen Martin-Cuadrado
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
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15
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Celussi M, Malfatti F, Ziveri P, Giani M, Del Negro P. Uptake-release dynamics of the inorganic and organic carbon pool mediated by planktonic prokaryotes in the deep Mediterranean Sea. Environ Microbiol 2016; 19:1163-1175. [PMID: 28026100 DOI: 10.1111/1462-2920.13641] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 11/25/2016] [Accepted: 12/03/2016] [Indexed: 11/28/2022]
Abstract
Understanding the ecosystem functioning in the dark portion of the ocean is a challenge that microbial ecologists are still facing. Due to the large volume, the global deep Ocean plays a central role in the regulation of climate, possibly buffering the rise of atmospheric carbon dioxide if processes of CO2 fixation compensate for respiration. We investigated the rates of several prokaryotic activities (dissolved and particulate primary production, heterotrophic carbon production and respiration) in meso- and bathypelagic waters of the Mediterranean Sea, covering all sub-basins. Chemosynthesis was the main process for C uptake. The rates of organic C (OC) excretion (or viral-induced cell lysis) inferred from the dissolved primary production measurements were noteworthy, being comparable to particulate primary production, and possibly contributing to the formation of non-sinking particulate organic matter. Inorganic C fixation rates were significantly higher than those reported for other deep-sea systems, probably as a consequence of the persistently higher temperature of dark Mediterranean waters or to phylogenetically diverse communities involved in the process. Primary production was negatively correlated with dissolved organic carbon concentration and showed an inverse pattern to heterotrophic carbon production, indicating a niche partitioning between heterotrophs and autotrophs. In sum, the deep Mediterranean Sea harbors active autotrophic communities able to fix inorganic carbon faster than the heterotrophic carbon production rates.
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Affiliation(s)
- Mauro Celussi
- OGS (Istituto Nazionale di Oceanografia e di Geofisica Sperimentale), Oceanography Division, via A. Piccard 54, Trieste, 34151, Italy
| | - Francesca Malfatti
- OGS (Istituto Nazionale di Oceanografia e di Geofisica Sperimentale), Oceanography Division, via A. Piccard 54, Trieste, 34151, Italy
| | - Patrizia Ziveri
- Institute of Environmental Science and Technology, Autonomous University of Barcelona (UAB), Bellaterra, 08193, Spain.,ICREA, Pg. Lluis Companys 23, Barcelona, 08010, Spain
| | - Michele Giani
- OGS (Istituto Nazionale di Oceanografia e di Geofisica Sperimentale), Oceanography Division, via A. Piccard 54, Trieste, 34151, Italy
| | - Paola Del Negro
- OGS (Istituto Nazionale di Oceanografia e di Geofisica Sperimentale), Oceanography Division, via A. Piccard 54, Trieste, 34151, Italy
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16
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Li Z, Wang Y, Li J, Liu F, He L, He Y, Wang S. Metagenomic Analysis of Genes Encoding Nutrient Cycling Pathways in the Microbiota of Deep-Sea and Shallow-Water Sponges. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:659-671. [PMID: 27819120 DOI: 10.1007/s10126-016-9725-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 10/14/2016] [Indexed: 05/20/2023]
Abstract
Sponges host complex symbiotic communities, but to date, the whole picture of the metabolic potential of sponge microbiota remains unclear, particularly the difference between the shallow-water and deep-sea sponge holobionts. In this study, two completely different sponges, shallow-water sponge Theonella swinhoei from the South China Sea and deep-sea sponge Neamphius huxleyi from the Indian Ocean, were selected to compare their whole symbiotic communities and metabolic potential, particularly in element transformation. Phylogenetically diverse bacteria, archaea, fungi, and algae were detected in both shallow-water sponge T. swinhoei and deep-sea sponge N. huxleyi, and different microbial community structures were indicated between these two sponges. Metagenome-based gene abundance analysis indicated that, though the two sponge microbiota have similar core functions, they showed different potential strategies in detailed metabolic processes, e.g., in the transformation and utilization of carbon, nitrogen, phosphorus, and sulfur by corresponding microbial symbionts. This study provides insight into the putative metabolic potentials of the microbiota associated with the shallow-water and deep-sea sponges at the whole community level, extending our knowledge of the sponge microbiota's functions, the association of sponge- microbes, as well as the adaption of sponge microbiota to the marine environment.
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Affiliation(s)
- Zhiyong Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China.
| | - Yuezhu Wang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, People's Republic of China
| | - Jinlong Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Fang Liu
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Liming He
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Ying He
- Laboratory of Marine Oceanography, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Shenyue Wang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, People's Republic of China
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17
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Westra ER, Dowling AJ, Broniewski JM, van Houte S. Evolution and Ecology of CRISPR. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-121415-032428] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Edze R. Westra
- Environment and Sustainability Institute and Centre for Ecology and Conservation, Biosciences, University of Exeter, Tremough Campus, Penryn TR10 9FE, United Kingdom;
| | - Andrea J. Dowling
- Environment and Sustainability Institute and Centre for Ecology and Conservation, Biosciences, University of Exeter, Tremough Campus, Penryn TR10 9FE, United Kingdom;
| | - Jenny M. Broniewski
- Environment and Sustainability Institute and Centre for Ecology and Conservation, Biosciences, University of Exeter, Tremough Campus, Penryn TR10 9FE, United Kingdom;
| | - Stineke van Houte
- Environment and Sustainability Institute and Centre for Ecology and Conservation, Biosciences, University of Exeter, Tremough Campus, Penryn TR10 9FE, United Kingdom;
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18
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Yakimov MM, Crisafi F, Messina E, Smedile F, Lopatina A, Denaro R, Pieper DH, Golyshin PN, Giuliano L. Analysis of defence systems and a conjugative IncP-1 plasmid in the marine polyaromatic hydrocarbons-degrading bacterium Cycloclasticus sp. 78-ME. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:508-519. [PMID: 27345842 DOI: 10.1111/1758-2229.12424] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/24/2016] [Indexed: 06/06/2023]
Abstract
Marine prokaryotes have evolved a broad repertoire of defence systems to protect their genomes from lateral gene transfer including innate or acquired immune systems and infection-induced programmed cell suicide and dormancy. Here we report on the analysis of multiple defence systems present in the genome of the strain Cycloclasticus sp. 78-ME isolated from petroleum deposits of the tanker 'Amoco Milford Haven'. Cycloclasticus are ubiquitous bacteria globally important in polyaromatic hydrocarbons degradation in marine environments. Two 'defence islands' were identified in 78-ME genome: the first harbouring CRISPR-Cas with toxin-antitoxin system, while the second was composed by an array of genes for toxin-antitoxin and restriction-modification proteins. Among all identified spacers of CRISPR-Cas system only seven spacers match sequences of phages and plasmids. Furthermore, a conjugative plasmid p7ME01, which belongs to a new IncP-1θ ancestral archetype without any accessory mobile elements was found in 78-ME. Our results provide the context to the co-occurrence of diverse defence mechanisms in the genome of Cycloclasticus sp. 78-ME, which protect the genome of this highly specialized PAH-degrader. This study contributes to the further understanding of complex networks established in petroleum-based microbial communities.
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Affiliation(s)
- Michail M Yakimov
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, Messina, 98122, Italy
| | - Francesca Crisafi
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, Messina, 98122, Italy
| | - Enzo Messina
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, Messina, 98122, Italy
| | - Francesco Smedile
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, Messina, 98122, Italy
| | - Anna Lopatina
- Institute of Molecular Genetics and Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Renata Denaro
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, Messina, 98122, Italy
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, HZI - Helmholtz Centre for Infection Research, Inhoffenstraße 7, Braunschweig, D-38124, Germany
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, ECW Bldg Deiniol Rd, Bangor, Gwynedd, LL57 2UW, United Kingdom
| | - Laura Giuliano
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, Messina, 98122, Italy
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19
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López-Pérez M, Kimes NE, Haro-Moreno JM, Rodriguez-Valera F. Not All Particles Are Equal: The Selective Enrichment of Particle-Associated Bacteria from the Mediterranean Sea. Front Microbiol 2016; 7:996. [PMID: 27446036 PMCID: PMC4916215 DOI: 10.3389/fmicb.2016.00996] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 06/09/2016] [Indexed: 11/13/2022] Open
Abstract
We have used two metagenomic approaches, direct sequencing of natural samples and sequencing after enrichment, to characterize communities of prokaryotes associated to particles. In the first approximation, different size filters (0.22 and 5 μm) were used to identify prokaryotic microbes of free-living and particle-attached bacterial communities in the Mediterranean water column. A subtractive metagenomic approach was used to characterize the dominant microbial groups in the large size fraction that were not present in the free-living one. They belonged mainly to Actinobacteria, Planctomycetes, Flavobacteria and Proteobacteria. In addition, marine microbial communities enriched by incubation with different kinds of particulate material have been studied by metagenomic assembly. Different particle kinds (diatomaceous earth, sand, chitin and cellulose) were colonized by very different communities of bacteria belonging to Roseobacter, Vibrio, Bacteriovorax, and Lacinutrix that were distant relatives of genomes already described from marine habitats. Besides, using assembly from deep metagenomic sequencing from the particle-specific enrichments we were able to determine a total of 20 groups of contigs (eight of them with >50% completeness) and reconstruct de novo five new genomes of novel species within marine clades (>79% completeness and <1.8% contamination). We also describe for the first time the genome of a marine Rhizobiales phage that seems to infect a broad range of Alphaproteobacteria and live in habitats as diverse as soil, marine sediment and water column. The metagenomic recruitment of the communities found by direct sequencing of the large size filter and by enrichment had nearly no overlap. These results indicate that these reconstructed genomes are part of the rare biosphere which exists at nominal levels under natural conditions.
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20
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Jin HM, Jeong HI, Kim KH, Hahn Y, Madsen EL, Jeon CO. Genome-wide transcriptional responses of Alteromonas naphthalenivorans SN2 to contaminated seawater and marine tidal flat sediment. Sci Rep 2016; 6:21796. [PMID: 26887987 PMCID: PMC4757865 DOI: 10.1038/srep21796] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 02/01/2016] [Indexed: 11/09/2022] Open
Abstract
A genome-wide transcriptional analysis of Alteromonas naphthalenivorans SN2 was performed to investigate its ecophysiological behavior in contaminated tidal flats and seawater. The experimental design mimicked these habitats that either added naphthalene or pyruvate; tidal flat-naphthalene (TF-N), tidal flat-pyruvate (TF-P), seawater-naphthalene (SW-N), and seawater-pyruvate (SW-P). The transcriptional profiles clustered by habitat (TF-N/TF-P and SW-N/SW-P), rather than carbon source, suggesting that the former may exert a greater influence on genome-wide expression in strain SN2 than the latter. Metabolic mapping of cDNA reads from strain SN2 based on KEGG pathway showed that metabolic and regulatory genes associated with energy metabolism, translation, and cell motility were highly expressed in all four test conditions, probably highlighting the copiotrophic properties of strain SN2 as an opportunistic marine r-strategist. Differential gene expression analysis revealed that strain SN2 displayed specific cellular responses to environmental variables (tidal flat, seawater, naphthalene, and pyruvate) and exhibited certain ecological fitness traits -- its notable PAH degradation capability in seasonally cold tidal flat might be reflected in elevated expression of stress response and chaperone proteins, while fast growth in nitrogen-deficient and aerobic seawater probably correlated with high expression of glutamine synthetase, enzymes utilizing nitrite/nitrate, and those involved in the removal of reactive oxygen species.
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Affiliation(s)
- Hyun Mi Jin
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea.,Freshwater Bioresources Utilization Division, Nakdonggang National Institute of Biological Resources, Gyeongsangbuk-do 37242, Republic of Korea
| | - Hye Im Jeong
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Kyung Hyun Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Yoonsoo Hahn
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Eugene L Madsen
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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21
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Sinha R, Clarke J, Benson AK. Alignment behaviors of short peptides provide a roadmap for functional profiling of metagenomic data. BMC Genomics 2015; 16:1080. [PMID: 26691573 PMCID: PMC4687345 DOI: 10.1186/s12864-015-2272-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 12/03/2015] [Indexed: 12/03/2022] Open
Abstract
Background Functional assignments for short-read metagenomic data pose a significant computational challenge due to perceived unpredictability of alignment behavior and the inability to infer useful functional information from translated protein-fragments/peptides. To address this problem, we have examined the predictability of short peptide alignments by systematically studying alignment behavior of large sets of short peptides generated from well-characterized proteins as well as hypothetical proteins in the KEGG database. Results Using test sets of peptides modeling the length and phylogenetic distributions of short-read metagenomic data, we observed that peptides from well-characterized proteins had indistinguishable alignments to proteins from the same orthologous family and proteins from different families. Nonetheless, the patterns contained remarkable phylogenetic and structural signals, with alignments of even very short peptides naturally restricted to their orthologous family and/or proteins having similar structural folds. In stark contrast, peptides from “hypothetical proteins” had only sparse hit patterns with low frequencies and much lower identities. By weighting the structure-driven alignments and filtering peptides with behaviors similar to those derived from “hypothetical proteins”, we demonstrate that the accuracy of abundance predictions of protein families is dramatically improved. Conclusions Evolutionary processes have dispersed protein folds across multiple protein families, precluding accurate functional assignment to short peptides, whose alignment behavior is non-random and driven by structure. Algorithms that filter sparse peptides and weight hit patterns of peptides from “known space” dramatically improve quantification of functions from diverse mixtures of peptides and should substantially improve applications of metagenomic analyses requiring accurate quantitative measures of functional families. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2272-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rohita Sinha
- Department of Food Science and Technology, University of Nebraska, 256 Food Innovation Complex, Lincoln, NE, 68588-6205, USA.
| | - Jennifer Clarke
- Department of Food Science and Technology, University of Nebraska, 256 Food Innovation Complex, Lincoln, NE, 68588-6205, USA. .,Department of Statistics, University of Nebraska, Lincoln, NE, 68583, USA. .,Quantitative Life Sciences Initiative, University of Nebraska, Lincoln, NE, 68583, USA.
| | - Andrew K Benson
- Department of Food Science and Technology, University of Nebraska, 256 Food Innovation Complex, Lincoln, NE, 68588-6205, USA.
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Suenaga H. Targeted metagenomics unveils the molecular basis for adaptive evolution of enzymes to their environment. Front Microbiol 2015; 6:1018. [PMID: 26441940 PMCID: PMC4585196 DOI: 10.3389/fmicb.2015.01018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 09/08/2015] [Indexed: 11/13/2022] Open
Abstract
Microorganisms have a wonderful ability to adapt rapidly to new or altered environmental conditions. Enzymes are the basis of metabolism in all living organisms and, therefore, enzyme adaptation plays a crucial role in the adaptation of microorganisms. Comparisons of homology and parallel beneficial mutations in an enzyme family provide valuable hints of how an enzyme adapted to an ecological system; consequently, a series of enzyme collections is required to investigate enzyme evolution. Targeted metagenomics is a promising tool for the construction of enzyme pools and for studying the adaptive evolution of enzymes. This perspective article presents a summary of targeted metagenomic approaches useful for this purpose.
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Affiliation(s)
- Hikaru Suenaga
- Bioproduction Research Institute - National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba, Japan
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Single cells within the Puerto Rico trench suggest hadal adaptation of microbial lineages. Appl Environ Microbiol 2015; 81:8265-76. [PMID: 26386059 DOI: 10.1128/aem.01659-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 09/12/2015] [Indexed: 11/20/2022] Open
Abstract
Hadal ecosystems are found at a depth of 6,000 m below sea level and below, occupying less than 1% of the total area of the ocean. The microbial communities and metabolic potential in these ecosystems are largely uncharacterized. Here, we present four single amplified genomes (SAGs) obtained from 8,219 m below the sea surface within the hadal ecosystem of the Puerto Rico Trench (PRT). These SAGs are derived from members of deep-sea clades, including the Thaumarchaeota and SAR11 clade, and two are related to previously isolated piezophilic (high-pressure-adapted) microorganisms. In order to identify genes that might play a role in adaptation to deep-sea environments, comparative analyses were performed with genomes from closely related shallow-water microbes. The archaeal SAG possesses genes associated with mixotrophy, including lipoylation and the glycine cleavage pathway. The SAR11 SAG encodes glycolytic enzymes previously reported to be missing from this abundant and cosmopolitan group. The other SAGs, which are related to piezophilic isolates, possess genes that may supplement energy demands through the oxidation of hydrogen or the reduction of nitrous oxide. We found evidence for potential trench-specific gene distributions, as several SAG genes were observed only in a PRT metagenome and not in shallower deep-sea metagenomes. These results illustrate new ecotype features that might perform important roles in the adaptation of microorganisms to life in hadal environments.
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Abstract
This review summarizes usage of genome-editing technologies for metagenomic studies; these studies are used to retrieve and modify valuable microorganisms for production, particularly in marine metagenomics. Organisms may be cultivable or uncultivable. Metagenomics is providing especially valuable information for uncultivable samples. The novel genes, pathways and genomes can be deducted. Therefore, metagenomics, particularly genome engineering and system biology, allows for the enhancement of biological and chemical producers and the creation of novel bioresources. With natural resources rapidly depleting, genomics may be an effective way to efficiently produce quantities of known and novel foods, livestock feed, fuels, pharmaceuticals and fine or bulk chemicals.
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Affiliation(s)
- Rimantas Kodzius
- Computational Bioscience Research Center (CBRC), Saudi Arabia; Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Saudi Arabia; King Abdullah University of Science and Technology (KAUST), Saudi Arabia.
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), Saudi Arabia; Biological and Environmental Sciences and Engineering Division (BESE), Saudi Arabia; King Abdullah University of Science and Technology (KAUST), Saudi Arabia.
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25
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Global diversity and biogeography of deep-sea pelagic prokaryotes. ISME JOURNAL 2015; 10:596-608. [PMID: 26251871 DOI: 10.1038/ismej.2015.137] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 06/15/2015] [Accepted: 07/01/2015] [Indexed: 11/09/2022]
Abstract
The deep-sea is the largest biome of the biosphere, and contains more than half of the whole ocean's microbes. Uncovering their general patterns of diversity and community structure at a global scale remains a great challenge, as only fragmentary information of deep-sea microbial diversity exists based on regional-scale studies. Here we report the first globally comprehensive survey of the prokaryotic communities inhabiting the bathypelagic ocean using high-throughput sequencing of the 16S rRNA gene. This work identifies the dominant prokaryotes in the pelagic deep ocean and reveals that 50% of the operational taxonomic units (OTUs) belong to previously unknown prokaryotic taxa, most of which are rare and appear in just a few samples. We show that whereas the local richness of communities is comparable to that observed in previous regional studies, the global pool of prokaryotic taxa detected is modest (~3600 OTUs), as a high proportion of OTUs are shared among samples. The water masses appear to act as clear drivers of the geographical distribution of both particle-attached and free-living prokaryotes. In addition, we show that the deep-oceanic basins in which the bathypelagic realm is divided contain different particle-attached (but not free-living) microbial communities. The combination of the aging of the water masses and a lack of complete dispersal are identified as the main drivers for this biogeographical pattern. All together, we identify the potential of the deep ocean as a reservoir of still unknown biological diversity with a higher degree of spatial complexity than hitherto considered.
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26
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Variations in Microbial Community Structure through the Stratified Water Column in the Tyrrhenian Sea (Central Mediterranean). JOURNAL OF MARINE SCIENCE AND ENGINEERING 2015. [DOI: 10.3390/jmse3030845] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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27
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Kleiner M, Wentrup C, Holler T, Lavik G, Harder J, Lott C, Littmann S, Kuypers MMM, Dubilier N. Use of carbon monoxide and hydrogen by a bacteria–animal symbiosis from seagrass sediments. Environ Microbiol 2015; 17:5023-35. [PMID: 26013766 PMCID: PMC4744751 DOI: 10.1111/1462-2920.12912] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 05/19/2015] [Indexed: 11/23/2022]
Abstract
The gutless marine worm Olavius algarvensis lives in symbiosis with chemosynthetic bacteria that provide nutrition by fixing carbon dioxide (CO2) into biomass using reduced sulfur compounds as energy sources. A recent metaproteomic analysis of the O. algarvensis symbiosis indicated that carbon monoxide (CO) and hydrogen (H2) might also be used as energy sources. We provide direct evidence that the O. algarvensis symbiosis consumes CO and H2. Single cell imaging using nanoscale secondary ion mass spectrometry revealed that one of the symbionts, the γ3‐symbiont, uses the energy from CO oxidation to fix CO2. Pore water analysis revealed considerable in‐situ concentrations of CO and H2 in the O. algarvensis environment, Mediterranean seagrass sediments. Pore water H2 concentrations (89–2147 nM) were up to two orders of magnitude higher than in seawater, and up to 36‐fold higher than previously known from shallow‐water marine sediments. Pore water CO concentrations (17–51 nM) were twice as high as in the overlying seawater (no literature data from other shallow‐water sediments are available for comparison). Ex‐situ incubation experiments showed that dead seagrass rhizomes produced large amounts of CO. CO production from decaying plant material could thus be a significant energy source for microbial primary production in seagrass sediments.
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Affiliation(s)
- Manuel Kleiner
- Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
- Department of Geoscience University of Calgary 2500 University Drive Calgary AB T2N 1N4 Canada
| | - Cecilia Wentrup
- Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
- Department of Microbiology and Ecosystem Science Division of Microbial Ecology University of Vienna Althanstr. 14 A‐1090 Vienna Austria
| | - Thomas Holler
- Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
| | - Gaute Lavik
- Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
| | - Jens Harder
- Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
| | - Christian Lott
- Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
- Elba Field Station HYDRA Institute for Marine Sciences Via del Forno 80 Campo nell'Elba LI 57034 Italy
| | - Sten Littmann
- Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
| | - Marcel M. M. Kuypers
- Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology Celsiusstrasse 1 Bremen 28359 Germany
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Ventosa A, de la Haba RR, Sánchez-Porro C, Papke RT. Microbial diversity of hypersaline environments: a metagenomic approach. Curr Opin Microbiol 2015; 25:80-7. [PMID: 26056770 DOI: 10.1016/j.mib.2015.05.002] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 04/29/2015] [Accepted: 05/01/2015] [Indexed: 10/23/2022]
Abstract
Recent studies based on metagenomics and other molecular techniques have permitted a detailed knowledge of the microbial diversity and metabolic activities of microorganisms in hypersaline environments. The current accepted model of community structure in hypersaline environments is that the square archaeon Haloquadratum waslbyi, the bacteroidete Salinibacter ruber and nanohaloarchaea are predominant members at higher salt concentrations, while more diverse archaeal and bacterial taxa are observed in habitats with intermediate salinities. Additionally, metagenomic studies may provide insight into the isolation and characterization of the principal microbes in these habitats, such as the recently described gammaproteobacterium Spiribacter salinus.
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Affiliation(s)
- Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain.
| | - Rafael R de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, 06269 Storrs, CT, USA
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La Cono V, Smedile F, La Spada G, Arcadi E, Genovese M, Ruggeri G, Genovese L, Giuliano L, Yakimov MM. Shifts in the meso- and bathypelagic archaea communities composition during recovery and short-term handling of decompressed deep-sea samples. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:450-459. [PMID: 25682761 DOI: 10.1111/1758-2229.12272] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 02/10/2015] [Indexed: 06/04/2023]
Abstract
Dark ocean microbial communities are actively involved in chemoautotrophic and anaplerotic fixation of bicarbonate. Thus, aphotic pelagic realm of the ocean might represent a significant sink of CO2 and source of primary production. However, the estimated metabolic activities in the dark ocean are fraught with uncertainties. Typically, deep-sea samples are recovered to the sea surface for downstream processing on deck. Shifts in ambient settings, associated with such treatments, can likely change the metabolic activity and community structure of deep-sea adapted autochthonous microbial populations. To estimate influence of recovery and short-term handling of deep-sea samples, we monitored the succession of bathypelagic microbial community during its 3 days long on deck incubation. We demonstrated that at the end of exposition, the deep-sea archaeal population decreased threefold, whereas the bacterial fraction doubled in size. As revealed by phylogenetic analyses of amoA gene transcripts, dominance of the active ammonium-oxidizing bathypelagic Thaumarchaeota groups shifted over time very fast. These findings demonstrated the simultaneous existence of various 'deep-sea ecotypes', differentially reacting to the sampling and downstream handling. Our study supports the hypothesis that metabolically active members of meso- and bathypelagic Thaumarchaeota possess the habitat-specific distribution, metabolic complexity and genetic divergence at subpopulation level.
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Affiliation(s)
- Violetta La Cono
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Francesco Smedile
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Gina La Spada
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Erika Arcadi
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Maria Genovese
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Gioacchino Ruggeri
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Lucrezia Genovese
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
| | - Laura Giuliano
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
- Mediterranean Science Commission (CIESM), 16 bd de Suisse, Monte Carlo, 98000, Monaco
| | - Michail M Yakimov
- Institute for Coastal Marine Environment, CNR, Spianata S. Raineri 86, 98122, Messina, Italy
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30
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Tseng CH, Chiang PW, Lai HC, Shiah FK, Hsu TC, Chen YL, Wen LS, Tseng CM, Shieh WY, Saeed I, Halgamuge S, Tang SL. Prokaryotic assemblages and metagenomes in pelagic zones of the South China Sea. BMC Genomics 2015; 16:219. [PMID: 25879764 PMCID: PMC4373125 DOI: 10.1186/s12864-015-1434-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 03/06/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Prokaryotic microbes, the most abundant organisms in the ocean, are remarkably diverse. Despite numerous studies of marine prokaryotes, the zonation of their communities in pelagic zones has been poorly delineated. By exploiting the persistent stratification of the South China Sea (SCS), we performed a 2-year, large spatial scale (10, 100, 1000, and 3000 m) survey, which included a pilot study in 2006 and comprehensive sampling in 2007, to investigate the biological zonation of bacteria and archaea using 16S rRNA tag and shotgun metagenome sequencing. RESULTS Alphaproteobacteria dominated the bacterial community in the surface SCS, where the abundance of Betaproteobacteria was seemingly associated with climatic activity. Gammaproteobacteria thrived in the deep SCS, where a noticeable amount of Cyanobacteria were also detected. Marine Groups II and III Euryarchaeota were predominant in the archaeal communities in the surface and deep SCS, respectively. Bacterial diversity was higher than archaeal diversity at all sampling depths in the SCS, and peaked at mid-depths, agreeing with the diversity pattern found in global water columns. Metagenomic analysis not only showed differential %GC values and genome sizes between the surface and deep SCS, but also demonstrated depth-dependent metabolic potentials, such as cobalamin biosynthesis at 10 m, osmoregulation at 100 m, signal transduction at 1000 m, and plasmid and phage replication at 3000 m. When compared with other oceans, urease at 10 m and both exonuclease and permease at 3000 m were more abundant in the SCS. Finally, enriched genes associated with nutrient assimilation in the sea surface and transposase in the deep-sea metagenomes exemplified the functional zonation in global oceans. CONCLUSIONS Prokaryotic communities in the SCS stratified with depth, with maximal bacterial diversity at mid-depth, in accordance with global water columns. The SCS had functional zonation among depths and endemically enriched metabolic potentials at the study site, in contrast to other oceans.
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Affiliation(s)
- Ching-Hung Tseng
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan.
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan.
| | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
| | - Hung-Chun Lai
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan.
| | - Fuh-Kwo Shiah
- Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan.
| | - Ting-Chang Hsu
- Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan.
| | - Yi-Lung Chen
- Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan.
| | - Liang-Saw Wen
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan.
| | - Chun-Mao Tseng
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan.
| | - Wung-Yang Shieh
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan.
| | - Isaam Saeed
- Optimisation and Pattern Recognition Research Group, Department of Mechanical Engineering, Melbourne School of Engineering, The University of Melbourne, Victoria, Australia.
| | - Saman Halgamuge
- Optimisation and Pattern Recognition Research Group, Department of Mechanical Engineering, Melbourne School of Engineering, The University of Melbourne, Victoria, Australia.
| | - Sen-Lin Tang
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan.
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan.
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Martin-Cuadrado AB, Garcia-Heredia I, Moltó AG, López-Úbeda R, Kimes N, López-García P, Moreira D, Rodriguez-Valera F. A new class of marine Euryarchaeota group II from the Mediterranean deep chlorophyll maximum. ISME JOURNAL 2014; 9:1619-34. [PMID: 25535935 DOI: 10.1038/ismej.2014.249] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 11/14/2014] [Accepted: 11/19/2014] [Indexed: 11/09/2022]
Abstract
We have analyzed metagenomic fosmid clones from the deep chlorophyll maximum (DCM), which, by genomic parameters, correspond to the 16S ribosomal RNA (rRNA)-defined marine Euryarchaeota group IIB (MGIIB). The fosmid collections associated with this group add up to 4 Mb and correspond to at least two species within this group. From the proposed essential genes contained in the collections, we infer that large sections of the conserved regions of the genomes of these microbes have been recovered. The genomes indicate a photoheterotrophic lifestyle, similar to that of the available genome of MGIIA (assembled from an estuarine metagenome in Puget Sound, Washington Pacific coast), with a proton-pumping rhodopsin of the same kind. Several genomic features support an aerobic metabolism with diversified substrate degradation capabilities that include xenobiotics and agar. On the other hand, these MGIIB representatives are non-motile and possess similar genome size to the MGIIA-assembled genome, but with a lower GC content. The large phylogenomic gap with other known archaea indicates that this is a new class of marine Euryarchaeota for which we suggest the name Thalassoarchaea. The analysis of recruitment from available metagenomes indicates that the representatives of group IIB described here are largely found at the DCM (ca. 50 m deep), in which they are abundant (up to 0.5% of the reads), and at the surface mostly during the winter mixing, which explains formerly described 16S rRNA distribution patterns. Their uneven representation in environmental samples that are close in space and time might indicate sporadic blooms.
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Affiliation(s)
- Ana-Belen Martin-Cuadrado
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Inmaculada Garcia-Heredia
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Aitor Gonzaga Moltó
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Rebeca López-Úbeda
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Nikole Kimes
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Purificación López-García
- Unité d'Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Orsay Cedex, France
| | - David Moreira
- Unité d'Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Orsay Cedex, France
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
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Palleronia abyssalis sp. nov., isolated from the deep Mediterranean Sea and the emended description of the genus Palleronia and of the species Palleronia marisminoris. Antonie van Leeuwenhoek 2014; 107:633-42. [DOI: 10.1007/s10482-014-0358-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/12/2014] [Indexed: 11/27/2022]
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Alcaide M, Stogios PJ, Lafraya Á, Tchigvintsev A, Flick R, Bargiela R, Chernikova TN, Reva ON, Hai T, Leggewie CC, Katzke N, La Cono V, Matesanz R, Jebbar M, Jaeger KE, Yakimov MM, Yakunin AF, Golyshin PN, Golyshina OV, Savchenko A, Ferrer M. Pressure adaptation is linked to thermal adaptation in salt-saturated marine habitats. Environ Microbiol 2014; 17:332-45. [PMID: 25330254 DOI: 10.1111/1462-2920.12660] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 10/01/2014] [Accepted: 10/02/2014] [Indexed: 12/22/2022]
Abstract
The present study provides a deeper view of protein functionality as a function of temperature, salt and pressure in deep-sea habitats. A set of eight different enzymes from five distinct deep-sea (3040-4908 m depth), moderately warm (14.0-16.5°C) biotopes, characterized by a wide range of salinities (39-348 practical salinity units), were investigated for this purpose. An enzyme from a 'superficial' marine hydrothermal habitat (65°C) was isolated and characterized for comparative purposes. We report here the first experimental evidence suggesting that in salt-saturated deep-sea habitats, the adaptation to high pressure is linked to high thermal resistance (P value = 0.0036). Salinity might therefore increase the temperature window for enzyme activity, and possibly microbial growth, in deep-sea habitats. As an example, Lake Medee, the largest hypersaline deep-sea anoxic lake of the Eastern Mediterranean Sea, where the water temperature is never higher than 16°C, was shown to contain halopiezophilic-like enzymes that are most active at 70°C and with denaturing temperatures of 71.4°C. The determination of the crystal structures of five proteins revealed unknown molecular mechanisms involved in protein adaptation to poly-extremes as well as distinct active site architectures and substrate preferences relative to other structurally characterized enzymes.
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Affiliation(s)
- María Alcaide
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain
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Yakimov MM, La Cono V, Smedile F, Crisafi F, Arcadi E, Leonardi M, Decembrini F, Catalfamo M, Bargiela R, Ferrer M, Golyshin PN, Giuliano L. Heterotrophic bicarbonate assimilation is the main process of de novo organic carbon synthesis in hadal zone of the Hellenic Trench, the deepest part of Mediterranean Sea. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:709-722. [PMID: 25756124 DOI: 10.1111/1758-2229.12192] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Ammonium-oxidizing chemoautotrophic members of Thaumarchaea are proposed to be the key players in the assimilation of bicarbonate in the dark (ABD). However, this process may also involve heterotrophic metabolic pathways, such as fixation of carbon dioxide (CO2) via various anaplerotic reactions. We collected samples from the depth of 4900 m at the Matapan-Vavilov Deep (MVD) station (Hellenic Trench, Eastern Mediterranean) and used the multiphasic approach to study the ABD mediators in this deep-sea ecosystem. At this depth, our analysis indicated the occurrence of actively CO2-fixing heterotrophic microbial assemblages dominated by Gammaproteobacteria with virtually no Thaumarchaea present. [14C]-bicarbonate incorporation experiments combined with shotgun [14C]-proteomic analysis identified a series of proteins of gammaproteobacterial origin. More than quarter of them were closely related with Alteromonas macleodii ‘deep ecotype’ AltDE, the predominant organism in the microbial community of MVD. The present study demonstrated that in the aphotic/hadal zone of the Mediterranean Sea, the assimilation of bicarbonate is associated with both chemolithoauto- and heterotrophic ABD. In some deep-sea areas, the latter may predominantly contribute to the de novo synthesis of organic carbon which points at the important and yet underestimated role heterotrophic bacterial populations can play the in global carbon cycle/sink in the ocean interior.
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Diversity of marine microbes in a changing Mediterranean Sea. RENDICONTI LINCEI-SCIENZE FISICHE E NATURALI 2014. [DOI: 10.1007/s12210-014-0333-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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López-Pérez M, Gonzaga A, Ivanova EP, Rodriguez-Valera F. Genomes of Alteromonas australica, a world apart. BMC Genomics 2014; 15:483. [PMID: 24942065 PMCID: PMC4119200 DOI: 10.1186/1471-2164-15-483] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 06/13/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alteromonas is a genus of marine bacteria that is very easy to isolate and grow in the laboratory. There are genomes available of the species Alteromonas macleodii from different locations around the world and an Alteromonas sp. isolated from a sediment in Korea. We have analyzed the genomes of two strains classified by 16S rRNA (>99% similarity) as the recently described species Alteromonas australica, and isolated from opposite ends of the world; A. australica DE170 was isolated in the South Adriatic (Mediterranean) at 1000 m depth while A. australica H17T was isolated from a sea water sample collected in St Kilda Beach, Tasman Sea. RESULTS Although these two strains belong to a clearly different species from A. macleodii, the overall synteny is well preserved and the flexible genomic islands seem to code for equivalent functions and be located at similar positions. Actually the genomes of all the Alteromonas species known to date seem to preserve synteny quite well with the only exception of the sediment isolate SN2. Among the specific metabolic features found for the A. australica isolates there is the degradation of xylan and production of cellulose as extracellular polymeric substance by DE170 or the potential ethanol/methanol degradation by H17T. CONCLUSIONS The genomes of the two A. australica isolates are not more different than those of strains of A. macleodii isolated from the same sample. Actually the recruitment from metagenomes indicates that all the available genomes are found in most tropical-temperate marine samples analyzed and that they live in consortia of several species and multiple clones within each. Overall the hydrolytic activities of the Alteromonas genus as a whole are impressive and fit with its known capabilities to exploit sudden inputs of organic matter in their environment.
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Affiliation(s)
| | | | | | - Francisco Rodriguez-Valera
- División de Microbiología, Evolutionary Genomics Group, Universidad Miguel Hernández, Apartado 18, San Juan, 03550 Alicante, Spain.
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Smedile F, Messina E, La Cono V, Yakimov MM. Comparative analysis of deep-sea bacterioplankton OMICS revealed the occurrence of habitat-specific genomic attributes. Mar Genomics 2014; 17:1-8. [PMID: 24937756 DOI: 10.1016/j.margen.2014.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/23/2014] [Accepted: 06/03/2014] [Indexed: 01/20/2023]
Abstract
Bathyal aphotic ocean represents the largest biotope on our planet, which sustains highly diverse but low-density microbial communities, with yet untapped genomic attributes, potentially useful for discovery of new biomolecules, industrial enzymes and pathways. In the last two decades, culture-independent approaches of high-throughput sequencing have provided new insights into structure and function of marine bacterioplankton, leading to unprecedented opportunities to accurately characterize microbial communities and their interactions with the environments. In the present review we focused on the analysis of relatively few deep-sea OMICS studies, completed thus far, to find the specific genomic patterns determining the lifeway and adaptation mechanisms of prokaryotes thriving in the dark deep ocean below the depth of 1000m. Phylogenomic and omic studies provided clear evidence that the bathyal microbial communities are distinct from the epipelagic counterparts and, along with generally larger genomes, possess their own habitat-specific genomic attributes. The high abundance in the deep ocean OMICS of the systems for environmental sensing, signal transduction and metabolic versatility as compared to the epipelagic counterparts is thought to enable the deep-sea bacterioplankton to rapidly adapt to changing environmental conditions associated with resource scarcity and high diversity of energy and carbon substrates in the bathyal biotopes. Together with a versatile heterotrophy, mixotrophy and anaplerosis are thought to enable the deep-sea bacterioplankton to cope with these environmental conditions.
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Affiliation(s)
- Francesco Smedile
- Institute for Coastal Marine Environment, CNR, Spianata S.Raineri 86, 98122 Messina, Italy
| | - Enzo Messina
- Institute for Coastal Marine Environment, CNR, Spianata S.Raineri 86, 98122 Messina, Italy
| | - Violetta La Cono
- Institute for Coastal Marine Environment, CNR, Spianata S.Raineri 86, 98122 Messina, Italy
| | - Michail M Yakimov
- Institute for Coastal Marine Environment, CNR, Spianata S.Raineri 86, 98122 Messina, Italy.
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Autotrophic microbe metagenomes and metabolic pathways differentiate adjacent Red Sea brine pools. Sci Rep 2014; 3:1748. [PMID: 23624511 PMCID: PMC3638166 DOI: 10.1038/srep01748] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 04/02/2013] [Indexed: 01/29/2023] Open
Abstract
In the Red Sea, two neighboring deep-sea brine pools, Atlantis II and Discovery, have been studied extensively, and the results have shown that the temperature and concentrations of metal and methane in Atlantis II have increased over the past decades. Therefore, we investigated changes in the microbial community and metabolic pathways. Here, we compared the metagenomes of the two pools to each other and to those of deep-sea water samples. Archaea were generally absent in the Atlantis II metagenome; Bacteria in the metagenome were typically heterotrophic and depended on aromatic compounds and other extracellular organic carbon compounds as indicated by enrichment of the related metabolic pathways. In contrast, autotrophic Archaea capable of CO2 fixation and methane oxidation were identified in Discovery but not in Atlantis II. Our results suggest that hydrothermal conditions and metal precipitation in the Atlantis II pool have resulted in elimination of the autotrophic community and methanogens.
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Li ZY, Wang YZ, He LM, Zheng HJ. Metabolic profiles of prokaryotic and eukaryotic communities in deep-sea sponge Neamphius huxleyi [corrected]. indicated by metagenomics. Sci Rep 2014; 4:3895. [PMID: 24463735 PMCID: PMC5379212 DOI: 10.1038/srep03895] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 01/08/2014] [Indexed: 01/29/2023] Open
Abstract
The whole metabolism of a sponge holobiont and the respective contributions of prokaryotic and eukaryotic symbionts and their associations with the sponge host remain largely unclear. Meanwhile, compared with shallow water sponges, deep-sea sponges are rarely understood. Here we report the metagenomic exploration of deep-sea sponge Neamphius huxleyi at the whole community level. Metagenomic data showed phylogenetically diverse prokaryotes and eukaryotes in Neamphius huxleyi. MEGAN and gene enrichment analyses indicated different metabolic potentials of prokaryotic symbionts from eukaryotic symbionts, especially in nitrogen and carbon metabolisms, and their molecular interactions with the sponge host. These results supported the hypothesis that prokaryotic and eukaryotic symbionts have different ecological roles and relationships with sponge host. Moreover, vigorous denitrification, and CO2 fixation by chemoautotrophic prokaryotes were suggested for this deep-sea sponge. The study provided novel insights into the respective potentials of prokaryotic and eukaryotic symbionts and their associations with deep-sea sponge Neamphius huxleyi.
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Affiliation(s)
- Zhi-Yong Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Yue-Zhu Wang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, P. R. China
| | - Li-Ming He
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Hua-Jun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, P. R. China
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Thrash JC, Temperton B, Swan BK, Landry ZC, Woyke T, DeLong EF, Stepanauskas R, Giovannoni SJ. Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype. ISME JOURNAL 2014; 8:1440-51. [PMID: 24451205 DOI: 10.1038/ismej.2013.243] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 11/07/2013] [Accepted: 12/10/2013] [Indexed: 11/09/2022]
Abstract
Bacterioplankton of the SAR11 clade are the most abundant microorganisms in marine systems, usually representing 25% or more of the total bacterial cells in seawater worldwide. SAR11 is divided into subclades with distinct spatiotemporal distributions (ecotypes), some of which appear to be specific to deep water. Here we examine the genomic basis for deep ocean distribution of one SAR11 bathytype (depth-specific ecotype), subclade Ic. Four single-cell Ic genomes, with estimated completeness of 55%-86%, were isolated from 770 m at station ALOHA and compared with eight SAR11 surface genomes and metagenomic datasets. Subclade Ic genomes dominated metagenomic fragment recruitment below the euphotic zone. They had similar COG distributions, high local synteny and shared a large number (69%) of orthologous clusters with SAR11 surface genomes, yet were distinct at the 16S rRNA gene and amino-acid level, and formed a separate, monophyletic group in phylogenetic trees. Subclade Ic genomes were enriched in genes associated with membrane/cell wall/envelope biosynthesis and showed evidence of unique phage defenses. The majority of subclade Ic-specfic genes were hypothetical, and some were highly abundant in deep ocean metagenomic data, potentially masking mechanisms for niche differentiation. However, the evidence suggests these organisms have a similar metabolism to their surface counterparts, and that subclade Ic adaptations to the deep ocean do not involve large variations in gene content, but rather more subtle differences previously observed deep ocean genomic data, like preferential amino-acid substitutions, larger coding regions among SAR11 clade orthologs, larger intergenic regions and larger estimated average genome size.
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Affiliation(s)
- J Cameron Thrash
- 1] Department of Microbiology, Oregon State University, Corvallis, OR, USA [2] Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Ben Temperton
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | - Brandon K Swan
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Zachary C Landry
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - Edward F DeLong
- 1] Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA [2] Center for Microbial Ecology: Research and Education, Honolulu, HI, USA
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López-Pérez M, Gonzaga A, Rodriguez-Valera F. Genomic diversity of "deep ecotype" Alteromonas macleodii isolates: evidence for Pan-Mediterranean clonal frames. Genome Biol Evol 2013; 5:1220-32. [PMID: 23729633 PMCID: PMC3698932 DOI: 10.1093/gbe/evt089] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
We have compared genomes of Alteromonas macleodii “deep ecotype” isolates from two deep Mediterranean sites and two surface samples from the Aegean and the English Channel. A total of nine different genomes were analyzed. They belong to five clonal frames (CFs) that differ among them by approximately 30,000 single-nucleotide polymorphisms (SNPs) over their core genomes. Two of the CFs contain three strains each with nearly identical genomes (∼100 SNPs over the core genome). One of the CFs had representatives that were isolated from samples taken more than 1,000 km away, 2,500 m deeper, and 5 years apart. These data mark the longest proven persistence of a CF in nature (outside of clinical settings). We have found evidence for frequent recombination events between or within CFs and even with the distantly related A. macleodii surface ecotype. The different CFs had different flexible genomic islands. They can be classified into two groups; one type is additive, that is, containing different numbers of gene cassettes, and is very variable in short time periods (they often varied even within a single CF). The other type was more stable and produced the complete replacement of a genomic fragment by another with different genes. Although this type was more conserved within each CF, we found examples of recombination among distantly related CFs including English Channel and Mediterranean isolates.
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Affiliation(s)
- Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
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Bioremediation of Southern Mediterranean oil polluted sites comes of age. N Biotechnol 2013; 30:743-8. [DOI: 10.1016/j.nbt.2013.05.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 04/21/2013] [Accepted: 05/10/2013] [Indexed: 11/21/2022]
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Han M, Li Z, Zhang F. The ammonia oxidizing and denitrifying prokaryotes associated with sponges from different sea areas. MICROBIAL ECOLOGY 2013; 66:427-436. [PMID: 23435827 DOI: 10.1007/s00248-013-0197-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 02/08/2013] [Indexed: 06/01/2023]
Abstract
Marine sponges have been suggested to play an important role in the marine nitrogen cycling. However, the role of sponge microbes in the nitrogen transformation remains limited, especially on the bacterial ammonia oxidization and denitrification. Hence, in the present study, using functional genes (amoA, nirS, nirK, and nxrA) involved in ammonia oxidization and denitrification and 16S rRNA genes for specific bacterial groups as markers, phylogenetically diverse prokaryotes including bacteria and archaea, which may be involved in the ammonia oxidization and denitrification processes in sponges, were revealed in seven sponge species. Ammonia oxidizers were found in all species, whereas three sponges (Placospongia sp., Acanthella sp., and Pericharax heteroraphis) harbor only ammonia-oxidizing bacteria (AOB), two sponges (Spirastrellidae diplastrella and Mycale fibrexilis) host only ammonia-oxidizing archaea (AOA), while the remaining two sponges (Haliclona sp. and Lamellomorpha sp.) harbor both AOB and AOA. S. diplastrella and Lamellomorpha sp. also harbor denitrifying bacteria. Nitrite reductase gene nirK was detected only in Lamellomorpha sp. with higher phylogenetic diversity than nirS gene observed only in S. diplastrella. The detected functional genes related to the ammonia oxidization and nitrite reduction in deep-sea and shallow-water sponges highlighted the potential ecological roles of prokaryotes in sponge-related nitrogen transformation.
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Affiliation(s)
- Minqi Han
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
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Affiliation(s)
| | | | - Juan L. Ramos
- CSIC- Estacion Experimental del Zaidin; Granada; Spain
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Gonzaga A, Martin-Cuadrado AB, López-Pérez M, Megumi Mizuno C, García-Heredia I, Kimes NE, Lopez-García P, Moreira D, Ussery D, Zaballos M, Ghai R, Rodriguez-Valera F. Polyclonality of concurrent natural populations of Alteromonas macleodii. Genome Biol Evol 2012; 4:1360-74. [PMID: 23212172 PMCID: PMC3542563 DOI: 10.1093/gbe/evs112] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2012] [Indexed: 01/28/2023] Open
Abstract
We have analyzed a natural population of the marine bacterium, Alteromonas macleodii, from a single sample of seawater to evaluate the genomic diversity present. We performed full genome sequencing of four isolates and 161 metagenomic fosmid clones, all of which were assigned to A. macleodii by sequence similarity. Out of the four strain genomes, A. macleodii deep ecotype (AltDE1) represented a different genome, whereas AltDE2 and AltDE3 were identical to the previously described AltDE. Although the core genome (~80%) had an average nucleotide identity of 98.51%, both AltDE and AltDE1 contained flexible genomic islands (fGIs), that is, genomic islands present in both genomes in the same genomic context but having different gene content. Some of the fGIs encode cell surface receptors known to be phage recognition targets, such as the O-chain of the lipopolysaccharide, whereas others have genes involved in physiological traits (e.g., nutrient transport, degradation, and metal resistance) denoting microniche specialization. The presence in metagenomic fosmids of genomic fragments differing from the sequenced strain genomes, together with the presence of new fGIs, indicates that there are at least two more A. macleodii clones present. The availability of three or more sequences overlapping the same genomic region also allowed us to estimate the frequency and distribution of recombination events among these different clones, indicating that these clustered near the genomic islands. The results indicate that this natural A. macleodii population has multiple clones with a potential for different phage susceptibility and exploitation of resources, within a seemingly unstructured habitat.
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Affiliation(s)
- Aitor Gonzaga
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Ana-Belen Martin-Cuadrado
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Carolina Megumi Mizuno
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Inmaculada García-Heredia
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Nikole E. Kimes
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | | | - David Moreira
- Unité d’Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, Orsay, France
| | - David Ussery
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
- Present address: Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Mila Zaballos
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | - Rohit Ghai
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Alicante, Spain
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