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Roveta C, Calcinai B, Girolametti F, Fernandes Couceiro J, Puce S, Annibaldi A, Costa R. The prokaryotic community of Chondrosia reniformis Nardo, 1847: from diversity to mercury detection. ZOOLOGY 2023; 158:126091. [PMID: 37003141 DOI: 10.1016/j.zool.2023.126091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 02/21/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023]
Abstract
Microbial communities inhabiting sponges are known to take part in many metabolic pathways, including nutrient cycles, and possibly also in the bioaccumulation of trace elements (TEs). Here, we used high-throughput, Illumina sequencing of 16S rRNA genes to characterize the prokaryotic communities present in the cortex and choanosome, respectively the external and internal body region of Chondrosia reniformis, and in the surrounding seawater. Furthermore, we estimated the total mercury content (THg) in these body regions of the sponge and in the corresponding microbial cell pellets. Fifteen prokaryotic phyla were detected in association with C. reniformis, 13 belonging to the domain Bacteria and two to the Archaea. No significant differences between the prokaryotic community composition of the two regions were found. Three lineages of ammonium-oxidizing organisms (Cenarchaeum symbiosum, Nitrosopumilus maritimus, and Nitrosococcus sp.) co-dominated the prokaryotic community, suggesting ammonium oxidation/nitrification as a key metabolic pathway within the microbiome of C. reniformis. In the sponge fractions, higher THg levels were found in the choanosome compared to the cortex. In contrast, comparable THg levels found in the microbial pellets obtained from both regions were significantly lower than those observed in the corresponding sponge fractions. Our work provides new insights into the prokaryotic communities and TEs distribution in different body parts of a model organism relevant for marine conservation and biotechnology. In this sense, this study paves the way for scientists to deepen the possible application of sponges not only as bioindicators, but also as bioremediation tools of metal polluted environments.
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Affiliation(s)
- Camilla Roveta
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy.
| | - Barbara Calcinai
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Federico Girolametti
- Department of Industrial Engineering and Mathematical Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Joana Fernandes Couceiro
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Stefania Puce
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Anna Annibaldi
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; Centre of Marine Sciences (CCMAR), University of Algarve, Portugal
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2
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Wei TS, Gao ZM, Gong L, Li QM, Zhou YL, Chen HG, He LS, Wang Y. Genome-centric view of the microbiome in a new deep-sea glass sponge species Bathydorus sp. Front Microbiol 2023; 14:1078171. [PMID: 36846759 PMCID: PMC9944714 DOI: 10.3389/fmicb.2023.1078171] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/12/2023] [Indexed: 02/10/2023] Open
Abstract
Sponges are widely distributed in the global ocean and harbor diverse symbiotic microbes with mutualistic relationships. However, sponge symbionts in the deep sea remain poorly studied at the genome level. Here, we report a new glass sponge species of the genus Bathydorus and provide a genome-centric view of its microbiome. We obtained 14 high-quality prokaryotic metagenome-assembled genomes (MAGs) affiliated with the phyla Nitrososphaerota, Pseudomonadota, Nitrospirota, Bdellovibrionota, SAR324, Bacteroidota, and Patescibacteria. In total, 13 of these MAGs probably represent new species, suggesting the high novelty of the deep-sea glass sponge microbiome. An ammonia-oxidizing Nitrososphaerota MAG B01, which accounted for up to 70% of the metagenome reads, dominated the sponge microbiomes. The B01 genome had a highly complex CRISPR array, which likely represents an advantageous evolution toward a symbiotic lifestyle and forceful ability to defend against phages. A sulfur-oxidizing Gammaproteobacteria species was the second most dominant symbiont, and a nitrite-oxidizing Nitrospirota species could also be detected, but with lower relative abundance. Bdellovibrio species represented by two MAGs, B11 and B12, were first reported as potential predatory symbionts in deep-sea glass sponges and have undergone dramatic genome reduction. Comprehensive functional analysis indicated that most of the sponge symbionts encoded CRISPR-Cas systems and eukaryotic-like proteins for symbiotic interactions with the host. Metabolic reconstruction further illustrated their essential roles in carbon, nitrogen, and sulfur cycles. In addition, diverse putative phages were identified from the sponge metagenomes. Our study expands the knowledge of microbial diversity, evolutionary adaption, and metabolic complementarity in deep-sea glass sponges.
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Affiliation(s)
- Tao-Shu Wei
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China,University of Chinese Academy of Sciences, Beijing, China
| | - Zhao-Ming Gao
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China,*Correspondence: Zhao-Ming Gao ✉
| | - Lin Gong
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Qing-Mei Li
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Ying-Li Zhou
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Hua-Guan Chen
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China,University of Chinese Academy of Sciences, Beijing, China
| | - Li-Sheng He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Yong Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China,Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China,Yong Wang ✉
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3
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Ai C, Tong A, Wen J, Chen R, Huang Y, Zhao C. Variations in the substrate composition and microbial community structure in the anaerobic fermentation process using the green algae Enteromorpha prolifera. FOOD PRODUCTION, PROCESSING AND NUTRITION 2022. [DOI: 10.1186/s43014-022-00110-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractEnteromorpha prolifera is a nutrient-rich green alga and abound in the Yellow Sea and the Bohai Sea of China. In this study, E. prolifera was anaerobically digested for biogas production. The variations of chemical compositions and microbial community structure as well as the physical structure of E. prolifera in anaerobic digestion process were investigated. This is the first report of multiple ways to deeply analysis the process of E. prolifera anaerobic digestion. Results from the present work showed that the biogas obtained from E. prolifera anaerobic digestion could achieve 409.7 mL•g− 1 TS with an average methane concentration of 53.2%, and the VFAs content in substrate played a vital role for driving the biogas production of flora. Moreover, S1 of Thermotogaceae and Cenarchaeum, the dominant bacteria and archaea in digestion flora, respectively, played important roles in degrading E. prolifera, acidizing slurry, and providing methanogenic substrate for methanogens.
Graphical Abstract
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4
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González-Castillo A, Carballo JL, Bautista-Guerrero E. Genomics, Phylogeny, and in Silico Phenotyping of Nitrosopumilus Genus. Curr Microbiol 2022; 80:3. [PMID: 36427110 DOI: 10.1007/s00284-022-03121-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 11/14/2022] [Indexed: 11/27/2022]
Abstract
The present study reports the first genome of Nitrosopumilus extracted from the marine sponge Thoosa mismalolli. The genomic study of Nitrosopumilus genus using seven genomes type strains (N. maritimus, N. piranensis, N. zosterae, N. ureiphilus, N. adriaticus, N. oxyclinae and N. cobalaminigenes), four genomes Candidatus species (Ca. N. koreensis, Ca. N. sp. AR2, Ca. N. salaria BD31, and SZUA-335), and six reference genomes (SI075, SI0036, SI0060, SI0034, SI0048, and bin36o) isolated from marine sponge, a tropical marine fish tank, dimly lit deep coastal waters, the lower euphotic zone of coastal waters, near-surface sediment, and MAG N. sp NMAG03 isolated from Thoosa mismalolli was performed. These genomes were characterized by means of a polyphasic approach comprising multilocus sequence analysis (MLSA) of 139 single-copy genes (SCG), core-pangenome, ANI, and in silico phenotypic characterization. We found that the genomes of the Nitrosopumilus genus formed three separate clusters (A, B, and C) based in 139 SCG sequence similarity. The genomes showed values between 75.2 and 99.5% for ANI, the core genome consisted of 168 gene families and the pangenome of 6,011 gene families. Based on the genomic analyses performed, the cluster A may contain a potential new species (NMAG03), and the cluster C could be represented by three new species of the genus. Finally, based on the results shown in this polyphasic approach, we support the use of the integrated approach for genomic analysis of poorly studied genera.
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Affiliation(s)
- Adrián González-Castillo
- Instituto de Ciencias del Mar Y Limnología, Universidad Nacional Autónoma de México (Unidad Académica Mazatlán), 82000, Mazatlán, México.
| | - José Luis Carballo
- Instituto de Ciencias del Mar Y Limnología, Universidad Nacional Autónoma de México (Unidad Académica Mazatlán), 82000, Mazatlán, México.,Departamento de Zoología, Laboratorio de Biología Marina, Universidad de Sevilla, Avda. Reina Mercedes 6, 41012, Seville, Spain
| | - Eric Bautista-Guerrero
- Laboratorio de Ecología Marina, Centro de Investigaciones Costeras, Centro Universitario de La Costa, Universidad de Guadalajara, Puerto Vallarta, México
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5
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Wang P, Li M, Dong L, Zhang C, Xie W. Comparative Genomics of Thaumarchaeota From Deep-Sea Sponges Reveal Their Niche Adaptation. Front Microbiol 2022; 13:869834. [PMID: 35859738 PMCID: PMC9289680 DOI: 10.3389/fmicb.2022.869834] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/30/2022] [Indexed: 11/17/2022] Open
Abstract
Thaumarchaeota account for a large portion of microbial symbionts in deep-sea sponges and are even dominant in some cases. In this study, we investigated three new sponge-associated Thaumarchaeota from the deep West Pacific Ocean. Thaumarchaeota were found to be the most dominant phylum in this sponge by both prokaryotic 16S rRNA amplicons and metagenomic sequencing. Fifty-seven published Thaumarchaeota genomes from sponges and other habitats were included for genomic comparison. Similar to shallow sponge-associated Thaumarchaeota, those Thaumarchaeota in deep-sea sponges have extended genome sizes and lower coding density compared with their free-living lineages. Thaumarchaeota in deep-sea sponges were specifically enriched in genes related to stress adapting, symbiotic adhesion and stability, host–microbe interaction and protein transportation. The genes involved in defense mechanisms, such as the restriction-modification system, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system, and toxin-antitoxin system were commonly enriched in both shallow and deep sponge-associated Thaumarchaeota. Our study demonstrates the significant effects of both depth and symbiosis on forming genomic characteristics of Thaumarchaeota, and provides novel insights into their niche adaptation in deep-sea sponges.
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Affiliation(s)
- Peng Wang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Minchun Li
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Liang Dong
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Cheng Zhang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Wei Xie
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- *Correspondence: Wei Xie,
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6
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Da Cunha V, Gaïa M, Forterre P. The expanding Asgard archaea and their elusive relationships with Eukarya. MLIFE 2022; 1:3-12. [PMID: 38818326 PMCID: PMC10989751 DOI: 10.1002/mlf2.12012] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/25/2022] [Accepted: 02/10/2022] [Indexed: 06/01/2024]
Abstract
The discovery of Asgard archaea and the exploration of their diversity over the last 6 years have deeply impacted the scientific community working on eukaryogenesis, rejuvenating an intense debate on the topology of the universal tree of life (uTol). Here, we discuss how this debate is impacted by two recent publications that expand the number of Asgard lineages and eukaryotic signature proteins (ESPs). We discuss some of the main difficulties that can impair the phylogenetic reconstructions of the uTol and suggest that the debate about its topology is not settled. We notably hypothesize the existence of horizontal gene transfers between ancestral Asgards and proto-eukaryotes that could result in the observed abnormal behaviors of some Asgard ESPs and universal marker proteins. This hypothesis is relevant regardless of the scenario considered regarding eukaryogenesis. It implies that the Asgards were already diversified before the last eukaryotic common ancestor and shared the same biotopes with proto-eukaryotes. We suggest that some Asgards might be still living in symbiosis today with modern Eukarya.
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Affiliation(s)
- Violette Da Cunha
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)Université Paris‐SaclayGif‐sur‐YvetteFrance
| | - Morgan Gaïa
- Génomique Métabolique, Génoscope, Institut François Jacob, CEA, CNRSUniv. Evry, Université Paris‐SaclayEvryFrance
| | - Patrick Forterre
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)Université Paris‐SaclayGif‐sur‐YvetteFrance
- Département de Microbiologie, Institut PasteurParisFrance
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7
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Medina-Chávez NO, Travisano M. Archaeal Communities: The Microbial Phylogenomic Frontier. Front Genet 2022; 12:693193. [PMID: 35154237 PMCID: PMC8826477 DOI: 10.3389/fgene.2021.693193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 11/22/2021] [Indexed: 11/17/2022] Open
Abstract
Archaea are a unique system for investigating the diversity of life. There are the most diverse group of organisms with the longest evolutionary history of life on Earth. Phylogenomic investigations reveal the complex evolutionary history of Archaea, overturning longstanding views of the history of life. They exist in the harshest environments and benign conditions, providing a system to investigate the basis for living in extreme environments. They are frequently members of microbial communities, albeit generally rare. Archaea were central in the evolution of Eukaryotes and can be used as a proxy for studying life on other planets. Future advances will depend not only upon phylogenomic studies but also on a better understanding of isolation and cultivation techniques.
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Affiliation(s)
- Nahui Olin Medina-Chávez
- Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, United States.,BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Michael Travisano
- Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, United States.,BioTechnology Institute, University of Minnesota, St. Paul, MN, United States.,Minnesota Center for the Philosophy of Science, University of Minnesota, Minneapolis, MN, United States
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8
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Li F, Leu A, Poff K, Carlson LT, Ingalls AE, DeLong EF. Planktonic Archaeal Ether Lipid Origins in Surface Waters of the North Pacific Subtropical Gyre. Front Microbiol 2021; 12:610675. [PMID: 34589060 PMCID: PMC8473941 DOI: 10.3389/fmicb.2021.610675] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 08/23/2021] [Indexed: 01/04/2023] Open
Abstract
Thaumarchaeota and Thermoplasmatota are the most abundant planktonic archaea in the sea. Thaumarchaeota contain tetraether lipids as their major membrane lipids, but the lipid composition of uncultured planktonic Thermoplasmatota representatives remains unknown. To address this knowledge gap, we quantified archaeal cells and ether lipids in open ocean depth profiles (0–200 m) of the North Pacific Subtropical Gyre. Planktonic archaeal community structure and ether lipid composition in the water column partitioned into two separate clusters: one above the deep chlorophyll maximum, the other within and below it. In surface waters, Thermoplasmatota densities ranged from 2.11 × 106 to 6.02 × 106 cells/L, while Thaumarchaeota were undetectable. As previously reported for Thaumarchaeota, potential homologs of archaeal tetraether ring synthases were present in planktonic Thermoplasmatota metagenomes. Despite the absence of Thaumarchaeota in surface waters, measurable amounts of intact polar ether lipids were found there. Based on cell abundance estimates, these surface water archaeal ether lipids contributed only 1.21 × 10–9 ng lipid/Thermoplasmatota cell, about three orders of magnitude less than that reported for Thaumarchaeota cells. While these data indicate that even if some tetraether and diether lipids may be derived from Thermoplasmatota, they would only comprise a small fraction of Thermoplasmatota total biomass. Therefore, while both MGI Thaumarchaeota and MGII/III Thermoplasmatota are potential biological sources of archaeal GDGTs, the Thaumarchaeota appear to be the major contributors of archaeal tetraether lipids in planktonic marine habitats. These results extend and confirm previous reports of planktonic archaeal lipid sources, and further emphasize the need for Thermoplasmatota cultivation, to better characterize the membrane lipid constituents of marine planktonic Thermoplasmatota, and more precisely define the sources and patterns of archaeal tetraether lipid distributions in marine plankton.
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Affiliation(s)
- Fuyan Li
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Andy Leu
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Kirsten Poff
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mânoa, Honolulu, HI, United States
| | - Laura T Carlson
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mânoa, Honolulu, HI, United States
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9
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Spatial separation of ribosomes and DNA in Asgard archaeal cells. ISME JOURNAL 2021; 16:606-610. [PMID: 34465898 PMCID: PMC8776820 DOI: 10.1038/s41396-021-01098-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 11/23/2022]
Abstract
The origin of the eukaryotic cell is a major open question in biology. Asgard archaea are the closest known prokaryotic relatives of eukaryotes, and their genomes encode various eukaryotic signature proteins, indicating some elements of cellular complexity prior to the emergence of the first eukaryotic cell. Yet, microscopic evidence to demonstrate the cellular structure of uncultivated Asgard archaea in the environment is thus far lacking. We used primer-free sequencing to retrieve 715 almost full-length Loki- and Heimdallarchaeota 16S rRNA sequences and designed novel oligonucleotide probes to visualize their cells in marine sediments (Aarhus Bay, Denmark) using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Super-resolution microscopy revealed 1–2 µm large, coccoid cells, sometimes occurring as aggregates. Remarkably, the DNA staining was spatially separated from ribosome-originated FISH signals by 50–280 nm. This suggests that the genomic material is condensed and spatially distinct in a particular location and could indicate compartmentalization or membrane invagination in Asgard archaeal cells.
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10
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Tahon G, Patricia Geesink, Ettema TJG. Expanding Archaeal Diversity and Phylogeny: Past, Present, and Future. Annu Rev Microbiol 2021; 75:359-381. [PMID: 34351791 DOI: 10.1146/annurev-micro-040921-050212] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The discovery of the Archaea is a major scientific hallmark of the twentieth century. Since then, important features of their cell biology, physiology, ecology, and diversity have been revealed. Over the course of some 40 years, the diversity of known archaea has expanded from 2 to about 30 phyla comprising over 20,000 species. Most of this archaeal diversity has been revealed by environmental 16S rRNA amplicon sequencing surveys using a broad range of universal and targeted primers. Of the few primers that target a large fraction of known archaeal diversity, all display a bias against recently discovered lineages, which limits studies aiming to survey overall archaeal diversity. Induced by genomic exploration of archaeal diversity, and improved phylogenomics approaches, archaeal taxonomic classification has been frequently revised. Due to computational limitations and continued discovery of new lineages, a stable archaeal phylogeny is not yet within reach. Obtaining phylogenetic and taxonomic consensus of archaea should be a high priority for the archaeal research community. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Guillaume Tahon
- Laboratory of Microbiology, Wageningen University and Research, 6700 EH Wageningen, The Netherlands; , ,
| | - Patricia Geesink
- Laboratory of Microbiology, Wageningen University and Research, 6700 EH Wageningen, The Netherlands; , ,
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University and Research, 6700 EH Wageningen, The Netherlands; , ,
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11
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Chekidhenkuzhiyil J, Anas A, Thomas P, Tharakan B, Nair S. Characterization of archaeal symbionts of sponges from the coral reef ecosystems of the Gulf of Mannar, Southeast coast of India. Saudi J Biol Sci 2021; 28:3783-3788. [PMID: 34220232 PMCID: PMC8241630 DOI: 10.1016/j.sjbs.2021.03.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/10/2021] [Accepted: 03/21/2021] [Indexed: 10/26/2022] Open
Abstract
Sponges accommodate a diverse group of microorganisms with varied metabolic capabilities. The bacterial associates of sponges are widely studied while our understanding of archaeal counterparts is scanty. In the present study, we report the archaeal associates of two sponges, Pseudoceratina purpurea (NCBI barcode: KX454492) and Cinachyra sp. (NCBI barcode: KX454495), found in the coral reef ecosystems of Gulf of Mannar, India. Archaea in the water column was predominated by members of class Halobacteria of Phylum Euryarchaeota (97%) followed by a minor fraction (3%) of Nitrosopumilus sp. of phylum Thaumarchaeota. Interestingly, Thaumarchaeota was identified as the sole archaeal population associated with the two sponges studied, among which Nitrosopumilus sp. occuppied 80 and 100% of the sequences in the clone library of P. purpurea and Cinachyra sp. respectively. Other archaea found in the P. purpurea were Nitrososphaera (10%) and unclassified ones (10%). The study identified Nitrosopumilus sp. as a unique symbiotic archaeon of sponges, P. purpurea and Cinachyra sp. The existence of host driven factors in selecting specific associates from a diverse group of archaea in the environment may need further investigations.
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Affiliation(s)
| | - Abdulaziz Anas
- CSIR-National Institute of Oceanography, Regional Centre, Cochin, Kerala 682 018, India
| | - P.A. Thomas
- Panachammoottil, Gandhipuram, Thiruvananthapuram, Kerala 695017, India
| | - Balu Tharakan
- CSIR-National Institute of Oceanography, Regional Centre, Cochin, Kerala 682 018, India
| | - Shanta Nair
- CSIR-National Institute of Oceanography, Regional Centre, Cochin, Kerala 682 018, India
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12
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Erngren I, Smit E, Pettersson C, Cárdenas P, Hedeland M. The Effects of Sampling and Storage Conditions on the Metabolite Profile of the Marine Sponge Geodia barretti. Front Chem 2021; 9:662659. [PMID: 34041223 PMCID: PMC8141568 DOI: 10.3389/fchem.2021.662659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/15/2021] [Indexed: 12/17/2022] Open
Abstract
Geodia barretti is a deep-sea marine sponge common in the north Atlantic and waters outside of Norway and Sweden. The sampling and subsequent treatment as well as storage of sponges for metabolomics analyses can be performed in different ways, the most commonly used being freezing (directly upon collection or later) or by storage in solvent, commonly ethanol, followed by freeze-drying. In this study we therefore investigated different sampling protocols and their effects on the detected metabolite profiles in liquid chromatography-mass spectrometry (LC-MS) using an untargeted metabolomics approach. Sponges (G. barretti) were collected outside the Swedish west coast and pieces from three sponge specimens were either flash frozen in liquid nitrogen, frozen later after the collection cruise, stored in ethanol or stored in methanol. The storage solvents as well as the actual sponge pieces were analyzed, all samples were analyzed with hydrophilic interaction liquid chromatography as well as reversed phase liquid chromatography with high resolution mass spectrometry using full-scan in positive and negative ionization mode. The data were evaluated using multivariate data analysis. The highest metabolite intensities were found in the frozen samples (flash frozen and frozen after sampling cruise) as well as in the storage solvents (methanol and ethanol). Metabolites extracted from the sponge pieces that had been stored in solvent were found in very low intensity, since the majority of metabolites were extracted to the solvents to a high degree. The exception being larger peptides and some lipids. The lowest variation between replicates were found in the flash frozen samples. In conclusion, the preferred method for sampling of sponges for metabolomics was found to be immediate freezing in liquid nitrogen. However, freezing the sponge samples after some time proved to be a reliable method as well, albeit with higher variation between the replicates. The study highlights the importance of saving ethanol extracts after preservation of specimens for biology studies; these valuable extracts could be further used in studies of natural products, chemosystematics or metabolomics.
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Affiliation(s)
- Ida Erngren
- Analytical Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Eva Smit
- BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Curt Pettersson
- Analytical Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Paco Cárdenas
- Pharmacognosy, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Mikael Hedeland
- Analytical Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
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13
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Ammonia-oxidizing archaea in biological interactions. J Microbiol 2021; 59:298-310. [DOI: 10.1007/s12275-021-1005-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 10/22/2022]
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14
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DeLong EF. Genome-enabled exploration of microbial ecology and evolution in the sea: a rising tide lifts all boats. Environ Microbiol 2021; 23:1301-1321. [PMID: 33459471 PMCID: PMC8049014 DOI: 10.1111/1462-2920.15403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 11/26/2022]
Abstract
As a young bacteriologist just launching my career during the early days of the 'microbial revolution' in the 1980s, I was fortunate to participate in some early discoveries, and collaborate in the development of cross-disciplinary methods now commonly referred to as "metagenomics". My early scientific career focused on applying phylogenetic and genomic approaches to characterize 'wild' bacteria, archaea and viruses in their natural habitats, with an emphasis on marine systems. These central interests have not changed very much for me over the past three decades, but knowledge, methodological advances and new theoretical perspectives about the microbial world certainly have. In this invited 'How we did it' perspective, I trace some of the trajectories of my lab's collective efforts over the years, including phylogenetic surveys of microbial assemblages in marine plankton and sediments, development of microbial community gene- and genome-enabled surveys, and application of genome-guided, cultivation-independent functional characterization of novel enzymes, pathways and their relationships to in situ biogeochemistry. Throughout this short review, I attempt to acknowledge, all the mentors, students, postdocs and collaborators who enabled this research. Inevitably, a brief autobiographical review like this cannot be fully comprehensive, so sincere apologies to any of my great colleagues who are not explicitly mentioned herein. I salute you all as well!
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Affiliation(s)
- Edward F DeLong
- Daniel K. Inouye Centre for Microbial Oceanography: Research and Education, University of Hawaii, Manoa, Honolulu, HI, 96822, USA
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15
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DeLong EF. Exploring Marine Planktonic Archaea: Then and Now. Front Microbiol 2021; 11:616086. [PMID: 33519774 PMCID: PMC7838436 DOI: 10.3389/fmicb.2020.616086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 12/18/2020] [Indexed: 12/24/2022] Open
Abstract
In 1977, Woese and Fox leveraged molecular phylogenetic analyses of ribosomal RNAs and identified a new microbial domain of life on Earth, the Archaebacteria (now known as Archaea). At the time of their discovery, only one archaebacterial group, the strictly anaerobic methanogens, was known. But soon, other phenotypically unrelated microbial isolates were shown to belong to the Archaea, many originating from extreme habitats, including extreme halophiles, extreme thermophiles, and thermoacidophiles. Since most Archaea seemed to inhabit extreme or strictly anoxic habitats, it came as a surprise in 1992 when two new lineages of archaea were reported to be abundant in oxygen rich, temperate marine coastal waters and the deep ocean. Since that time, studies of marine planktonic archaea have revealed many more surprises, including their unexpected ubiquity, unusual symbiotic associations, unpredicted physiologies and biogeochemistry, and global abundance. In this Perspective, early work conducted on marine planktonic Archaea by my lab group and others is discussed in terms of the relevant historical context, some of the original research motivations, and surprises and discoveries encountered along the way.
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Affiliation(s)
- Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography Research and Education, University of Hawai'i at Mănoa, Honolulu, HI, United States
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16
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Haber M, Burgsdorf I, Handley KM, Rubin-Blum M, Steindler L. Genomic Insights Into the Lifestyles of Thaumarchaeota Inside Sponges. Front Microbiol 2021; 11:622824. [PMID: 33537022 PMCID: PMC7848895 DOI: 10.3389/fmicb.2020.622824] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/14/2020] [Indexed: 11/28/2022] Open
Abstract
Sponges are among the oldest metazoans and their success is partly due to their abundant and diverse microbial symbionts. They are one of the few animals that have Thaumarchaeota symbionts. Here we compare genomes of 11 Thaumarchaeota sponge symbionts, including three new genomes, to free-living ones. Like their free-living counterparts, sponge-associated Thaumarchaeota can oxidize ammonia, fix carbon, and produce several vitamins. Adaptions to life inside the sponge host include enrichment in transposases, toxin-antitoxin systems and restriction modifications systems, enrichments previously reported also from bacterial sponge symbionts. Most thaumarchaeal sponge symbionts lost the ability to synthesize rhamnose, which likely alters their cell surface and allows them to evade digestion by the host. All but one archaeal sponge symbiont encoded a high-affinity, branched-chain amino acid transporter system that was absent from the analyzed free-living thaumarchaeota suggesting a mixotrophic lifestyle for the sponge symbionts. Most of the other unique features found in sponge-associated Thaumarchaeota, were limited to only a few specific symbionts. These features included the presence of exopolyphosphatases and a glycine cleavage system found in the novel genomes. Thaumarchaeota have thus likely highly specific interactions with their sponge host, which is supported by the limited number of host sponge species to which each of these symbionts is restricted.
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Affiliation(s)
- Markus Haber
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, České Budějovice, Czechia
| | - Ilia Burgsdorf
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Kim M. Handley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Maxim Rubin-Blum
- Israel Oceanographic and Limnological Research Institute, Haifa, Israel
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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17
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Archaeal communities of low and high microbial abundance sponges inhabiting the remote western Indian Ocean island of Mayotte. Antonie van Leeuwenhoek 2020; 114:95-112. [DOI: 10.1007/s10482-020-01503-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/25/2020] [Indexed: 12/11/2022]
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18
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Caballero S, Galeano AM, Lozano JD, Vives M. Description of the microbiota in epidermal mucus and skin of sharks ( Ginglymostoma cirratum and Negaprion brevirostris) and one stingray ( Hypanus americanus). PeerJ 2020; 8:e10240. [PMID: 33362953 PMCID: PMC7747685 DOI: 10.7717/peerj.10240] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/05/2020] [Indexed: 01/04/2023] Open
Abstract
Skin mucus in fish is the first barrier between the organism and the environment but the role of skin mucus in protecting fish against pathogens is not well understood. During copulation in sharks, the male bites the female generating wounds, which are then highly likely to become infected by opportunistic bacteria from the water or from the male shark's mouth. Describing the microbial component of epithelial mucus may allow future understanding of this first line of defense in sharks. In this study, we analyzed mucus and skin samples obtained from 19 individuals of two shark species and a stingray: the nurse shark (Ginglymostoma cirratum), the lemon shark (Negaprion brevirostris) and the southern stingray (Hypanus americanus). Total DNA was extracted from all samples, and the bacterial 16S rRNA gene (region V3-V4) was amplified and sequenced on the Ion Torrent Platform. Bacterial diversity (order) was higher in skin and mucus than in water. Order composition was more similar between the two shark species. Alpha-diversities (Shannon and Simpson) for OTUs (clusters of sequences defined by a 97% identity threshold for the16S rRNA gene) were high and there were non-significant differences between elasmobranch species or types of samples. We found orders of potentially pathogenic bacteria in water samples collected from the area where the animals were found, such as Pasteurellales (i.e., genus Pasteurella spp. and Haemophilus spp.) and Oceanospirillales (i.e., genus Halomonas spp.) but these were not found in the skin or mucus samples from any species. Some bacterial orders, such as Flavobacteriales, Vibrionales (i.e., genus Pseudoalteromonas), Lactobacillales and Bacillales were found only in mucus and skin samples. However, in a co-occurrence analyses, no significant relationship was found among these orders (strength less than 0.6, p-value > 0.01) but significant relationships were found among the order Trembayales, Fusobacteriales, and some previously described marine environmental Bacteria and Archaea, including Elusimicrobiales, Thermoproteales, Deinococcales and Desulfarculales. This is the first study focusing on elasmobranch microbial communities. The functional role and the benefits of these bacteria still needs understanding as well as the potential changes to microbial communities as a result of changing environmental conditions.
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Affiliation(s)
- Susana Caballero
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos, LEMVA, Biological Sciences Department, Universidad de los Andes, Bogota, Colombia
| | - Ana Maria Galeano
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos, LEMVA, Biological Sciences Department, Universidad de los Andes, Bogota, Colombia
| | - Juan Diego Lozano
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos, LEMVA, Biological Sciences Department, Universidad de los Andes, Bogota, Colombia
| | - Martha Vives
- Centro de Investigaciones Microbiológicas, CIMIC, Biological Sciences Department, Universidad de los Andes, Bogota, Colombia
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19
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Bibi F, Azhar EI. Analysis of bacterial communities in sponges and coral inhabiting Red Sea, using barcoded 454 pyrosequencing. Saudi J Biol Sci 2020; 28:847-854. [PMID: 33424375 PMCID: PMC7783839 DOI: 10.1016/j.sjbs.2020.11.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 11/18/2022] Open
Abstract
Microbial communities are linked with marine sponge are diverse in their structure and function. Our understanding of the sponge-associated microbial diversity is limited especially from Red Sea in Saudi Arabia where few species of sponges have been studied. Here we used pyrosequencing to study two marine sponges and coral species sampled from Obhur region from Red sea in Jeddah. A total of 168 operational taxonomic units (OTUs) were identified from Haliclona caerulea, Stylissa carteri and Rhytisma fulvum. Taxonomic identification of tag sequences of 16S ribosomal RNA revealed 6 different bacterial phyla and 9 different classes. A proportion of unclassified reads were was also observed in sponges and coral sample. We found diverse bacterial communities associated with two sponges and a coral sample. Diversity and richness estimates based on OUTs revealed that sponge H. caerulea had significantly high bacterial diversity. The identified OTUs showed unique clustering in three sponge samples as revealed by Principal coordinate analysis (PCoA). Proteobacteria (88-95%) was dominant phyla alonwith Bacteroidetes, Planctomycetes, Cyanobacteria, Firmicutes and Nitrospirae. Seventeen different genera were identified where genus Pseudoalteromonas was dominant in all three samples. This is first study to assess bacterial communities of sponge and coral sample that have never been studied before to unravel their microbial communities using 454-pyrosequencing method.
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Affiliation(s)
- Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
- Corresponding author at: Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
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20
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Abstract
Host-associated microbial communities have an important role in shaping the health and fitness of plants and animals. Most studies have focused on the bacterial, fungal or viral communities, but often the archaeal component has been neglected. The archaeal community, the so-called archaeome, is now increasingly recognized as an important component of host-associated microbiomes. It is composed of various lineages, including mainly Methanobacteriales and Methanomassiliicoccales (Euryarchaeota), as well as representatives of the Thaumarchaeota. Host-archaeome interactions have mostly been delineated from methanogenic archaea in the gastrointestinal tract, where they contribute to substantial methane production and are potentially also involved in disease-relevant processes. In this Review, we discuss the diversity and potential roles of the archaea associated with protists, plants and animals. We also present the current understanding of the archaeome in humans, the specific adaptations involved in interaction with the resident microbial community as well as with the host, and the roles of the archaeome in both health and disease.
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21
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de Oliveira BFR, Carr CM, Dobson ADW, Laport MS. Harnessing the sponge microbiome for industrial biocatalysts. Appl Microbiol Biotechnol 2020; 104:8131-8154. [PMID: 32827049 DOI: 10.1007/s00253-020-10817-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/29/2020] [Accepted: 08/05/2020] [Indexed: 12/31/2022]
Abstract
Within the marine sphere, host-associated microbiomes are receiving growing attention as prolific sources of novel biocatalysts. Given the known biocatalytic potential of poriferan microbial inhabitants, this review focuses on enzymes from the sponge microbiome, with special attention on their relevant properties and the wide range of their potential biotechnological applications within various industries. Cultivable bacterial and filamentous fungal isolates account for the majority of the enzymatic sources. Hydrolases, mainly glycoside hydrolases and carboxylesterases, are the predominant reported group of enzymes, with varying degrees of tolerance to alkaline pH and growing salt concentrations being common. Prospective areas for the application of these microbial enzymes include biorefinery, detergent, food and effluent treatment industries. Finally, alternative strategies to identify novel biocatalysts from the sponge microbiome are addressed, with an emphasis on modern -omics-based approaches that are currently available in the enzyme research arena. By providing this current overview of the field, we hope to not only increase the appetite of researchers to instigate forthcoming studies but also to stress how basic and applied research can pave the way for new biocatalysts from these symbiotic microbial communities in a productive fashion. KEY POINTS: • The sponge microbiome is a burgeoning source of industrial biocatalysts. • Sponge microbial enzymes have useful habitat-related traits for several industries. • Strategies are provided for the future discovery of microbial enzymes from sponges.
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Affiliation(s)
- Bruno Francesco Rodrigues de Oliveira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. .,School of Microbiology, University College Cork, Cork, Ireland.
| | - Clodagh M Carr
- School of Microbiology, University College Cork, Cork, Ireland
| | - Alan D W Dobson
- School of Microbiology, University College Cork, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland
| | - Marinella Silva Laport
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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22
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Qin W, Zheng Y, Zhao F, Wang Y, Urakawa H, Martens-Habbena W, Liu H, Huang X, Zhang X, Nakagawa T, Mende DR, Bollmann A, Wang B, Zhang Y, Amin SA, Nielsen JL, Mori K, Takahashi R, Virginia Armbrust E, Winkler MKH, DeLong EF, Li M, Lee PH, Zhou J, Zhang C, Zhang T, Stahl DA, Ingalls AE. Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea. ISME JOURNAL 2020; 14:2595-2609. [PMID: 32636492 PMCID: PMC7490402 DOI: 10.1038/s41396-020-0710-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 06/16/2020] [Accepted: 06/25/2020] [Indexed: 12/29/2022]
Abstract
Ammonia-oxidizing archaea (AOA) are among the most abundant and ubiquitous microorganisms in the ocean, exerting primary control on nitrification and nitrogen oxides emission. Although united by a common physiology of chemoautotrophic growth on ammonia, a corresponding high genomic and habitat variability suggests tremendous adaptive capacity. Here, we compared 44 diverse AOA genomes, 37 from species cultivated from samples collected across diverse geographic locations and seven assembled from metagenomic sequences from the mesopelagic to hadopelagic zones of the deep ocean. Comparative analysis identified seven major marine AOA genotypic groups having gene content correlated with their distinctive biogeographies. Phosphorus and ammonia availabilities as well as hydrostatic pressure were identified as selective forces driving marine AOA genotypic and gene content variability in different oceanic regions. Notably, AOA methylphosphonate biosynthetic genes span diverse oceanic provinces, reinforcing their importance for methane production in the ocean. Together, our combined comparative physiological, genomic, and metagenomic analyses provide a comprehensive view of the biogeography of globally abundant AOA and their adaptive radiation into a vast range of marine and terrestrial habitats.
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Affiliation(s)
- Wei Qin
- School of Oceanography, University of Washington, Seattle, WA, USA.
| | - Yue Zheng
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Feng Zhao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China. .,University of Chinese Academy of Sciences, Beijing, China.
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Hidetoshi Urakawa
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Davie, FL, USA
| | - Haodong Liu
- Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
| | - Xiaowu Huang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hong Kong, China
| | - Xinxu Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Tatsunori Nakagawa
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Daniel R Mende
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, USA
| | | | - Baozhan Wang
- Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Sciences and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Shady A Amin
- Department of Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Jeppe L Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Koji Mori
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Kisarazu, Chiba, Japan
| | - Reiji Takahashi
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | | | - Mari-K H Winkler
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, USA
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Po-Heng Lee
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hong Kong, China.,Department of Civil and Environmental Engineering, Imperial College London, London, UK
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.,Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,School of Environment, Tsinghua University, Beijing, China
| | - Chuanlun Zhang
- Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA, USA.
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23
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Oren A, Garrity GM, Parker CT, Chuvochina M, Trujillo ME. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2020; 70:3956-4042. [DOI: 10.1099/ijsem.0.003789] [Citation(s) in RCA: 782] [Impact Index Per Article: 195.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M. Garrity
- NamesforLife, LLC, PO Box 769, Okemos MI 48805-0769, USA
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| | | | - Maria Chuvochina
- Australian Centre for Ecogenomics, University of Queensland, St. Lucia QLD 4072, Brisbane, Australia
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007, Salamanca, Spain
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24
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Cleary DFR, Polónia ARM, Reijnen BT, Berumen ML, de Voogd NJ. Prokaryote Communities Inhabiting Endemic and Newly Discovered Sponges and Octocorals from the Red Sea. MICROBIAL ECOLOGY 2020; 80:103-119. [PMID: 31932882 DOI: 10.1007/s00248-019-01465-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
In the present study, we assessed prokaryotic communities of demosponges, a calcareous sponge, octocorals, sediment and seawater in coral reef habitat of the central Red Sea, including endemic species and species new to science. Goals of the study were to compare the prokaryotic communities of demosponges with the calcareous sponge and octocorals and to assign preliminary high microbial abundance (HMA) or low microbial abundance (LMA) status to the sponge species based on compositional trait data. Based on the compositional data, we were able to assign preliminary LMA or HMA status to all sponge species. Certain species, however, had traits of both LMA and HMA species. For example, the sponge Ectyoplasia coccinea, which appeared to be a LMA species, had traits, including a relatively high abundance of Chloroflexi members, that were more typical of HMA species. This included dominant OTUs assigned to two different classes within the Chloroflexi. The calcareous sponge clustered together with seawater, the known LMA sponge Stylissa carteri and other presumable LMA species. The two dominant OTUs of this species were assigned to the Deltaproteobacteria and had no close relatives in the GenBank database. The octocoral species in the present study had prokaryotic communities that were distinct from sediment, seawater and all sponge species. These were characterised by OTUs assigned to the orders Rhodospirillales, Cellvibrionales, Spirochaetales and the genus Endozoicomonas, which were rare or absent in samples from other biotopes.
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Affiliation(s)
- D F R Cleary
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| | - A R M Polónia
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - B T Reijnen
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - M L Berumen
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - N J de Voogd
- Marine Biodiversity, Naturalis Biodiversity Center, Leiden, The Netherlands
- Institute of Environmental Sciences, Environmental Biology Department, Leiden University, Leiden, The Netherlands
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25
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Zhong H, Lehtovirta-Morley L, Liu J, Zheng Y, Lin H, Song D, Todd JD, Tian J, Zhang XH. Novel insights into the Thaumarchaeota in the deepest oceans: their metabolism and potential adaptation mechanisms. MICROBIOME 2020; 8:78. [PMID: 32482169 PMCID: PMC7265257 DOI: 10.1186/s40168-020-00849-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/27/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Marine Group I (MGI) Thaumarchaeota, which play key roles in the global biogeochemical cycling of nitrogen and carbon (ammonia oxidizers), thrive in the aphotic deep sea with massive populations. Recent studies have revealed that MGI Thaumarchaeota were present in the deepest part of oceans-the hadal zone (depth > 6000 m, consisting almost entirely of trenches), with the predominant phylotype being distinct from that in the "shallower" deep sea. However, little is known about the metabolism and distribution of these ammonia oxidizers in the hadal water. RESULTS In this study, metagenomic data were obtained from 0-10,500 m deep seawater samples from the Mariana Trench. The distribution patterns of Thaumarchaeota derived from metagenomics and 16S rRNA gene sequencing were in line with that reported in previous studies: abundance of Thaumarchaeota peaked in bathypelagic zone (depth 1000-4000 m) and the predominant clade shifted in the hadal zone. Several metagenome-assembled thaumarchaeotal genomes were recovered, including a near-complete one representing the dominant hadal phylotype of MGI. Using comparative genomics, we predict that unexpected genes involved in bioenergetics, including two distinct ATP synthase genes (predicted to be coupled with H+ and Na+ respectively), and genes horizontally transferred from other extremophiles, such as those encoding putative di-myo-inositol-phosphate (DIP) synthases, might significantly contribute to the success of this hadal clade under the extreme condition. We also found that hadal MGI have the genetic potential to import a far higher range of organic compounds than their shallower water counterparts. Despite this trait, hadal MDI ammonia oxidation and carbon fixation genes are highly transcribed providing evidence they are likely autotrophic, contributing to the primary production in the aphotic deep sea. CONCLUSIONS Our study reveals potentially novel adaptation mechanisms of deep-sea thaumarchaeotal clades and suggests key functions of deep-sea Thaumarchaeota in carbon and nitrogen cycling. Video Abstract.
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Affiliation(s)
- Haohui Zhong
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Laura Lehtovirta-Morley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Jiwen Liu
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yanfen Zheng
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Heyu Lin
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Delei Song
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Jiwei Tian
- Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266100, China.
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Blank PN, Barnett AA, Ronnebaum TA, Alderfer KE, Gillott BN, Christianson DW, Himmelberger JA. Structural studies of geranylgeranylglyceryl phosphate synthase, a prenyltransferase found in thermophilic Euryarchaeota. Acta Crystallogr D Struct Biol 2020; 76:542-557. [PMID: 32496216 PMCID: PMC7271946 DOI: 10.1107/s2059798320004878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 04/05/2020] [Indexed: 12/26/2022] Open
Abstract
Archaea are uniquely adapted to thrive in harsh environments, and one of these adaptations involves the archaeal membrane lipids, which are characterized by their isoprenoid alkyl chains connected via ether linkages to glycerol 1-phosphate. The membrane lipids of the thermophilic and acidophilic euryarchaeota Thermoplasma volcanium are exclusively glycerol dibiphytanyl glycerol tetraethers. The first committed step in the biosynthetic pathway of these archaeal lipids is the formation of the ether linkage between glycerol 1-phosphate and geranylgeranyl diphosphate, and is catalyzed by the enzyme geranylgeranylglyceryl phosphate synthase (GGGPS). The 1.72 Å resolution crystal structure of GGGPS from T. volcanium (TvGGGPS) in complex with glycerol and sulfate is reported here. The crystal structure reveals TvGGGPS to be a dimer, which is consistent with the absence of the aromatic anchor residue in helix α5a that is required for hexamerization in other GGGPS homologs; the hexameric quaternary structure in GGGPS is thought to provide thermostability. A phylogenetic analysis of the Euryarchaeota and a parallel ancestral state reconstruction investigated the relationship between optimal growth temperature and the ancestral sequences. The presence of an aromatic anchor residue is not explained by temperature as an ecological parameter. An examination of the active site of the TvGGGPS dimer revealed that it may be able to accommodate longer isoprenoid substrates, supporting an alternative pathway of isoprenoid membrane-lipid synthesis.
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Affiliation(s)
- P. N. Blank
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - A. A. Barnett
- Department of Biology, DeSales University, 2755 Station Avenue, Center Valley, PA 18034, USA
| | - T. A. Ronnebaum
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - K. E. Alderfer
- Department of Chemistry and Physics, DeSales University, 2755 Station Avenue, Center Valley, PA 18034, USA
| | - B. N. Gillott
- Department of Chemistry and Physics, DeSales University, 2755 Station Avenue, Center Valley, PA 18034, USA
| | - D. W. Christianson
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA
| | - J. A. Himmelberger
- Department of Chemistry and Physics, DeSales University, 2755 Station Avenue, Center Valley, PA 18034, USA
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27
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Santiago Á, Razo-Hernández RS, Pastor N. Revealing the Structural Contributions to Thermal Adaptation of the TATA-Box Binding Protein: Molecular Dynamics and QSPR Analyses. J Chem Inf Model 2020; 60:866-879. [PMID: 31917925 DOI: 10.1021/acs.jcim.9b00824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The TATA-box binding protein (TBP) is an important element of the transcription machinery in archaea and eukaryotic organisms. TBP is expressed in organisms adapted to different temperatures, indicating a robust structure, and experimental studies have shown that the mid-unfolding temperature (Tm) of TBP is directly correlated with the optimal growth temperature (OGT) of the organism. To understand which are the relevant structural requirements for its stability, we present the first structural and dynamic computational study of TBPs, combining molecular dynamics (MD) simulations and a quantitative structure-property relationship (QSPR) over a set of TBPs of organisms adapted to different temperatures. We found that the main structural properties of TBP used to adapt to high temperatures are an increase in the ease of desolvation of charged residues at the surface, an increase in the local resiliency, the presence of Leu clusters in the protein core, and an increase in the loss of hydrophobic packing in the N-terminal subdomain. In view of our results, we consider that TBP is a good model to study thermal adaptation, and our analysis opens the possibility of performing protein engineering on TBPs to study transcription at high or low temperatures.
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Affiliation(s)
- Ángel Santiago
- Laboratorio de Dinámica de Proteínas, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas , Universidad Autónoma del Estado de Morelos , Av. Universidad 1001, Col. Chamilpa , Cuernavaca , Morelos 62209 , México
| | - Rodrigo Said Razo-Hernández
- Laboratorio de Dinámica de Proteínas, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas , Universidad Autónoma del Estado de Morelos , Av. Universidad 1001, Col. Chamilpa , Cuernavaca , Morelos 62209 , México
| | - Nina Pastor
- Laboratorio de Dinámica de Proteínas, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas , Universidad Autónoma del Estado de Morelos , Av. Universidad 1001, Col. Chamilpa , Cuernavaca , Morelos 62209 , México.,Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología , Universidad Nacional Autónoma de México , Av. Universidad 2001, Col. Chamilpa , Cuernavaca , Morelos 62210 , México
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Zhang F, Jonas L, Lin H, Hill RT. Microbially mediated nutrient cycles in marine sponges. FEMS Microbiol Ecol 2019; 95:5582607. [DOI: 10.1093/femsec/fiz155] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 10/04/2019] [Indexed: 01/05/2023] Open
Abstract
ABSTRACTEfficient nutrient cycles mediated by symbiotic microorganisms with their hosts are vital to support the high productivity of coral reef ecosystems. In these ecosystems, marine sponges are important habitat-forming organisms in the benthic community and harbor abundant microbial symbionts. However, few studies have reviewed the critical microbially mediated nutrient cycling processes in marine sponges. To bridge this gap, in this review article, we summarize existing knowledge and recent advances in understanding microbially mediated carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) cycles in sponges, propose a conceptual model that describes potential interactions and constraints in the major nutrient cycles, and suggest that shifting redox state induced by animal behavior like sponge pumping can exert great influence on the activities of symbiotic microbial communities. Constraints include the lack of knowledge on spatial and temporal variations and host behavior; more studies are needed in these areas. Sponge microbiomes may have a significant impact on the nutrient cycles in the world’s coral reef ecosystems.
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Affiliation(s)
- Fan Zhang
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Columbus Center, 701 East Pratt Street, Baltimore Maryland 21202, USA
| | - Lauren Jonas
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Columbus Center, 701 East Pratt Street, Baltimore Maryland 21202, USA
| | - Hanzhi Lin
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Columbus Center, 701 East Pratt Street, Baltimore Maryland 21202, USA
| | - Russell T Hill
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Columbus Center, 701 East Pratt Street, Baltimore Maryland 21202, USA
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Zhang S, Song W, Wemheuer B, Reveillaud J, Webster N, Thomas T. Comparative Genomics Reveals Ecological and Evolutionary Insights into Sponge-Associated Thaumarchaeota. mSystems 2019; 4:e00288-19. [PMID: 31409660 PMCID: PMC6697440 DOI: 10.1128/msystems.00288-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/22/2019] [Indexed: 01/25/2023] Open
Abstract
Thaumarchaeota are frequently reported to associate with marine sponges (phylum Porifera); however, little is known about the features that distinguish them from their free-living thaumarchaeal counterparts. In this study, thaumarchaeal metagenome-assembled genomes (MAGs) were reconstructed from metagenomic data sets derived from the marine sponges Hexadella detritifera, Hexadella cf. detritifera, and Stylissa flabelliformis Phylogenetic and taxonomic analyses revealed that the three thaumarchaeal MAGs represent two new species within the genus Nitrosopumilus and one novel genus, for which we propose the names "Candidatus UNitrosopumilus hexadellus," "Candidatus UNitrosopumilus detritiferus," and "Candidatus UCenporiarchaeum stylissum" (the U superscript indicates that the taxon is uncultured). Comparison of these genomes to data from the Sponge Earth Microbiome Project revealed that "Ca UCenporiarchaeum stylissum" has been exclusively detected in sponges and can hence be classified as a specialist, while "Ca UNitrosopumilus detritiferus" and "Ca UNitrosopumilus hexadellus" are also detected outside the sponge holobiont and likely lead a generalist lifestyle. Comparison of the sponge-associated MAGs to genomes of free-living Thaumarchaeota revealed signatures that indicate functional features of a sponge-associated lifestyle, and these features were related to nutrient transport and metabolism, restriction-modification, defense mechanisms, and host interactions. Each species exhibited distinct functional traits, suggesting that they have reached different stages of evolutionary adaptation and/or occupy distinct ecological niches within their sponge hosts. Our study therefore offers new evolutionary and ecological insights into the symbiosis between sponges and their thaumarchaeal symbionts.IMPORTANCE Sponges represent ecologically important models to understand the evolution of symbiotic interactions of metazoans with microbial symbionts. Thaumarchaeota are commonly found in sponges, but their potential adaptations to a host-associated lifestyle are largely unknown. Here, we present three novel sponge-associated thaumarchaeal species and compare their genomic and predicted functional features with those of closely related free-living counterparts. We found different degrees of specialization of these thaumarchaeal species to the sponge environment that is reflected in their host distribution and their predicted molecular and metabolic properties. Our results indicate that Thaumarchaeota may have reached different stages of evolutionary adaptation in their symbiosis with sponges.
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Affiliation(s)
- Shan Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- Center for Marine Science & Innovation, University of New South Wales, Sydney, Australia
| | - Weizhi Song
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- Center for Marine Science & Innovation, University of New South Wales, Sydney, Australia
| | - Bernd Wemheuer
- Center for Marine Science & Innovation, University of New South Wales, Sydney, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Julie Reveillaud
- ASTRE, INRA, CIRAD, University of Montpellier, Montpellier, France
| | - Nicole Webster
- Australian Institute of Marine Science, Townsville, Australia
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Australia
| | - Torsten Thomas
- Center for Marine Science & Innovation, University of New South Wales, Sydney, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
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Villegas-Plazas M, Wos-Oxley ML, Sanchez JA, Pieper DH, Thomas OP, Junca H. Variations in Microbial Diversity and Metabolite Profiles of the Tropical Marine Sponge Xestospongia muta with Season and Depth. MICROBIAL ECOLOGY 2019; 78:243-256. [PMID: 30413836 DOI: 10.1007/s00248-018-1285-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 10/30/2018] [Indexed: 06/08/2023]
Abstract
Xestospongia muta is among the most emblematic sponge species inhabiting coral reefs of the Caribbean Sea. Besides being the largest sponge species growing in the Caribbean, it is also known to produce secondary metabolites. This study aimed to assess the effect of depth and season on the symbiotic bacterial dynamics and major metabolite profiles of specimens of X. muta thriving in a tropical marine biome (Portobelo Bay, Panamá), which allow us to determine whether variability patterns are similar to those reported for subtropical latitudes. The bacterial assemblages were characterized using Illumina deep-sequencing and metabolomic profiles using UHPLC-DAD-ELSD from five depths (ranging 9-28 m) across two seasons (spring and autumn). Diverse symbiotic communities, representing 24 phyla with a predominance of Proteobacteria and Chloroflexi, were found. Although several thousands of OTUs were determined, most of them belong to the rare biosphere and only 23 to a core community. There was a significant difference between the structure of the microbial communities in respect to season (autumn to spring), with a further significant difference between depths only in autumn. This was partially mirrored in the metabolome profile, where the overall metabolite composition did not differ between seasons, but a significant depth gradient was observed in autumn. At the phyla level, Cyanobacteria, Firmicutes, Actinobacteria, and Spirochaete showed a mild-moderate correlation with the metabolome profile. The metabolomic profiles were mainly characterized by known brominated polyunsaturated fatty acids. This work presents findings about the composition and dynamics of the microbial assemblages of X. muta expanding and confirming current knowledge about its remarkable diversity and geographic variability as observed in this tropical marine biome.
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Affiliation(s)
- Marcela Villegas-Plazas
- RG Microbial Ecology: Metabolism, Genomics & Evolution, Div Ecogenomics & Holobionts, Microbiomas Foundation, LT11A, Chía, 250008, Colombia
| | - Melissa L Wos-Oxley
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Honorary Research Associate, South Australian Museum, Adelaide, Australia
| | - Juan A Sanchez
- Laboratorio de Biología Molecular Marina (BIOMMAR), Departmento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Olivier P Thomas
- Marine Biodiscovery, School of Chemistry and Ryan Institute, National University of Ireland Galway (NUI Galway), University Road, Galway, H91 TK33, Ireland
| | - Howard Junca
- RG Microbial Ecology: Metabolism, Genomics & Evolution, Div Ecogenomics & Holobionts, Microbiomas Foundation, LT11A, Chía, 250008, Colombia.
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31
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Lopes-dos-Santos RMA, De Troch M, Bossier P, Van Stappen G. Labelling halophilic Archaea using 13C and 15N stable isotopes: a potential tool to investigate haloarchaea consumption by metazoans. Extremophiles 2019; 23:359-365. [DOI: 10.1007/s00792-019-01084-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/15/2019] [Indexed: 11/30/2022]
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32
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Neave MJ, Apprill A, Aeby G, Miyake S, Voolstra CR. Microbial Communities of Red Sea Coral Reefs. CORAL REEFS OF THE RED SEA 2019. [DOI: 10.1007/978-3-030-05802-9_4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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33
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García-Bonilla E, Brandão PFB, Pérez T, Junca H. Stable and Enriched Cenarchaeum symbiosum and Uncultured Betaproteobacteria HF1 in the Microbiome of the Mediterranean Sponge Haliclona fulva (Demospongiae: Haplosclerida). MICROBIAL ECOLOGY 2019; 77:25-36. [PMID: 29766224 DOI: 10.1007/s00248-018-1201-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 05/03/2018] [Indexed: 06/08/2023]
Abstract
Sponges harbor characteristic microbiomes derived from symbiotic relationships shaping their lifestyle and survival. Haliclona fulva is encrusting marine sponge species dwelling in coralligenous accretions or semidark caves of the Mediterranean Sea and the near Atlantic Ocean. In this work, we characterized the abundance and core microbial community composition found in specimens of H. fulva by means of electron microscopy and 16S amplicon Illumina sequencing. We provide evidence of its low microbial abundance (LMA) nature. We found that the H. fulva core microbiome is dominated by sequences belonging to the orders Nitrosomonadales and Cenarchaeales. Seventy percent of the reads assigned to these phylotypes grouped in a very small number of high-frequency operational taxonomic units, representing niche-specific species Cenarchaeum symbiosum and uncultured Betaproteobacteria HF1, a new eubacterial ribotype variant found in H. fulva. The microbial composition of H. fulva is quite distinct from those reported in sponge species of the same Haliclona genus. We also detected evidence of an excretion/capturing loop between these abundant microorganisms and planktonic microbes by analyzing shifts in seawater planktonic microbial content exposed to healthy sponge specimens maintained in aquaria. Our results suggest that horizontal transmission is very likely the main mechanism for symbionts' acquisition by H. fulva. So far, this is the first shallow water sponge species harboring such a specific and predominant assemblage composed of these eubacterial and archaeal ribotypes. Our data suggests that this symbiotic relationship is very stable over time, indicating that the identified core microbial symbionts may play key roles in the holobiont functioning.
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Affiliation(s)
- Erika García-Bonilla
- RG Microbial Ecology: Metabolism, Genomics & Evolution, Div Ecogenomics & Holobionts, Microbiomas Foundation, LT 11, Chía, 250008, Colombia
| | - Pedro F B Brandão
- Laboratorio de Microbiología Ambiental y Aplicada, Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia, Avenida Carrera 30 No. 45-03, Bogotá, Colombia
| | - Thierry Pérez
- Station Marine d'Endoume SME - IMBE, Institut Méditerranéen de Biodiversité et d'Ecologie Marine et Continentale, UMR 7263 CNRS, Aix-Marseille Université, IRD, Avignon Université, Rue Batterie des Lions, 13007, Marseille, France
| | - Howard Junca
- RG Microbial Ecology: Metabolism, Genomics & Evolution, Div Ecogenomics & Holobionts, Microbiomas Foundation, LT 11, Chía, 250008, Colombia.
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34
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BluePharmTrain: Biology and Biotechnology of Marine Sponges. GRAND CHALLENGES IN MARINE BIOTECHNOLOGY 2018. [DOI: 10.1007/978-3-319-69075-9_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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35
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Rodrigues-Oliveira T, Belmok A, Vasconcellos D, Schuster B, Kyaw CM. Archaeal S-Layers: Overview and Current State of the Art. Front Microbiol 2017; 8:2597. [PMID: 29312266 PMCID: PMC5744192 DOI: 10.3389/fmicb.2017.02597] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/12/2017] [Indexed: 01/01/2023] Open
Abstract
In contrast to bacteria, all archaea possess cell walls lacking peptidoglycan and a number of different cell envelope components have also been described. A paracrystalline protein surface layer, commonly referred to as S-layer, is present in nearly all archaea described to date. S-layers are composed of only one or two proteins and form different lattice structures. In this review, we summarize current understanding of archaeal S-layer proteins, discussing topics such as structure, lattice type distribution among archaeal phyla and glycosylation. The hexagonal lattice type is dominant within the phylum Euryarchaeota, while in the Crenarchaeota this feature is mainly associated with specific orders. S-layers exclusive to the Crenarchaeota have also been described, which are composed of two proteins. Information regarding S-layers in the remaining archaeal phyla is limited, mainly due to organism description through only culture-independent methods. Despite the numerous applied studies using bacterial S-layers, few reports have employed archaea as a study model. As such, archaeal S-layers represent an area for exploration in both basic and applied research.
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Affiliation(s)
- Thiago Rodrigues-Oliveira
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
| | - Aline Belmok
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
| | - Deborah Vasconcellos
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
| | - Bernhard Schuster
- Department of NanoBiotechnology, Institute for Synthetic Bioarchitectures, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Cynthia M. Kyaw
- Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
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36
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Qin W, Heal KR, Ramdasi R, Kobelt JN, Martens-Habbena W, Bertagnolli AD, Amin SA, Walker CB, Urakawa H, Könneke M, Devol AH, Moffett JW, Armbrust EV, Jensen GJ, Ingalls AE, Stahl DA. Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota. Int J Syst Evol Microbiol 2017; 67:5067-5079. [PMID: 29034851 DOI: 10.1099/ijsem.0.002416] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four mesophilic, neutrophilic, and aerobic marine ammonia-oxidizing archaea, designated strains SCM1T, HCA1T, HCE1T and PS0T, were isolated from a tropical marine fish tank, dimly lit deep coastal waters, the lower euphotic zone of coastal waters, and near-surface sediment in the Puget Sound estuary, respectively. Cells are straight or slightly curved small rods, 0.15-0.26 µm in diameter and 0.50-1.59 µm in length. Motility was not observed, although strain PS0T possesses genes associated with archaeal flagella and chemotaxis, suggesting it may be motile under some conditions. Cell membranes consist of glycerol dibiphytanyl glycerol tetraether (GDGT) lipids, with crenarchaeol as the major component. Strain SCM1T displays a single surface layer (S-layer) with p6 symmetry, distinct from the p3-S-layer reported for the soil ammonia-oxidizing archaeon Nitrososphaera viennensis EN76T. Respiratory quinones consist of fully saturated and monounsaturated menaquinones with 6 isoprenoid units in the side chain. Cells obtain energy from ammonia oxidation and use carbon dioxide as carbon source; addition of an α-keto acid (α-ketoglutaric acid) was necessary to sustain growth of strains HCA1T, HCE1T, and PS0T. Strain PS0T uses urea as a source of ammonia for energy production and growth. All strains synthesize vitamin B1 (thiamine), B2 (riboflavin), B6 (pyridoxine), and B12 (cobalamin). Optimal growth occurs between 25 and 32 °C, between pH 6.8 and 7.3, and between 25 and 37 ‰ salinity. All strains have a low mol% G+C content of 33.0-34.2. Strains are related by 98 % or greater 16S rRNA gene sequence identity, sharing ~85 % 16S rRNA gene sequence identity with Nitrososphaera viennensis EN76T. All four isolates are well separated by phenotypic and genotypic characteristics and are here assigned to distinct species within the genus Nitrosopumilus gen. nov. Isolates SCM1T (=ATCC TSD-97T =NCIMB 15022T), HCA1T (=ATCC TSD-96T), HCE1T (=ATCC TSD-98T), and PS0T (=ATCC TSD-99T) are type strains of the species Nitrosopumilusmaritimus sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., respectively. In addition, we propose the family Nitrosopumilaceae fam. nov. and the order Nitrosopumilales ord. nov. within the class Nitrososphaeria.
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Affiliation(s)
- Wei Qin
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Katherine R Heal
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Rasika Ramdasi
- Division of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Julia N Kobelt
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Willm Martens-Habbena
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
- Department of Microbiology and Cell Science and Fort Lauderdale Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Florida, FL, USA
| | - Anthony D Bertagnolli
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shady A Amin
- Department of Chemistry, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Christopher B Walker
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Hidetoshi Urakawa
- Department of Marine and Ecological Sciences, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Martin Könneke
- Marine Archaea Group, MARUM-Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Allan H Devol
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - James W Moffett
- Departments of Biological Sciences and Earth Sciences and Civil and Environmental Engineering, University of Southern California, Los Angeles, CA, USA
| | | | - Grant J Jensen
- Division of Biology, California Institute of Technology, Pasadena, CA, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
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37
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Cleary DFR, Polónia ARM. Bacterial and archaeal communities inhabiting mussels, sediment and water in Indonesian anchialine lakes. Antonie Van Leeuwenhoek 2017; 111:237-257. [PMID: 29027059 DOI: 10.1007/s10482-017-0944-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/13/2017] [Indexed: 11/24/2022]
Abstract
Anchialine lakes are a globally rare and unique ecosystem consisting of saline lakes surrounded by land and isolated from the surrounding marine environment. These lakes host a unique flora and fauna including numerous endemic species. Relatively few studies have, however, studied the prokaryote communities present in these lakes and compared them with the surrounding 'open water' marine environment. In the present study, we used a 16S rRNA gene barcoded pyrosequencing approach to examine prokaryote (Bacteria and Archaea) composition in three distinct biotopes (sediment, water and the mussel Brachidontes sp.) inhabiting four habitats, namely, three marine lakes and the surrounding marine environment of Berau, Indonesia. Biotope and habitat proved significant predictors of variation in bacterial and archaeal composition and higher taxon abundance. Most bacterial sequences belonged to OTUs assigned to the Proteobacteria. Compared to sediment and water, mussels had relatively high abundances of the classes Mollicutes and Epsilonproteobacteria. Most archaeal sequences, in turn, belonged to OTUs assigned to the Crenarchaeota with the relative abundance of crenarchaeotes highest in mussel samples. For both Bacteria and Archaea, the main variation in composition was between water samples on the one hand and sediment and mussel samples on the other. Sediment and mussels also shared much more OTUs than either shared with water. Abundant bacterial OTUs in mussels were related to organisms previously obtained from corals, oysters and the deepsea mussel Bathymodiolus manusensis. Abundant archaeal OTUs in mussels, in contrast, were closely related to organisms previously obtained from sediment.
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Affiliation(s)
- D F R Cleary
- CESAM and Department of Biology, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| | - A R M Polónia
- CESAM and Department of Biology, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
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Siliakus MF, van der Oost J, Kengen SWM. Adaptations of archaeal and bacterial membranes to variations in temperature, pH and pressure. Extremophiles 2017; 21:651-670. [PMID: 28508135 PMCID: PMC5487899 DOI: 10.1007/s00792-017-0939-x] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 04/29/2017] [Indexed: 12/30/2022]
Abstract
The cytoplasmic membrane of a prokaryotic cell consists of a lipid bilayer or a monolayer that shields the cellular content from the environment. In addition, the membrane contains proteins that are responsible for transport of proteins and metabolites as well as for signalling and energy transduction. Maintenance of the functionality of the membrane during changing environmental conditions relies on the cell's potential to rapidly adjust the lipid composition of its membrane. Despite the fundamental chemical differences between bacterial ester lipids and archaeal ether lipids, both types are functional under a wide range of environmental conditions. We here provide an overview of archaeal and bacterial strategies of changing the lipid compositions of their membranes. Some molecular adjustments are unique for archaea or bacteria, whereas others are shared between the two domains. Strikingly, shared adjustments were predominantly observed near the growth boundaries of bacteria. Here, we demonstrate that the presence of membrane spanning ether-lipids and methyl branches shows a striking relationship with the growth boundaries of archaea and bacteria.
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Affiliation(s)
- Melvin F Siliakus
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
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Zhou H, Liu B, Wang Q, Sun J, Xie G, Ren N, Ren ZJ, Xing D. Pulse electromagnetic fields enhance extracellular electron transfer in magnetic bioelectrochemical systems. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:238. [PMID: 29075322 PMCID: PMC5644122 DOI: 10.1186/s13068-017-0929-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 10/10/2017] [Indexed: 05/15/2023]
Abstract
BACKGROUND Microbial extracellular electron transfer (EET) is essential in driving the microbial interspecies interaction and redox reactions in bioelectrochemical systems (BESs). Magnetite (Fe3O4) and magnetic fields (MFs) were recently reported to promote microbial EET, but the mechanisms of MFs stimulation of EET and current generation in BESs are not known. This study investigates the behavior of current generation and EET in a state-of-the-art pulse electromagnetic field (PEMF)-assisted magnetic BES (PEMF-MBES), which was equipped with magnetic carbon particle (Fe3O4@N-mC)-coated electrodes. Illumina Miseq sequencing of 16S rRNA gene amplicons was also conducted to reveal the changes of microbial communities and interactions on the anode in response to magnetic field. RESULTS PEMF had significant influences on current generation. When reactors were operated in microbial fuel cell (MFC) mode with pulse electromagnetic field (PEMF-MMFCs), power densities increased by 25.3-36.0% compared with no PEMF control MFCs (PEMF-OFF-MMFCs). More interestingly, when PEMF was removed, the power density dropped by 25.7%, while when PEMF was reintroduced, the value was restored to the previous level. Illumina sequencing of 16S rRNA gene amplicon and principal component analysis (PCA) based on operational taxonomic units (OTUs) indicate that PEMFs led to the shifts in microbial community and changes in species evenness that decreased biofilm microbial diversity. Geobacter spp. were found dominant in all anode biofilms, but the relative abundance in PEMF-MMFCs (86.1-90.0%) was higher than in PEMF-OFF-MMFCs (82.5-82.7%), indicating that the magnetic field enriched Geobacter on the anode. The current generation of Geobacter-inoculated microbial electrolysis cells (MECs) presented the same change regularity, the accordingly increase or decrease corresponding with switch of PEMF, which confirmed the reversible stimulation of PEMFs on microbial electron transfer. CONCLUSION The pulse electromagnetic field (PEMF) showed significant influence on state-of-the-art pulse magnetic bioelectrochemical systems (PEMF-MBES) in terms of current generation and microbial ecology. EET was instantaneously and reversibly enhanced in MBESs inoculated with either mixed-culture or Geobacter. PEMF notably decreased bacterial and archaeal diversities of the anode biofilms in MMFCs via changing species evenness rather than species richness, and facilitated specific enrichment of exoelectrogenic bacteria (Geobacter) on the anode surface. This study demonstrates a new magnetic approach for understanding and facilitating microbial electrochemical activities.
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Affiliation(s)
- Huihui Zhou
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Nangang District, P.O. Box 2614, Harbin, 150090 Heilongjiang China
| | - Bingfeng Liu
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Nangang District, P.O. Box 2614, Harbin, 150090 Heilongjiang China
| | - Qisong Wang
- School of Electrical Engineering and Automation, Harbin Institute of Technology, Harbin, 150001 China
| | - Jianmin Sun
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Nangang District, P.O. Box 2614, Harbin, 150090 Heilongjiang China
- The Academy of Fundamental and Interdisciplinary Science, Harbin Institute of Technology, Harbin, 150080 China
| | - Guojun Xie
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Nangang District, P.O. Box 2614, Harbin, 150090 Heilongjiang China
| | - Nanqi Ren
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Nangang District, P.O. Box 2614, Harbin, 150090 Heilongjiang China
| | - Zhiyong Jason Ren
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, CO 80309 USA
| | - Defeng Xing
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 73 Huanghe Road, Nangang District, P.O. Box 2614, Harbin, 150090 Heilongjiang China
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Samson RY, Dobro MJ, Jensen GJ, Bell SD. The Structure, Function and Roles of the Archaeal ESCRT Apparatus. Subcell Biochem 2017; 84:357-377. [PMID: 28500532 DOI: 10.1007/978-3-319-53047-5_12] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Although morphologically resembling bacteria, archaea constitute a distinct domain of life with a closer affiliation to eukaryotes than to bacteria. This similarity is seen in the machineries for a number of essential cellular processes, including DNA replication and gene transcription. Perhaps surprisingly, given their prokaryotic morphology, some archaea also possess a core cell division apparatus that is related to that involved in the final stages of membrane abscission in vertebrate cells, the ESCRT machinery.
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Affiliation(s)
- Rachel Y Samson
- Department of Molecular and Cellular Biochemistry, Indiana University, Simon Hall MSB, 212 S Hawthorne Drive, Bloomington, IN, 47405, USA
| | - Megan J Dobro
- School of Natural Science, Hampshire College, Amherst, MA, 01002, USA
| | - Grant J Jensen
- Division of Biology, California Institute of Technology, Pasadena, CA, 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Stephen D Bell
- Department of Molecular and Cellular Biochemistry, Indiana University, Simon Hall MSB, 212 S Hawthorne Drive, Bloomington, IN, 47405, USA.
- Department of Biology, Indiana University, Simon Hall MSB, 212 S Hawthorne Drive, Bloomington, IN, 47405, USA.
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Comparison of archaeal and bacterial communities in two sponge species and seawater from an Indonesian coral reef environment. Mar Genomics 2016; 29:69-80. [DOI: 10.1016/j.margen.2016.04.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/28/2016] [Accepted: 04/28/2016] [Indexed: 12/17/2022]
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López-Legentil S, Turon X, Erwin PM. Feeding cessation alters host morphology and bacterial communities in the ascidian Pseudodistoma crucigaster. Front Zool 2016; 13:2. [PMID: 26770257 PMCID: PMC4712478 DOI: 10.1186/s12983-016-0134-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 01/07/2016] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Ascidians can associate with abundant and diverse consortia of microbial symbionts, yet these communities remain unexamined for the majority of host ascidians and little is known about host-symbiont interactions. METHODS We coupled electron microscopy and 16S rRNA gene tag pyrosequencing to investigate the bacterial communities associated with the colonial ascidian Pseudodistoma crucigaster, a species endemic to the Mediterranean Sea that has a life cycle with two phases: actively-filtering (active) and non-filtering (resting) forms. RESULTS Resting colonies exhibited a reduced branchial sac (feeding apparatus) and a thickened cuticle. Electron microscope images also suggested higher abundance of colonizing microorganisms on surfaces of resting colonies. Accordingly, bacterial sequences associated with environmental sources (sediment and biofilms, >99 % similarity) were detected exclusively in resting colonies. Bacterial communities of P. crucigaster colonies (active and resting) were dominated by 3 core taxa affiliated (>94 % similarity) with previously described symbiotic Alphaproteobacteria in marine invertebrates. Shifts in rare bacteria were detected when ascidians entered the resting phase, including the appearance of strictly anaerobic lineages and nitrifying bacterial guilds. CONCLUSIONS These findings suggest that physical (thickened cuticle) and metabolic (feeding cessation) changes in host ascidians have cascading effects on associated bacteria, where modified oxygen concentrations and chemical substrates for microbial metabolism may create anaerobic microhabitats and promote colonization by environmental microorganisms.
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Affiliation(s)
- Susanna López-Legentil
- Department of Biology & Marine Biology, and Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, 28409 Wilmington, USA
| | - Xavier Turon
- Center for Advanced Studies of Blanes (CEAB-CSIC), Accés Cala S. Francesc 14, 17300 Blanes Girona, Spain
| | - Patrick M Erwin
- Department of Biology & Marine Biology, and Center for Marine Science, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, 28409 Wilmington, USA
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Sedimentary archaeal amoA gene abundance reflects historic nutrient level and salinity fluctuations in Qinghai Lake, Tibetan Plateau. Sci Rep 2015; 5:18071. [PMID: 26666501 PMCID: PMC4678299 DOI: 10.1038/srep18071] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/10/2015] [Indexed: 11/09/2022] Open
Abstract
Integration of DNA derived from ancient phototrophs with their characteristic lipid biomarkers has been successfully employed to reconstruct paleoenvironmental conditions. However, it is poorly known that whether the DNA and lipids of microbial functional aerobes (such as ammonia-oxidizing archaea: AOA) can be used for reconstructing past environmental conditions. Here we identify and quantify the AOA amoA genes (encoding the alpha subunit of ammonia monooxygenases) preserved in a 5.8-m sediment core (spanning the last 18,500 years) from Qinghai Lake. Parallel analyses revealed that low amoA gene abundance corresponded to high total organic carbon (TOC) and salinity, while high amoA gene abundance corresponded to low TOC and salinity. In the Qinghai Lake region, TOC can serve as an indicator of paleo-productivity and paleo-precipitation, which is related to historic nutrient input and salinity. So our data suggest that temporal variation of AOA amoA gene abundance preserved in Qinghai Lake sediment may reflect the variations of nutrient level and salinity throughout the late Pleistocene and Holocene in the Qinghai Lake region.
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Salhi A, Essack M, Radovanovic A, Marchand B, Bougouffa S, Antunes A, Simoes MF, Lafi FF, Motwalli OA, Bokhari A, Malas T, Amoudi SA, Othum G, Allam I, Mineta K, Gao X, Hoehndorf R, C Archer JA, Gojobori T, Bajic VB. DESM: portal for microbial knowledge exploration systems. Nucleic Acids Res 2015; 44:D624-33. [PMID: 26546514 PMCID: PMC4702830 DOI: 10.1093/nar/gkv1147] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 10/19/2015] [Indexed: 12/31/2022] Open
Abstract
Microorganisms produce an enormous variety of chemical compounds. It is of general interest for microbiology and biotechnology researchers to have means to explore information about molecular and genetic basis of functioning of different microorganisms and their ability for bioproduction. To enable such exploration, we compiled 45 topic-specific knowledgebases (KBs) accessible through DESM portal (www.cbrc.kaust.edu.sa/desm). The KBs contain information derived through text-mining of PubMed information and complemented by information data-mined from various other resources (e.g. ChEBI, Entrez Gene, GO, KOBAS, KEGG, UniPathways, BioGrid). All PubMed records were indexed using 4 538 278 concepts from 29 dictionaries, with 1 638 986 records utilized in KBs. Concepts used are normalized whenever possible. Most of the KBs focus on a particular type of microbial activity, such as production of biocatalysts or nutraceuticals. Others are focused on specific categories of microorganisms, e.g. streptomyces or cyanobacteria. KBs are all structured in a uniform manner and have a standardized user interface. Information exploration is enabled through various searches. Users can explore statistically most significant concepts or pairs of concepts, generate hypotheses, create interactive networks of associated concepts and export results. We believe DESM will be a useful complement to the existing resources to benefit microbiology and biotechnology research.
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Affiliation(s)
- Adil Salhi
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Magbubah Essack
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Aleksandar Radovanovic
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | | | - Salim Bougouffa
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Andre Antunes
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Marta Filipa Simoes
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Feras F Lafi
- King Abdullah University of Science and Technology (KAUST), Center for Desert Agriculture (CDA), Thuwal 23955-6900, Kingdom of Saudi Arabia King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Olaa A Motwalli
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Ameerah Bokhari
- King Abdullah University of Science and Technology (KAUST), Center for Desert Agriculture (CDA), Thuwal 23955-6900, Kingdom of Saudi Arabia King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Tariq Malas
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Soha Al Amoudi
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Ghofran Othum
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Intikhab Allam
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Katsuhiko Mineta
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Robert Hoehndorf
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - John A C Archer
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Takashi Gojobori
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Vladimir B Bajic
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal 23955-6900, Kingdom of Saudi Arabia
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Cleary DFR, de Voogd NJ, Polónia ARM, Freitas R, Gomes NCM. Composition and Predictive Functional Analysis of Bacterial Communities in Seawater, Sediment and Sponges in the Spermonde Archipelago, Indonesia. MICROBIAL ECOLOGY 2015; 70:889-903. [PMID: 26072397 DOI: 10.1007/s00248-015-0632-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 05/21/2015] [Indexed: 05/23/2023]
Abstract
In this study, we used a 16S rRNA gene barcoded pyrosequencing approach to sample bacterial communities from six biotopes, namely, seawater, sediment and four sponge species (Stylissa carteri, Stylissa massa, Xestospongia testudinaria and Hyrtios erectus) inhabiting coral reefs of the Spermonde Archipelago, South Sulawesi, Indonesia. Samples were collected along a pronounced onshore to offshore environmental gradient. Our goals were to (1) compare higher taxon abundance among biotopes, (2) test to what extent variation in bacterial composition can be explained by the biotope versus environment, (3) identify dominant (>300 sequences) bacterial operational taxonomic units (OTUs) and their closest known relatives and (4) assign putative functions to the sponge bacterial communities using a recently developed predictive metagenomic approach. We observed marked differences in bacterial composition and the relative abundance of the most abundant phyla, classes and orders among sponge species, seawater and sediment. Although all biotopes housed compositionally distinct bacterial communities, there were three prominent clusters. These included (1) both Stylissa species and seawater, (2) X. testudinaria and H. erectus and (3) sediment. Bacterial communities sampled from the same biotope, but different environments (based on proximity to the coast) were much more similar than bacterial communities from different biotopes in the same environment. The biotope thus appears to be a much more important structuring force than the surrounding environment. There were concomitant differences in the predicted counts of KEGG orthologs (KOs) suggesting that bacterial communities housed in different sponge species, sediment and seawater perform distinct functions. In particular, the bacterial communities of both Stylissa species were predicted to be enriched for KOs related to chemotaxis, nitrification and denitrification whereas bacterial communities in X. testudinaria and H. erectus were predicted to be enriched for KOs related to the toxin-antitoxin (TA) system, nutrient starvation and heavy metal export.
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Affiliation(s)
- Daniel F R Cleary
- Departamento de Biologia, Centro de Estudos do Ambiente e do Mar (CESAM), Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| | - Nicole J de Voogd
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, The Netherlands
| | - Ana R M Polónia
- Departamento de Biologia, Centro de Estudos do Ambiente e do Mar (CESAM), Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Rossana Freitas
- Departamento de Biologia, Centro de Estudos do Ambiente e do Mar (CESAM), Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Newton C M Gomes
- Departamento de Biologia, Centro de Estudos do Ambiente e do Mar (CESAM), Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
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Acosta S, Carela M, Garcia-Gonzalez A, Gines M, Vicens L, Cruet R, Massey SE. DNA Repair Is Associated with Information Content in Bacteria, Archaea, and DNA Viruses. J Hered 2015; 106:644-59. [PMID: 26320243 DOI: 10.1093/jhered/esv055] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 07/07/2015] [Indexed: 11/13/2022] Open
Abstract
The concept of a "proteomic constraint" proposes that DNA repair capacity is positively correlated with the information content of a genome, which can be approximated to the size of the proteome (P). This in turn implies that DNA repair genes are more likely to be present in genomes with larger values of P. This stands in contrast to the common assumption that informational genes have a core function and so are evenly distributed across organisms. We examined the presence/absence of 18 DNA repair genes in bacterial genomes. A positive relationship between gene presence and P was observed for 17 genes in the total dataset, and 16 genes when only nonintracellular bacteria were examined. A marked reduction of DNA repair genes was observed in intracellular bacteria, consistent with their reduced value of P. We also examined archaeal and DNA virus genomes, and show that the presence of DNA repair genes is likewise related to a larger value of P. In addition, the products of the bacterial genes mutY, vsr, and ndk, involved in the correction of GC/AT mutations, are strongly associated with reduced genome GC content. We therefore propose that a reduction in information content leads to a loss of DNA repair genes and indirectly to a reduction in genome GC content in bacteria by exposure to the underlying AT mutation bias. The reduction in P may also indirectly lead to the increase in substitution rates observed in intracellular bacteria via loss of DNA repair genes.
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Affiliation(s)
- Sharlene Acosta
- From the Department of Biology, University of Puerto Rico-Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico (Acosta, Carela, Garcia-Gonzalez, Gines, Vicens, Cruet, and Massey)
| | - Miguelina Carela
- From the Department of Biology, University of Puerto Rico-Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico (Acosta, Carela, Garcia-Gonzalez, Gines, Vicens, Cruet, and Massey)
| | - Aurian Garcia-Gonzalez
- From the Department of Biology, University of Puerto Rico-Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico (Acosta, Carela, Garcia-Gonzalez, Gines, Vicens, Cruet, and Massey)
| | - Mariela Gines
- From the Department of Biology, University of Puerto Rico-Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico (Acosta, Carela, Garcia-Gonzalez, Gines, Vicens, Cruet, and Massey)
| | - Luis Vicens
- From the Department of Biology, University of Puerto Rico-Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico (Acosta, Carela, Garcia-Gonzalez, Gines, Vicens, Cruet, and Massey)
| | - Ricardo Cruet
- From the Department of Biology, University of Puerto Rico-Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico (Acosta, Carela, Garcia-Gonzalez, Gines, Vicens, Cruet, and Massey)
| | - Steven E Massey
- From the Department of Biology, University of Puerto Rico-Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico (Acosta, Carela, Garcia-Gonzalez, Gines, Vicens, Cruet, and Massey).
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From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems. Cell Mol Life Sci 2015; 72:4287-308. [PMID: 26254872 PMCID: PMC4611022 DOI: 10.1007/s00018-015-2004-1] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 07/23/2015] [Accepted: 07/28/2015] [Indexed: 12/30/2022]
Abstract
Microorganisms and the viruses that infect them are the most numerous biological entities on Earth and enclose its greatest biodiversity and genetic reservoir. With strength in their numbers, these microscopic organisms are major players in the cycles of energy and matter that sustain all life. Scientists have only scratched the surface of this vast microbial world through culture-dependent methods. Recent developments in generating metagenomes, large random samples of nucleic acid sequences isolated directly from the environment, are providing comprehensive portraits of the composition, structure, and functioning of microbial communities. Moreover, advances in metagenomic analysis have created the possibility of obtaining complete or nearly complete genome sequences from uncultured microorganisms, providing important means to study their biology, ecology, and evolution. Here we review some of the recent developments in the field of metagenomics, focusing on the discovery of genetic novelty and on methods for obtaining uncultured genome sequences, including through the recycling of previously published datasets. Moreover we discuss how metagenomics has become a core scientific tool to characterize eco-evolutionary patterns of microbial ecosystems, thus allowing us to simultaneously discover new microbes and study their natural communities. We conclude by discussing general guidelines and challenges for modeling the interactions between uncultured microorganisms and viruses based on the information contained in their genome sequences. These models will significantly advance our understanding of the functioning of microbial ecosystems and the roles of microbes in the environment.
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Yang Q, Franco CMM, Zhang W. Sponge-associated actinobacterial diversity: validation of the methods of actinobacterial DNA extraction and optimization of 16S rRNA gene amplification. Appl Microbiol Biotechnol 2015; 99:8731-40. [PMID: 26245685 DOI: 10.1007/s00253-015-6875-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/16/2015] [Accepted: 07/21/2015] [Indexed: 11/26/2022]
Abstract
Experiments were designed to validate the two common DNA extraction protocols (CTAB-based method and DNeasy Blood & Tissue Kit) used to effectively recover actinobacterial DNA from sponge samples in order to study the sponge-associated actinobacterial diversity. This was done by artificially spiking sponge samples with actinobacteria (spores, mycelia and a combination of the two). Our results demonstrated that both DNA extraction methods were effective in obtaining DNA from the sponge samples as well as the sponge samples spiked with different amounts of actinobacteria. However, it was noted that in the presence of the sponge, the bacterial 16S rRNA gene could not be amplified unless the combined DNA template was diluted. To test the hypothesis that the extracted sponge DNA contained inhibitors, dilutions of the DNA extracts were tested for six sponge species representing five orders. The results suggested that the inhibitors were co-extracted with the sponge DNA, and a high dilution of this DNA was required for the successful PCR amplification for most of the samples. The optimized PCR conditions, including primer selection, PCR reaction system and program optimization, further improved the PCR performance. However, no single PCR condition was found to be suitable for the diverse sponge samples using various primer sets. These results highlight for the first time that the DNA extraction methods used are effective in obtaining actinobacterial DNA and that the presence of inhibitors in the sponge DNA requires high dilution coupled with fine tuning of the PCR conditions to achieve success in the study of sponge-associated actinobacterial diversity.
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Affiliation(s)
- Qi Yang
- Centre for Marine Bioproducts Development, Adelaide, SA, 5042, Australia
- Department of Medical Biotechnology, School of Medicine, Flinders University, Adelaide, SA, 5042, Australia
| | - Christopher M M Franco
- Centre for Marine Bioproducts Development, Adelaide, SA, 5042, Australia.
- Department of Medical Biotechnology, School of Medicine, Flinders University, Adelaide, SA, 5042, Australia.
| | - Wei Zhang
- Centre for Marine Bioproducts Development, Adelaide, SA, 5042, Australia.
- Department of Medical Biotechnology, School of Medicine, Flinders University, Adelaide, SA, 5042, Australia.
- Centre for Marine Drugs, Renji Hospital, Shanghai Jiaotong University, Shanghai, 200240, China.
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Hong JK, Cho JC. Environmental Variables Shaping the Ecological Niche of Thaumarchaeota in Soil: Direct and Indirect Causal Effects. PLoS One 2015; 10:e0133763. [PMID: 26241328 PMCID: PMC4524719 DOI: 10.1371/journal.pone.0133763] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 07/01/2015] [Indexed: 11/18/2022] Open
Abstract
To find environmental variables (EVs) shaping the ecological niche of the archaeal phylum Thaumarchaeota in terrestrial environments, we determined the abundance of Thaumarchaeota in various soil samples using real-time PCR targeting thaumarchaeotal 16S rRNA gene sequences. We employed our previously developed primer, THAUM-494, which had greater coverage for Thaumarchaeota and lower tolerance to nonthaumarchaeotal taxa than previous Thaumarchaeota-directed primers. The relative abundance estimates (RVs) of Thaumarchaeota (RTHAUM), Archaea (RARCH), and Bacteria (RBACT) were subjected to a series of statistical analyses. Redundancy analysis (RDA) showed a significant (p < 0.05) canonical relationship between RVs and EVs. Negative causal relationships between RTHAUM and nutrient level-related EVs were observed in an RDA biplot. These negative relationships were further confirmed by correlation and regression analyses. Total nitrogen content (TN) appeared to be the EV that affected RTHAUM most strongly, and total carbon content (TC), which reflected the content of organic matter (OM), appeared to be the EV that affected it least. However, in the path analysis, a path model indicated that TN might be a mediator EV that could be controlled directly by the OM. Additionally, another path model implied that water content (WC) might also indirectly affect RTHAUM by controlling ammonium nitrogen (NH4+-N) level through ammonification. Thus, although most directly affected by NH4+-N, RTHAUM could be ultimately determined by OM content, suggesting that Thaumarchaeota could prefer low-OM or low-WC conditions, because either of these EVs could subsequently result in low levels of NH4+-N in soil.
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Affiliation(s)
- Jin-Kyung Hong
- Institute of Environmental Sciences and Department of Environmental Sciences, Hankuk University of Foreign Studies, Yong-In, Korea
| | - Jae-Chang Cho
- Institute of Environmental Sciences and Department of Environmental Sciences, Hankuk University of Foreign Studies, Yong-In, Korea
- * E-mail:
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Polymenakou PN, Christakis CA, Mandalakis M, Oulas A. Pyrosequencing analysis of microbial communities reveals dominant cosmopolitan phylotypes in deep-sea sediments of the eastern Mediterranean Sea. Res Microbiol 2015; 166:448-457. [PMID: 25908548 DOI: 10.1016/j.resmic.2015.03.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 01/22/2015] [Accepted: 03/23/2015] [Indexed: 10/23/2022]
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