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Abdallah RZ, Elbehery AHA, Ahmed SF, Ouf A, Malash MN, Liesack W, Siam R. Deciphering the functional and structural complexity of the Solar Lake flat mat microbial benthic communities. mSystems 2024; 9:e0009524. [PMID: 38727215 PMCID: PMC11237645 DOI: 10.1128/msystems.00095-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 04/04/2024] [Indexed: 06/19/2024] Open
Abstract
The Solar Lake in Taba, Egypt, encompasses one of the few modern-day microbial mats' systems metabolically analogous to Precambrian stromatolites. Solar Lake benthic communities and their adaptation to the Lake's unique limnological cycle have not been described for over two decades. In this study, we revisit the flat mat and describe the summer's shallow water versus exposed microbial community; the latter occurs in response to the seasonal partial receding of water. We employed metagenomic NovaSeq-6000 shotgun sequencing and 16S rRNA, mcrA, and dsrB quantitative PCR. A total of 292 medium-to-high-quality metagenome-assembled genomes (MAGs) were reconstructed. At the structural level, Candidatus Aenigmatarchaeota, Micrarchaeota, and Omnitrophota MAGs were exclusively detected in the shallow-water mats, whereas Halobacteria and Myxococcota MAGs were specific to the exposed microbial mat. Functionally, genes involved in reactive oxygen species (ROS) detoxification and osmotic pressure were more abundant in the exposed than in the shallow-water microbial mats, whereas genes involved in sulfate reduction/oxidation and nitrogen fixation were ubiquitously detected. Genes involved in the utilization of methylated amines for methane production were predominant when compared with genes associated with alternative methanogenesis pathways. Solar Lake methanogen MAGs belonged to Methanosarcinia, Bathyarchaeia, Candidatus Methanofastidiosales, and Archaeoglobales. The latter had the genetic capacity for anaerobic methane oxidation. Moreover, Coleofasciculus chthonoplastes, previously reported to dominate the winter shallow-water flat mat, had a substantial presence in the summer. These findings reveal the taxonomic and biochemical microbial zonation of the exposed and shallow-water Solar Lake flat mat benthic community and their capacity to ecologically adapt to the summer water recession. IMPORTANCE Fifty-five years ago, the extremophilic "Solar Lake" was discovered on the Red Sea shores, garnering microbiologists' interest worldwide from the 1970s to 1990s. Nevertheless, research on the lake paused at the turn of the millennium. In our study, we revisited the Solar Lake benthic community using a genome-centric approach and described the distinct microbial communities in the exposed versus shallow-water mat unveiling microbial zonation in the benthic communities surrounding the Solar Lake. Our findings highlighted the unique structural and functional adaptations employed by these microbial mat communities. Moreover, we report new methanogens and phototrophs, including an intriguing methanogen from the Archaeoglobales family. We describe how the Solar Lake's flat mat microbial community adapts to stressors like oxygen intrusion and drought due to summer water level changes, which provides insights into the genomic strategies of microbial communities to cope with altered and extreme environmental conditions.
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Affiliation(s)
- Rehab Z Abdallah
- Biology department, The American University in Cairo, Cairo, Egypt
| | - Ali H A Elbehery
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City, Egypt
| | - Shimaa F Ahmed
- Biology department, The American University in Cairo, Cairo, Egypt
| | - Amged Ouf
- Biology department, The American University in Cairo, Cairo, Egypt
| | - Mohamed N Malash
- Microbiology and Immunology Department, Faculty of Pharmacy, Ahram Canadian University, 6th of October City, Giza, Egypt
| | - Werner Liesack
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Rania Siam
- Biology department, The American University in Cairo, Cairo, Egypt
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2
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Xing Q, Zhang S, Tao X, Mesbah NM, Mao X, Wang H, Wiegel J, Zhao B. The polyextremophile Natranaerobius thermophilus adopts a dual adaptive strategy to long-term salinity stress, simultaneously accumulating compatible solutes and K . Appl Environ Microbiol 2024; 90:e0014524. [PMID: 38578096 PMCID: PMC11107154 DOI: 10.1128/aem.00145-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/15/2024] [Indexed: 04/06/2024] Open
Abstract
The bacterium Natranaerobius thermophilus is an extremely halophilic alkalithermophile that can thrive under conditions of high salinity (3.3-3.9 M Na+), alkaline pH (9.5), and elevated temperature (53°C). To understand the molecular mechanisms of salt adaptation in N. thermophilus, it is essential to investigate the protein, mRNA, and key metabolite levels on a molecular basis. Based on proteome profiling of N. thermophilus under 3.1, 3.7, and 4.3 M Na+ conditions compared to 2.5 M Na+ condition, we discovered that a hybrid strategy, combining the "compatible solute" and "salt-in" mechanisms, was utilized for osmotic adjustment dur ing the long-term salinity adaptation of N. thermophilus. The mRNA level of key proteins and the intracellular content of compatible solutes and K+ support this conclusion. Specifically, N. thermophilus employs the glycine betaine ABC transporters (Opu and ProU families), Na+/solute symporters (SSS family), and glutamate and proline synthesis pathways to adapt to high salinity. The intracellular content of compatible solutes, including glycine betaine, glutamate, and proline, increases with rising salinity levels in N. thermophilus. Additionally, the upregulation of Na+/ K+/ H+ transporters facilitates the maintenance of intracellular K+ concentration, ensuring cellular ion homeostasis under varying salinities. Furthermore, N. thermophilus exhibits cytoplasmic acidification in response to high Na+ concentrations. The median isoelectric points of the upregulated proteins decrease with increasing salinity. Amino acid metabolism, carbohydrate and energy metabolism, membrane transport, and bacterial chemotaxis activities contribute to the adaptability of N. thermophilus under high salt stress. This study provides new data that support further elucidating the complex adaptation mechanisms of N. thermophilus under multiple extremes.IMPORTANCEThis study represents the first report of simultaneous utilization of two salt adaptation mechanisms within the Clostridia class in response to long-term salinity stress.
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Affiliation(s)
- Qinghua Xing
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shanshan Zhang
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
- Luo Yang Branch of Institute of Computing Technology, Chinese Academy of Sciences, Luoyang, China
| | - Xinyi Tao
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Noha M. Mesbah
- Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Xinwei Mao
- Department of Civil Engineering, Stony Brook University, Stony Brook, New York, USA
| | - Haisheng Wang
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Juergen Wiegel
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Baisuo Zhao
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing, China
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3
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Dick JM, Tan J. Chemical Links Between Redox Conditions and Estimated Community Proteomes from 16S rRNA and Reference Protein Sequences. MICROBIAL ECOLOGY 2023; 85:1338-1355. [PMID: 35503575 DOI: 10.1007/s00248-022-01988-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/28/2022] [Indexed: 05/10/2023]
Abstract
Environmental influences on community structure are often assessed through multivariate analyses in order to relate microbial abundances to separately measured physicochemical variables. However, genes and proteins are themselves chemical entities; in combination with genome databases, differences in microbial abundances directly encode for chemical variability. We predicted that the carbon oxidation state of estimated community proteomes, obtained by combining taxonomic abundances from published 16S rRNA gene sequencing datasets with reference microbial proteomes from the NCBI Reference Sequence (RefSeq) database, would reflect environmental oxidation-reduction conditions. Analysis of multiple datasets confirms the geobiochemical predictions for environmental redox gradients in hydrothermal systems, stratified lakes and marine environments, and shale gas wells. The geobiochemical signal is largest for the steep redox gradients associated with hydrothermal systems and between injected water and produced fluids from shale gas wells, demonstrating that microbial community composition can be a chemical proxy for environmental redox gradients. Although estimates of oxidation state from 16S amplicon and metagenomic sequences are correlated, the 16S-based estimates show stronger associations with redox gradients in some environments.
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Affiliation(s)
- Jeffrey M Dick
- Key Laboratory of Metallogenic Prediction of Nonferrous Metals and Geological Environment Monitoring, Ministry of Education, School of Geosciences and Info-Physics, Central South University, Changsha, 410083, China.
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.
| | - Jingqiang Tan
- Key Laboratory of Metallogenic Prediction of Nonferrous Metals and Geological Environment Monitoring, Ministry of Education, School of Geosciences and Info-Physics, Central South University, Changsha, 410083, China
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4
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Espinosa-Asuar L, Monroy-Guzmán C, Madrigal-Trejo D, Navarro-Miranda M, Sánchez-Pérez J, Buenrostro Muñoz J, Villar J, Cifuentes Camargo JF, Kalambokidis M, Esquivel-Hernandez DA, Viladomat Jasso M, Escalante AE, Velez P, Figueroa M, Martinez-Cardenas A, Ramirez-Barahona S, Gasca-Pineda J, Eguiarte LE, Souza V. Diversity of an uncommon elastic hypersaline microbial mat along a small-scale transect. PeerJ 2022; 10:e13579. [PMID: 35757167 PMCID: PMC9220918 DOI: 10.7717/peerj.13579] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/22/2022] [Indexed: 01/17/2023] Open
Abstract
We evaluated the microbial diversity and metabolome profile of an uncommon hypersaline elastic microbial mat from Cuatro Ciénegas Basin (CCB) in the Chihuahuan Desert of Coahuila, México. We collected ten samples on a small scale transect (1.5-m) and described its microbial diversity through NGS-based ITS and 16S rDNA gene sequencing. A very low number of taxa comprised a considerable proportion of the mat and were shared across all sampling points, whereas the rare biosphere was more phylogenetically diverse (Faith's Phylogenetic Diversity (FPD) index) and phylogenetically disperse (using a null model distribution of Phylogenetic Species Clustering (nmdPSC)) than the abundant (high read count) taxa for both analyzed libraries. We also found a distinctive metabolome profile for each sample and were able to tentatively annotate several classes of compounds with relevant biological properties.
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Affiliation(s)
- Laura Espinosa-Asuar
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CdMx, México
| | - Camila Monroy-Guzmán
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CdMx, México
| | - David Madrigal-Trejo
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CdMx, México
| | - Marisol Navarro-Miranda
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CdMx, México
| | - Jazmin Sánchez-Pérez
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CdMx, México
| | - Jhoselinne Buenrostro Muñoz
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CdMx, México
| | - Juan Villar
- Pontifica Universidad Javeriana, Bogotá D.C., Colombia
| | | | - Maria Kalambokidis
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CdMx, México
| | - Diego A. Esquivel-Hernandez
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CdMx, México
| | - Mariette Viladomat Jasso
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CdMx, México
| | - Ana E. Escalante
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, CdMx, México
| | - Patricia Velez
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, CdMx, México
| | - Mario Figueroa
- Facultad de Química, Universidad Nacional Autónoma de México, CdMx, México
| | | | - Santiago Ramirez-Barahona
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, CdMx, México
| | - Jaime Gasca-Pineda
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CdMx, México
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CdMx, México
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CdMx, México
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5
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Ghosh UU, Ali H, Ghosh R, Kumar A. Bacterial streamers as colloidal systems: Five grand challenges. J Colloid Interface Sci 2021; 594:265-278. [PMID: 33765646 DOI: 10.1016/j.jcis.2021.02.102] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 12/21/2022]
Abstract
Bacteria can thrive in biofilms, which are intricately organized communities with cells encased in a self-secreted matrix of extracellular polymeric substances (EPS). Imposed hydrodynamic stresses can transform this active colloidal dispersion of bacteria and EPS into slender thread-like entities called streamers. In this perspective article, the reader is introduced to the world of such deformable 'bacteria-EPS' composites that are a subclass of the generic flow-induced colloidal structures. While bacterial streamers have been shown to form in a variety of hydrodynamic conditions (turbulent and creeping flows), its abiotic analogues have only been demonstrated in low Reynolds number (Re < 1) particle-laden polymeric flows. Streamers are relevant to a variety of situations ranging from natural formations in caves and river beds to clogging of biomedical devices and filtration membranes. A critical review of the relevant biophysical aspects of streamer formation phenomena and unique attributes of its material behavior are distilled to unveil five grand scientific challenges. The coupling between colloidal hydrodynamics, device geometry and streamer formation are highlighted.
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Affiliation(s)
- Udita U Ghosh
- Department of Mechanical Engineering, Indian Institute of Science, Bangalore, India
| | - Hessein Ali
- Department of Mechanical and Aerospace Engineering, University of Central Florida, Orlando, FL 32816, USA
| | - Ranajay Ghosh
- Department of Mechanical and Aerospace Engineering, University of Central Florida, Orlando, FL 32816, USA.
| | - Aloke Kumar
- Department of Mechanical Engineering, Indian Institute of Science, Bangalore, India.
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Wani GA, Khan MA, Dar MA, Shah MA, Reshi ZA. Next Generation High Throughput Sequencing to Assess Microbial Communities: An Application Based on Water Quality. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2021; 106:727-733. [PMID: 33774727 DOI: 10.1007/s00128-021-03195-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 03/13/2021] [Indexed: 06/12/2023]
Abstract
Traditional techniques to identify different contaminants (biological or chemical) in the waters are slow, laborious, and can require specialized expertise. Hence, the rapid determination of water quality using more sensitive and reliable metagenomic based approaches attains special importance. Metagenomics deals with the study of genetic material that is recovered from microbial communities present in environmental samples. In traditional techniques cultivation-based methodologies were used to describe the diversity of microorganisms in environmental samples. It has failed to function as a robust marker because of limited taxonomic and phylogenetic implications. In this backdrop, high-throughput DNA sequencing approaches have proven very powerful in microbial source tracking because of investigating the full variety of genome-based analysis such as microbial genetic diversity and population structure played by them. Next generation sequencing technologies can reveal a greater proportion of microbial communities that have not been reported earlier by traditional techniques. The present review highlights the shift from traditional techniques for the basic study of community composition to next-generation sequencing (NGS) platforms and their potential applications to the biomonitoring of water quality in relation to human health.
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Affiliation(s)
- Gowher A Wani
- Department of Botany, University of Kashmir, Srinagar, Jammu & Kashmir, 190 006, India.
| | - Mohd Asgar Khan
- Department of Botany, University of Kashmir, Srinagar, Jammu & Kashmir, 190 006, India
| | - Mudasir A Dar
- Department of Botany, University of Kashmir, Srinagar, Jammu & Kashmir, 190 006, India
| | - Manzoor A Shah
- Department of Botany, University of Kashmir, Srinagar, Jammu & Kashmir, 190 006, India
| | - Zafar A Reshi
- Department of Botany, University of Kashmir, Srinagar, Jammu & Kashmir, 190 006, India
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7
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Sonbol S, Siam R. The association of group IIB intron with integrons in hypersaline environments. Mob DNA 2021; 12:8. [PMID: 33648565 PMCID: PMC7923331 DOI: 10.1186/s13100-021-00234-2] [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: 12/12/2020] [Accepted: 01/27/2021] [Indexed: 11/25/2022] Open
Abstract
Background Group II introns are mobile genetic elements used as efficient gene targeting tools. They function as both ribozymes and retroelements. Group IIC introns are the only class reported so far to be associated with integrons. In order to identify group II introns linked with integrons and CALINS (cluster of attC sites lacking a neighboring integron integrase) within halophiles, we mined for integrons in 28 assembled metagenomes from hypersaline environments and publically available 104 halophilic genomes using Integron Finder followed by blast search for group II intron reverse transcriptases (RT)s. Results We report the presence of different group II introns associated with integrons and integron-related sequences denoted by UHB.F1, UHB.I2, H.ha.F1 and H.ha.F2. The first two were identified within putative integrons in the metagenome of Tanatar-5 hypersaline soda lake, belonging to IIC and IIB intron classes, respectively at which the first was a truncated intron. Other truncated introns H.ha.F1 and H.ha.F2 were also detected in a CALIN within the extreme halophile Halorhodospira halochloris, both belonging to group IIB introns. The intron-encoded proteins (IEP) s identified within group IIB introns belonged to different classes: CL1 class in UHB.I2 and bacterial class E in H.ha.Fa1 and H.ha.F2. A newly identified insertion sequence (ISHahl1) of IS200/605 superfamily was also identified adjacent to H. halochloris CALIN. Finally, an abundance of toxin-antitoxin (TA) systems was observed within the identified integrons. Conclusion So far, this is the first investigation of group II introns within integrons in halophilic genomes and metagenomes from hypersaline environments. We report the presence of group IIB introns associated with integrons or CALINs. This study provides the basis for understanding the role of group IIB introns in the evolution of halophiles and their potential biotechnological role. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-021-00234-2.
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Affiliation(s)
- Sarah Sonbol
- Biology Department and the Graduate Program of Biotechnology, School of Sciences and Engineering, the American University in Cairo, New Cairo, Cairo, 11835, Egypt
| | - Rania Siam
- Biology Department and the Graduate Program of Biotechnology, School of Sciences and Engineering, the American University in Cairo, New Cairo, Cairo, 11835, Egypt. .,University of Medicine and Health Sciences, Basseterre, Saint Kitts and Nevis.
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8
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Depthwise microbiome and isotopic profiling of a moderately saline microbial mat in a solar saltern. Sci Rep 2020; 10:20686. [PMID: 33244085 PMCID: PMC7693307 DOI: 10.1038/s41598-020-77622-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 11/09/2020] [Indexed: 11/23/2022] Open
Abstract
The solar salterns in Tuticorin, India, are man-made, saline to hypersaline systems hosting some uniquely adapted populations of microorganisms and eukaryotic algae that have not been fully characterized. Two visually different microbial mats (termed ‘white’ and ‘green’) developing on the reservoir ponds (53 PSU) were isolated from the salterns. Firstly, archaeal and bacterial diversity in different vertical layers of the mats were analyzed. Culture-independent 16S rRNA gene analysis revealed that both bacteria and archaea were rich in their diversity. The top layers had a higher representation of halophilic archaea Halobacteriaceae, phylum Chloroflexi, and classes Anaerolineae, Delta- and Gamma- Proteobacteria than the deeper sections, indicating that a salinity gradient exists within the mats. Limited presence of Cyanobacteria and detection of algae-associated bacteria, such as Phycisphaerae, Phaeodactylibacter and Oceanicaulis likely implied that eukaryotic algae and other phototrophs could be the primary producers within the mat ecosystem. Secondly, predictive metabolic pathway analysis using the 16S rRNA gene data revealed that in addition to the regulatory microbial functions, methane and nitrogen metabolisms were prevalent. Finally, stable carbon and nitrogen isotopic compositions determined from both mat samples showed that the δ13Corg and δ15Norg values increased slightly with depth, ranging from − 16.42 to − 14.73‰, and 11.17 to 13.55‰, respectively. The isotopic signature along the microbial mat profile followed a pattern that is distinctive to the community composition and net metabolic activities, and comparable to saline mats in other salterns. The results and discussions presented here by merging culture-independent studies, predictive metabolic analyses and isotopic characterization, provide a collective strategy to understand the compositional and functional characteristics of microbial mats in saline environments.
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9
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Jarett JK, Džunková M, Schulz F, Roux S, Paez-Espino D, Eloe-Fadrosh E, Jungbluth SP, Ivanova N, Spear JR, Carr SA, Trivedi CB, Corsetti FA, Johnson HA, Becraft E, Kyrpides N, Stepanauskas R, Woyke T. Insights into the dynamics between viruses and their hosts in a hot spring microbial mat. ISME JOURNAL 2020; 14:2527-2541. [PMID: 32661357 PMCID: PMC7490370 DOI: 10.1038/s41396-020-0705-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 06/03/2020] [Accepted: 06/11/2020] [Indexed: 12/28/2022]
Abstract
Our current knowledge of host-virus interactions in biofilms is limited to computational predictions based on laboratory experiments with a small number of cultured bacteria. However, natural biofilms are diverse and chiefly composed of uncultured bacteria and archaea with no viral infection patterns and lifestyle predictions described to date. Herein, we predict the first DNA sequence-based host-virus interactions in a natural biofilm. Using single-cell genomics and metagenomics applied to a hot spring mat of the Cone Pool in Mono County, California, we provide insights into virus-host range, lifestyle and distribution across different mat layers. Thirty-four out of 130 single cells contained at least one viral contig (26%), which, together with the metagenome-assembled genomes, resulted in detection of 59 viruses linked to 34 host species. Analysis of single-cell amplification kinetics revealed a lack of active viral replication on the single-cell level. These findings were further supported by mapping metagenomic reads from different mat layers to the obtained host-virus pairs, which indicated a low copy number of viral genomes compared to their hosts. Lastly, the metagenomic data revealed high layer specificity of viruses, suggesting limited diffusion to other mat layers. Taken together, these observations indicate that in low mobility environments with high microbial abundance, lysogeny is the predominant viral lifestyle, in line with the previously proposed "Piggyback-the-Winner" theory.
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Affiliation(s)
- Jessica K Jarett
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,AnimalBiome, Oakland, CA, USA
| | - Mária Džunková
- Department of Energy Joint Genome Institute, Berkeley, CA, USA. .,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Frederik Schulz
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Simon Roux
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David Paez-Espino
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Emiley Eloe-Fadrosh
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sean P Jungbluth
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - John R Spear
- Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, USA
| | | | | | | | - Hope A Johnson
- California State University Fullerton, Fullerton, CA, USA
| | - Eric Becraft
- University of North Alabama, Florence, AL, USA.,Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Nikos Kyrpides
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Tanja Woyke
- Department of Energy Joint Genome Institute, Berkeley, CA, USA. .,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,University of California, Merced, CA, USA.
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10
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Context-dependent dynamics lead to the assembly of functionally distinct microbial communities. Nat Commun 2020; 11:1440. [PMID: 32188849 PMCID: PMC7080782 DOI: 10.1038/s41467-020-15169-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 02/18/2020] [Indexed: 11/15/2022] Open
Abstract
Niche construction through interspecific interactions can condition future community states on past ones. However, the extent to which such history dependency can steer communities towards functionally different states remains a subject of active debate. Using bacterial communities collected from wild pitchers of the carnivorous pitcher plant, Sarracenia purpurea, we test the effects of history on composition and function across communities assembled in synthetic pitcher plant microcosms. We find that the diversity of assembled communities is determined by the diversity of the system at early, pre-assembly stages. Species composition is also contingent on early community states, not only because of differences in the species pool, but also because the same species have different dynamics in different community contexts. Importantly, compositional differences are proportional to differences in function, as profiles of resource use are strongly correlated with composition, despite convergence in respiration rates. Early differences in community structure can thus propagate to mature communities, conditioning their functional repertoire. Historical contingency can affect community composition and function, but the extent to which this occurs is unclear. Here the authors use pitcher plant microbial communities to demonstrate that community dynamics and key metabolic functions at equilibrium depend on history and initial composition.
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11
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Dillon ML, Hawes I, Jungblut AD, Mackey TJ, Eisen JA, Doran PT, Sumner DY. Energetic and Environmental Constraints on the Community Structure of Benthic Microbial Mats in Lake Fryxell, Antarctica. FEMS Microbiol Ecol 2020; 96:fiz207. [PMID: 31905236 PMCID: PMC6974422 DOI: 10.1093/femsec/fiz207] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 01/03/2020] [Indexed: 11/13/2022] Open
Abstract
Ecological communities are regulated by the flow of energy through environments. Energy flow is typically limited by access to photosynthetically active radiation (PAR) and oxygen concentration (O2). The microbial mats growing on the bottom of Lake Fryxell, Antarctica, have well-defined environmental gradients in PAR and (O2). We analyzed the metagenomes of layers from these microbial mats to test the extent to which access to oxygen and light controls community structure. We found variation in the diversity and relative abundances of Archaea, Bacteria and Eukaryotes across three (O2) and PAR conditions: high (O2) and maximum PAR, variable (O2) with lower maximum PAR, and low (O2) and maximum PAR. We found distinct communities structured by the optimization of energy use on a millimeter-scale across these conditions. In mat layers where (O2) was saturated, PAR structured the community. In contrast, (O2) positively correlated with diversity and affected the distribution of dominant populations across the three habitats, suggesting that meter-scale diversity is structured by energy availability. Microbial communities changed across covarying gradients of PAR and (O2). The comprehensive metagenomic analysis suggests that the benthic microbial communities in Lake Fryxell are structured by energy flow across both meter- and millimeter-scales.
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Affiliation(s)
- Megan L Dillon
- Lawrence Berkeley National Laboratory Climate and Ecosystem Sciences Division 70A-2245B, One Cyclotron Rd Berkeley, CA 94720 510-486-5538
- Department of Earth and Planetary Sciences, University of California, Davis One Shields Ave Davis, CA 95616, USA
| | - Ian Hawes
- Coastal Marine Field Station, University of Waikato, 58 Cross Rd Sulphur Point Tauranga 3110, New Zealand
| | - Anne D Jungblut
- Life Sciences Department, Natural History Museum, Cromwell Rd South Kensington London SW7 5BD, UK
| | - Tyler J Mackey
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Ave Cambridge, MA 02139-4307, USA
| | - Jonathan A Eisen
- Department of Evolution and Ecology, University of California, Davis, One Shields Ave Davis, CA USA
| | - Peter T Doran
- Geology and Geophysics, Louisiana State University, E235 Howe Russell Kniffen Baton Rouge, LA 70803 USA
| | - Dawn Y Sumner
- Department of Earth and Planetary Sciences, University of California, Davis One Shields Ave Davis, CA 95616, USA
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12
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Narayan NR, Weinmaier T, Laserna-Mendieta EJ, Claesson MJ, Shanahan F, Dabbagh K, Iwai S, DeSantis TZ. Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences. BMC Genomics 2020; 21:56. [PMID: 31952477 PMCID: PMC6967091 DOI: 10.1186/s12864-019-6427-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 12/24/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Shotgun metagenomic sequencing reveals the potential in microbial communities. However, lower-cost 16S ribosomal RNA (rRNA) gene sequencing provides taxonomic, not functional, observations. To remedy this, we previously introduced Piphillin, a software package that predicts functional metagenomic content based on the frequency of detected 16S rRNA gene sequences corresponding to genomes in regularly updated, functionally annotated genome databases. Piphillin (and similar tools) have previously been evaluated on 16S rRNA data processed by the clustering of sequences into operational taxonomic units (OTUs). New techniques such as amplicon sequence variant error correction are in increased use, but it is unknown if these techniques perform better in metagenomic content prediction pipelines, or if they should be treated the same as OTU data in respect to optimal pipeline parameters. RESULTS To evaluate the effect of 16S rRNA sequence analysis method (clustering sequences into OTUs vs amplicon sequence variant error correction into amplicon sequence variants (ASVs)) on the ability of Piphillin to predict functional metagenomic content, we evaluated Piphillin-predicted functional content from 16S rRNA sequence data processed through OTU clustering and error correction into ASVs compared to corresponding shotgun metagenomic data. We show a strong correlation between metagenomic data and Piphillin-predicted functional content resulting from both 16S rRNA sequence analysis methods. Differential abundance testing with Piphillin-predicted functional content exhibited a low false positive rate (< 0.05) while capturing a large fraction of the differentially abundant features resulting from corresponding metagenomic data. However, Piphillin prediction performance was optimal at different cutoff parameters depending on 16S rRNA sequence analysis method. Using data analyzed with amplicon sequence variant error correction, Piphillin outperformed comparable tools, for instance exhibiting 19% greater balanced accuracy and 54% greater precision compared to PICRUSt2. CONCLUSIONS Our results demonstrate that raw Illumina sequences should be processed for subsequent Piphillin analysis using amplicon sequence variant error correction (with DADA2 or similar methods) and run using a 99% ID cutoff for Piphillin, while sequences generated on platforms other than Illumina should be processed via OTU clustering (e.g., UPARSE) and run using a 96% ID cutoff for Piphillin. Piphillin is publicly available for academic users (Piphillin server. http://piphillin.secondgenome.com/.).
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Affiliation(s)
- Nicole R. Narayan
- Informatics Department, Second Genome Inc., South San Francisco, California, USA
| | - Thomas Weinmaier
- Informatics Department, Second Genome Inc., South San Francisco, California, USA
| | - Emilio J. Laserna-Mendieta
- APC Microbiome Ireland, University College Cork, Co., Cork, Ireland
- School of Microbiology, University College Cork, Co., Cork, Ireland
| | - Marcus J. Claesson
- APC Microbiome Ireland, University College Cork, Co., Cork, Ireland
- School of Microbiology, University College Cork, Co., Cork, Ireland
| | - Fergus Shanahan
- APC Microbiome Ireland, University College Cork, Co., Cork, Ireland
- Department of Medicine, University College Cork, Co., Cork, Ireland
| | - Karim Dabbagh
- Informatics Department, Second Genome Inc., South San Francisco, California, USA
| | - Shoko Iwai
- Informatics Department, Second Genome Inc., South San Francisco, California, USA
| | - Todd Z. DeSantis
- Informatics Department, Second Genome Inc., South San Francisco, California, USA
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13
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Dick JM, Yu M, Tan J, Lu A. Changes in Carbon Oxidation State of Metagenomes Along Geochemical Redox Gradients. Front Microbiol 2019; 10:120. [PMID: 30804909 PMCID: PMC6378307 DOI: 10.3389/fmicb.2019.00120] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 01/18/2019] [Indexed: 01/01/2023] Open
Abstract
There is widespread interest in how geochemistry affects the genomic makeup of microbial communities, but the possible impacts of oxidation-reduction (redox) conditions on the chemical composition of biomacromolecules remain largely unexplored. Here we document systematic changes in the carbon oxidation state, a metric derived from the chemical formulas of biomacromolecular sequences, using published metagenomic and metatranscriptomic datasets from 18 studies representing different marine and terrestrial environments. We find that the carbon oxidation states of DNA, as well as proteins inferred from coding sequences, follow geochemical redox gradients associated with mixing and cooling of hot spring fluids in Yellowstone National Park (USA) and submarine hydrothermal fluids. Thermodynamic calculations provide independent predictions for the environmental shaping of the gene and protein composition of microbial communities in these systems. On the other hand, the carbon oxidation state of DNA is negatively correlated with oxygen concentration in marine oxygen minimum zones. In this case, a thermodynamic model is not viable, but the low carbon oxidation state of DNA near the ocean surface reflects a low GC content, which can be attributed to genome reduction in organisms adapted to low-nutrient conditions. We also present evidence for a depth-dependent increase of oxidation state at the species level, which might be associated with alteration of DNA through horizontal gene transfer and/or selective degradation of relatively reduced (AT-rich) extracellular DNA by heterotrophic bacteria. Sediments exhibit even more complex behavior, where carbon oxidation state minimizes near the sulfate-methane transition zone and rises again at depth; markedly higher oxidation states are also associated with older freshwater-dominated sediments in the Baltic Sea that are enriched in iron oxides and have low organic carbon. This geobiochemical study of carbon oxidation state reveals a new aspect of environmental information in metagenomic sequences, and provides a reference frame for future studies that may use ancient DNA sequences as a paleoredox indicator.
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Affiliation(s)
- Jeffrey M. Dick
- Key Laboratory of Metallogenic Prediction of Nonferrous Metals and Geological Environment Monitoring, Ministry of Education, Central South University, Changsha, China
- School of Geosciences and Info-Physics, Central South University, Changsha, China
| | - Miao Yu
- Key Laboratory of Metallogenic Prediction of Nonferrous Metals and Geological Environment Monitoring, Ministry of Education, Central South University, Changsha, China
- School of Geosciences and Info-Physics, Central South University, Changsha, China
| | - Jingqiang Tan
- Key Laboratory of Metallogenic Prediction of Nonferrous Metals and Geological Environment Monitoring, Ministry of Education, Central South University, Changsha, China
- School of Geosciences and Info-Physics, Central South University, Changsha, China
| | - Anhuai Lu
- Key Laboratory of Metallogenic Prediction of Nonferrous Metals and Geological Environment Monitoring, Ministry of Education, Central South University, Changsha, China
- School of Geosciences and Info-Physics, Central South University, Changsha, China
- School of Earth and Space Sciences, Peking University, Beijing, China
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14
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Coban O, Williams M, Bebout BM. Mechanisms of nitrogen attenuation from seawater by two microbial mats. WATER RESEARCH 2018; 147:373-381. [PMID: 30326399 DOI: 10.1016/j.watres.2018.09.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 08/21/2018] [Accepted: 09/23/2018] [Indexed: 06/08/2023]
Abstract
Microbial mats, due to their high microbial diversity, have the potential to express most biogeochemical cycling processes, highlighting their prospective use in bioremediation of various environmental contaminants. In this study the mechanisms of nitrogen attenuation were investigated in naturally occurring microbial mats from Elkhorn Slough, Monterey Bay, CA, USA, and Baja California Sur, Mexico. Key processes responsible for this removal were evaluated using quantification of functional genes related to nitrification, denitrification, and nitrogen fixation. Both microbial mats were capable of removing high (up to 2 mM) concentrations of ammonium and nitrate. Ammonium assimilation rates measured for Elkhorn Slough mats showed that this process was responsible for most of the ammonium uptake in these mats. While Elkhorn Slough mats did not show any evidence of nitrogen removal pathways other than microbial assimilation, Baja mats exhibited the potential for nitrification, denitrification, and DNRA as well as assimilation. The results of this study demonstrate the potential of microbial mats for bioremediation of nitrogenous pollutants independent of the mechanisms responsible for their removal.
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Affiliation(s)
- Oksana Coban
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, 94035, USA.
| | - MiKalley Williams
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Brad M Bebout
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, 94035, USA
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15
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De Anda V, Zapata-Peñasco I, Blaz J, Poot-Hernández AC, Contreras-Moreira B, González-Laffitte M, Gámez-Tamariz N, Hernández-Rosales M, Eguiarte LE, Souza V. Understanding the Mechanisms Behind the Response to Environmental Perturbation in Microbial Mats: A Metagenomic-Network Based Approach. Front Microbiol 2018; 9:2606. [PMID: 30555424 PMCID: PMC6280815 DOI: 10.3389/fmicb.2018.02606] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 10/11/2018] [Indexed: 12/26/2022] Open
Abstract
To date, it remains unclear how anthropogenic perturbations influence the dynamics of microbial communities, what general patterns arise in response to disturbance, and whether it is possible to predict them. Here, we suggest the use of microbial mats as a model of study to reveal patterns that can illuminate the ecological processes underlying microbial dynamics in response to stress. We traced the responses to anthropogenic perturbation caused by water depletion in microbial mats from Cuatro Cienegas Basin (CCB), Mexico, by using a time-series spatially resolved analysis in a novel combination of three computational approaches. First, we implemented MEBS (Multi-genomic Entropy-Based Score) to evaluate the dynamics of major biogeochemical cycles across spatio-temporal scales with a single informative value. Second, we used robust Time Series-Ecological Networks (TS-ENs) to evaluate the total percentage of interactions at different taxonomic levels. Lastly, we utilized network motifs to characterize specific interaction patterns. Our results indicate that microbial mats from CCB contain an enormous taxonomic diversity with at least 100 phyla, mainly represented by members of the rare biosphere (RB). Statistical ecological analyses point out a clear involvement of anaerobic guilds related to sulfur and methane cycles during wet versus dry conditions, where we find an increase in fungi, photosynthetic, and halotolerant taxa. TS-ENs indicate that in wet conditions, there was an equilibrium between cooperation and competition (positive and negative relationships, respectively), while under dry conditions there is an over-representation of negative relationships. Furthermore, most of the keystone taxa of the TS-ENs at family level are members of the RB and the microbial mat core highlighting their crucial role within the community. Our results indicate that microbial mats are more robust to perturbation due to redundant functions that are likely shared among community members in the highly connected TS-ENs with density values close to one (≈0.9). Finally, we provide evidence that suggests that a large taxonomic diversity where all community members interact with each other (low modularity), the presence of permanent of low-abundant taxa, and an increase in competition can be potential buffers against environmental disturbance in microbial mats.
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Affiliation(s)
- Valerie De Anda
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Icoquih Zapata-Peñasco
- Dirección de Investigación en Transformación de Hidrocarburos, Instituto Mexicano del Petróleo, Eje Central Lázaro Cárdenas, Ciudad de México, Mexico
| | - Jazmín Blaz
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Augusto Cesar Poot-Hernández
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, UNAM, Ciudad Universitaria, Ciudad de México, Mexico
| | - Bruno Contreras-Moreira
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Zaragoza, Spain
- Fundación ARAID, Zaragoza, Spain
| | | | - Niza Gámez-Tamariz
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | | | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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16
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Ugarte A, Vicedomini R, Bernardes J, Carbone A. A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling. MICROBIOME 2018; 6:149. [PMID: 30153857 PMCID: PMC6114274 DOI: 10.1186/s40168-018-0532-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 08/13/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Biochemical and regulatory pathways have until recently been thought and modelled within one cell type, one organism and one species. This vision is being dramatically changed by the advent of whole microbiome sequencing studies, revealing the role of symbiotic microbial populations in fundamental biochemical functions. The new landscape we face requires the reconstruction of biochemical and regulatory pathways at the community level in a given environment. In order to understand how environmental factors affect the genetic material and the dynamics of the expression from one environment to another, we want to evaluate the quantity of gene protein sequences or transcripts associated to a given pathway by precisely estimating the abundance of protein domains, their weak presence or absence in environmental samples. RESULTS MetaCLADE is a novel profile-based domain annotation pipeline based on a multi-source domain annotation strategy. It applies directly to reads and improves identification of the catalog of functions in microbiomes. MetaCLADE is applied to simulated data and to more than ten metagenomic and metatranscriptomic datasets from different environments where it outperforms InterProScan in the number of annotated domains. It is compared to the state-of-the-art non-profile-based and profile-based methods, UProC and HMM-GRASPx, showing complementary predictions to UProC. A combination of MetaCLADE and UProC improves even further the functional annotation of environmental samples. CONCLUSIONS Learning about the functional activity of environmental microbial communities is a crucial step to understand microbial interactions and large-scale environmental impact. MetaCLADE has been explicitly designed for metagenomic and metatranscriptomic data and allows for the discovery of patterns in divergent sequences, thanks to its multi-source strategy. MetaCLADE highly improves current domain annotation methods and reaches a fine degree of accuracy in annotation of very different environments such as soil and marine ecosystems, ancient metagenomes and human tissues.
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Affiliation(s)
- Ari Ugarte
- Sorbonne Université, UPMC-Univ P6, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 4 Place Jussieu, Paris, 75005 France
| | - Riccardo Vicedomini
- Sorbonne Université, UPMC-Univ P6, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 4 Place Jussieu, Paris, 75005 France
- Sorbonne Université, UPMC-Univ P6, CNRS, Institut des Sciences du Calcul et des Donnees, 4 Place Jussieu, Paris, 75005 France
| | - Juliana Bernardes
- Sorbonne Université, UPMC-Univ P6, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 4 Place Jussieu, Paris, 75005 France
| | - Alessandra Carbone
- Sorbonne Université, UPMC-Univ P6, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 4 Place Jussieu, Paris, 75005 France
- Institut Universitaire de France, Paris, 75005 France
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17
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Wong HL, White RA, Visscher PT, Charlesworth JC, Vázquez-Campos X, Burns BP. Disentangling the drivers of functional complexity at the metagenomic level in Shark Bay microbial mat microbiomes. ISME JOURNAL 2018; 12:2619-2639. [PMID: 29980796 DOI: 10.1038/s41396-018-0208-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 04/27/2018] [Accepted: 06/01/2018] [Indexed: 11/09/2022]
Abstract
The functional metagenomic potential of Shark Bay microbial mats was examined for the first time at a millimeter scale, employing shotgun sequencing of communities via the Illumina NextSeq 500 platform in conjunction with defined chemical analyses. A detailed functional metagenomic profile has elucidated key pathways and facilitated inference of critical microbial interactions. In addition, 87 medium-to-high-quality metagenome-assembled genomes (MAG) were assembled, including potentially novel bins under the deep-branching archaeal Asgard group (Thorarchaetoa and Lokiarchaeota). A range of pathways involved in carbon, nitrogen, sulfur, and phosphorus cycles were identified in mat metagenomes, with the Wood-Ljungdahl pathway over-represented and inferred as a major carbon fixation mode. The top five sets of genes were affiliated to sulfate assimilation (cysNC cysNCD, sat), methanogenesis (hdrABC), Wood-Ljungdahl pathways (cooS, coxSML), phosphate transport (pstB), and copper efflux (copA). Polyhydroxyalkanoate (PHA) synthase genes were over-represented at the surface, with PHA serving as a potential storage of fixed carbon. Sulfur metabolism genes were highly represented, in particular complete sets of genes responsible for both assimilatory and dissimilatory sulfate reduction. Pathways of environmental adaptation (UV, hypersalinity, oxidative stress, and heavy metal resistance) were also delineated, as well as putative viral defensive mechanisms (core genes of the CRISPR, BREX, and DISARM systems). This study provides new metagenome-based models of how biogeochemical cycles and adaptive responses may be partitioned in the microbial mats of Shark Bay.
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Affiliation(s)
- Hon Lun Wong
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia.,Australian Centre for Astrobiology, University of New South Wales Sydney, Sydney, NSW, Australia
| | - Richard Allen White
- Institute of Biological Chemistry, Washington State University, Pullman, USA
| | - Pieter T Visscher
- Australian Centre for Astrobiology, University of New South Wales Sydney, Sydney, NSW, Australia.,Department of Marine Sciences, University of Connecticut, Storrs, CT, USA
| | - James C Charlesworth
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia.,Australian Centre for Astrobiology, University of New South Wales Sydney, Sydney, NSW, Australia
| | - Xabier Vázquez-Campos
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia. .,Australian Centre for Astrobiology, University of New South Wales Sydney, Sydney, NSW, Australia.
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18
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Prieto-Barajas CM, Valencia-Cantero E, Santoyo G. Microbial mat ecosystems: Structure types, functional diversity, and biotechnological application. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2017.11.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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19
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Terrisse F, Cravo-Laureau C, Noël C, Cagnon C, Dumbrell AJ, McGenity TJ, Duran R. Variation of Oxygenation Conditions on a Hydrocarbonoclastic Microbial Community Reveals Alcanivorax and Cycloclasticus Ecotypes. Front Microbiol 2017; 8:1549. [PMID: 28861063 PMCID: PMC5562018 DOI: 10.3389/fmicb.2017.01549] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/31/2017] [Indexed: 12/26/2022] Open
Abstract
Deciphering the ecology of marine obligate hydrocarbonoclastic bacteria (MOHCB) is of crucial importance for understanding their success in occupying distinct niches in hydrocarbon-contaminated marine environments after oil spills. In marine coastal sediments, MOHCB are particularly subjected to extreme fluctuating conditions due to redox oscillations several times a day as a result of mechanical (tide, waves and currents) and biological (bioturbation) reworking of the sediment. The adaptation of MOHCB to the redox oscillations was investigated by an experimental ecology approach, subjecting a hydrocarbon-degrading microbial community to contrasting oxygenation regimes including permanent anoxic conditions, anoxic/oxic oscillations and permanent oxic conditions. The most ubiquitous MOHCB, Alcanivorax and Cycloclasticus, showed different behaviors, especially under anoxic/oxic oscillation conditions, which were more favorable for Alcanivorax than for Cycloclasticus. The micro-diversity of 16S rRNA gene transcripts from these genera revealed specific ecotypes for different oxygenation conditions and their dynamics. It is likely that such ecotypes allow the colonization of distinct ecological niches that may explain the success of Alcanivorax and Cycloclasticus in hydrocarbon-contaminated coastal sediments during oil-spills.
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Affiliation(s)
- Fanny Terrisse
- IPREM UMR CNRS 5254, Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'AdourPau, France
| | - Cristiana Cravo-Laureau
- IPREM UMR CNRS 5254, Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'AdourPau, France
| | - Cyril Noël
- IPREM UMR CNRS 5254, Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'AdourPau, France
| | - Christine Cagnon
- IPREM UMR CNRS 5254, Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'AdourPau, France
| | - Alex J Dumbrell
- School of Biological Sciences, University of EssexColchester, United Kingdom
| | - Terry J McGenity
- School of Biological Sciences, University of EssexColchester, United Kingdom
| | - Robert Duran
- IPREM UMR CNRS 5254, Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'AdourPau, France
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20
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Cobo-Simón M, Tamames J. Relating genomic characteristics to environmental preferences and ubiquity in different microbial taxa. BMC Genomics 2017; 18:499. [PMID: 28662636 PMCID: PMC5492924 DOI: 10.1186/s12864-017-3888-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 06/21/2017] [Indexed: 11/10/2022] Open
Abstract
Background Despite the important role that microorganisms play in environmental processes, the low percentage of cultured microbes (5%) has limited, until now, our knowledge of their ecological strategies. However, the development of high-throughput sequencing has generated a huge amount of genomic and metagenomic data without the need of culturing that can be used to study ecological questions. This study aims to estimate the functional capabilities, genomic sizes and 16S copy number of different taxa in relation to their ubiquity and their environmental preferences. Results To achieve this goal, we compiled data regarding the presence of each prokaryotic genera in diverse environments. Then, genomic characteristics such as genome size, 16S rRNA gene copy number, and functional content of the genomes were related to their ubiquity and different environmental preferences of the corresponding taxa. The results showed clear correlations between genomic characteristics and environmental conditions. Conclusions Ubiquity and adaptation were linked to genome size, while 16S copy number was not directly related to ubiquity. We observed that different combinations of these two characteristics delineate the different environments. Besides, the analysis of functional classes showed some clear signatures linked to particular environments. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3888-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marta Cobo-Simón
- Systems Biology Programme, Centro Nacional de Biotecnología (CNB-CSIC), C/Darwin 3, 28049, Madrid, Spain
| | - Javier Tamames
- Systems Biology Programme, Centro Nacional de Biotecnología (CNB-CSIC), C/Darwin 3, 28049, Madrid, Spain.
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21
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Mobberley JM, Lindemann SR, Bernstein HC, Moran JJ, Renslow RS, Babauta J, Hu D, Beyenal H, Nelson WC. Organismal and spatial partitioning of energy and macronutrient transformations within a hypersaline mat. FEMS Microbiol Ecol 2017; 93:3071443. [PMID: 28334407 PMCID: PMC5812542 DOI: 10.1093/femsec/fix028] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 03/13/2017] [Indexed: 02/06/2023] Open
Abstract
Phototrophic mat communities are model ecosystems for studying energy cycling and elemental transformations because complete biogeochemical cycles occur over millimeter-to-centimeter scales. Characterization of energy and nutrient capture within hypersaline phototrophic mats has focused on specific processes and organisms; however, little is known about community-wide distribution of and linkages between these processes. To investigate energy and macronutrient capture and flow through a structured community, the spatial and organismal distribution of metabolic functions within a compact hypersaline mat community from Hot Lake have been broadly elucidated through species-resolved metagenomics and geochemical, microbial diversity and metabolic gradient measurements. Draft reconstructed genomes of 34 abundant organisms revealed three dominant cyanobacterial populations differentially distributed across the top layers of the mat suggesting niche separation along light and oxygen gradients. Many organisms contained diverse functional profiles, allowing for metabolic response to changing conditions within the mat. Organisms with partial nitrogen and sulfur metabolisms were widespread indicating dependence on metabolite exchange. In addition, changes in community spatial structure were observed over the diel. These results indicate that organisms within the mat community have adapted to the temporally dynamic environmental gradients in this hypersaline mat through metabolic flexibility and fluid syntrophic interactions, including shifts in spatial arrangements.
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Affiliation(s)
- Jennifer M Mobberley
- Biological Science Division, Earth and Environmental Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Stephen R Lindemann
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN 47907, USA.,Department of Nutrition Science, Purdue University, West Lafayette, IN 47907, USA
| | - Hans C Bernstein
- Biological Science Division, Earth and Environmental Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA.,The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
| | - James J Moran
- Chemical and Biological Signature Sciences, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Ryan S Renslow
- Biological Science Division, Earth and Environmental Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA.,The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
| | - Jerome Babauta
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
| | - Dehong Hu
- Environmental Molecular Sciences Laboratory, Earth and Environmental Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Haluk Beyenal
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
| | - William C Nelson
- Biological Science Division, Earth and Environmental Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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22
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Wong HL, Visscher PT, White RA, Smith DL, Patterson MM, Burns BP. Dynamics of archaea at fine spatial scales in Shark Bay mat microbiomes. Sci Rep 2017; 7:46160. [PMID: 28397816 PMCID: PMC5387419 DOI: 10.1038/srep46160] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 03/09/2017] [Indexed: 01/07/2023] Open
Abstract
The role of archaea in microbial mats is poorly understood. Delineating the spatial distribution of archaea with mat depth will enable resolution of putative niches in these systems. In the present study, high throughput amplicon sequencing was undertaken in conjunction with analysis of key biogeochemical properties of two mats (smooth and pustular) from Shark Bay, Australia. One-way analysis of similarity tests indicated the archaeal community structures of smooth and pustular mats were significantly different (global R = 1, p = 0.1%). Smooth mats possessed higher archaeal diversity, dominated by Parvarchaeota. The methanogenic community in smooth mats was dominated by hydrogenotrophic Methanomicrobiales, as well as methylotrophic Methanosarcinales, Methanococcales, Methanobacteriales and Methanomassiliicoccaceae. Pustular mats were enriched with Halobacteria and Parvarchaeota. Key metabolisms (bacterial and archaeal) were measured, and the rates of oxygen production/consumption and sulfate reduction were up to four times higher in smooth than in pustular mats. Methane production peaked in the oxic layers and was up to seven-fold higher in smooth than pustular mats. The finding of an abundance of anaerobic methanogens enriched at the surface where oxygen levels were highest, coupled with peak methane production in the oxic zone, suggests putative surface anoxic niches in these microbial mats.
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Affiliation(s)
- Hon Lun Wong
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia.,Australian Centre for Astrobiology, University of New South Wales Sydney, Australia
| | - Pieter T Visscher
- Department of Marine Sciences, University of Connecticut, USA.,Australian Centre for Astrobiology, University of New South Wales Sydney, Australia
| | - Richard Allen White
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Daniela-Lee Smith
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
| | | | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia.,Australian Centre for Astrobiology, University of New South Wales Sydney, Australia
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23
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Saghaï A, Zivanovic Y, Moreira D, Benzerara K, Bertolino P, Ragon M, Tavera R, López-Archilla AI, López-García P. Comparative metagenomics unveils functions and genome features of microbialite-associated communities along a depth gradient. Environ Microbiol 2016; 18:4990-5004. [PMID: 27422734 PMCID: PMC5477898 DOI: 10.1111/1462-2920.13456] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 07/13/2016] [Indexed: 12/15/2022]
Abstract
Modern microbialites are often used as analogs of Precambrian stromatolites; therefore, studying the metabolic interplay within their associated microbial communities can help formulating hypotheses on their formation and long-term preservation within the fossil record. We performed a comparative metagenomic analysis of microbialite samples collected at two sites and along a depth gradient in Lake Alchichica (Mexico). The community structure inferred from single-copy gene family identification and long-contig (>10 kb) assignation, consistently with previous rRNA gene surveys, showed a wide prokaryotic diversity dominated by Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria, and Bacteroidetes, while eukaryotes were largely dominated by green algae or diatoms. Functional analyses based on RefSeq, COG and SEED assignations revealed the importance of housekeeping functions, with an overrepresentation of genes involved in carbohydrate metabolism, as compared with other metabolic capacities. The search for genes diagnostic of specific metabolic functions revealed the important involvement of Alphaproteobacteria in anoxygenic photosynthesis and sulfide oxidation, and Cyanobacteria in oxygenic photosynthesis and nitrogen fixation. Surprisingly, sulfate reduction appeared negligible. Comparative analyses suggested functional similarities among various microbial mat and microbialite metagenomes as compared with soil or oceans, but showed differences in microbial processes among microbialite types linked to local environmental conditions.
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Affiliation(s)
- Aurélien Saghaï
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Yvan Zivanovic
- Institut de Biologie Intégrative de la Cellule, CNRS, Université Paris-Sud Orsay, Université Paris-Saclay, France
| | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Karim Benzerara
- Institut de Minéralogie et de Physique des Matériaux et de Cosmochimie, CNRS, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, Sorbonne Universités, Paris, France
| | - Paola Bertolino
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Marie Ragon
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Rosaluz Tavera
- Departamento de Ecología y Recursos Naturales, Universidad Nacional Autónoma de México, DF Mexico, Mexico
| | | | - Purificación López-García
- Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France
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24
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Abstract
“Slime” played a brief and spectacular role in the 19th century founded by the theory of primordial slime by Ernst Haeckel. However, that substance was never found and eventually abandoned. Further scientific attention slowly began in the 1930s referring to slime as a microbial product and then was inspired by “How bacteria stick” by Costerton et al. in 1978, and the matrix material was considered to be polysaccharides. Later, it turned out that proteins, nucleic acids and lipids were major other constituents of the extracellular polymeric substances (EPS), an acronym which was highly discussed. The role of the EPS matrix turns out to be fundamental for biofilms, in terms of keeping cells in proximity and allowing for extended interaction, resource capture, mechanical strength and other properties, which emerge from the life of biofilm organisms, including enhanced tolerance to antimicrobials and other stress. The EPS components are extremely complex and dynamic and fulfil many functional roles, turning biofilms into the most ubiquitous and successful form of life on Earth.
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25
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Iwai S, Weinmaier T, Schmidt BL, Albertson DG, Poloso NJ, Dabbagh K, DeSantis TZ. Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes. PLoS One 2016; 11:e0166104. [PMID: 27820856 PMCID: PMC5098786 DOI: 10.1371/journal.pone.0166104] [Citation(s) in RCA: 196] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 10/07/2016] [Indexed: 01/30/2023] Open
Abstract
Functional analysis of a clinical microbiome facilitates the elucidation of mechanisms by which microbiome perturbation can cause a phenotypic change in the patient. The direct approach for the analysis of the functional capacity of the microbiome is via shotgun metagenomics. An inexpensive method to estimate the functional capacity of a microbial community is through collecting 16S rRNA gene profiles then indirectly inferring the abundance of functional genes. This inference approach has been implemented in the PICRUSt and Tax4Fun software tools. However, those tools have important limitations since they rely on outdated functional databases and uncertain phylogenetic trees and require very specific data pre-processing protocols. Here we introduce Piphillin, a straightforward algorithm independent of any proposed phylogenetic tree, leveraging contemporary functional databases and not obliged to any singular data pre-processing protocol. When all three inference tools were evaluated against actual shotgun metagenomics, Piphillin was superior in predicting gene composition in human clinical samples compared to both PICRUSt and Tax4Fun (p<0.01 and p<0.001, respectively) and Piphillin’s ability to predict disease associations with specific gene orthologs exhibited a 15% increase in balanced accuracy compared to PICRUSt. From laboratory animal samples, no performance advantage was observed for any one of the tools over the others and for environmental samples all produced unsatisfactory predictions. Our results demonstrate that functional inference using the direct method implemented in Piphillin is preferable for clinical biospecimens. Piphillin is publicly available for academic use at http://secondgenome.com/Piphillin.
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Affiliation(s)
- Shoko Iwai
- Informatics Department, Second Genome Inc., South San Francisco, California, United States of America
| | - Thomas Weinmaier
- Informatics Department, Second Genome Inc., South San Francisco, California, United States of America
| | - Brian L. Schmidt
- Bluestone Center for Clinical Research and the Department of Oral and Maxillofacial Surgery, New York University College of Dentistry, New York, New York, United States of America
| | - Donna G. Albertson
- Bluestone Center for Clinical Research and the Department of Oral and Maxillofacial Surgery, New York University College of Dentistry, New York, New York, United States of America
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
| | - Neil J. Poloso
- Research and External Scientific Innovation Department, Allergan PLC, Irvine, California, United States of America
| | - Karim Dabbagh
- Informatics Department, Second Genome Inc., South San Francisco, California, United States of America
| | - Todd Z. DeSantis
- Informatics Department, Second Genome Inc., South San Francisco, California, United States of America
- * E-mail:
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26
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Use of Comparative Genomics To Characterize the Diversity of Acinetobacter baumannii Surveillance Isolates in a Health Care Institution. Antimicrob Agents Chemother 2016; 60:5933-41. [PMID: 27458211 DOI: 10.1128/aac.00477-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 07/05/2016] [Indexed: 01/19/2023] Open
Abstract
Despite the increasing prevalence of the nosocomial pathogen Acinetobacter baumannii, little is known about which genomic components contribute to clinical presentation of this important pathogen. Most whole-genome comparisons of A. baumannii have focused on specific genomic regions associated with phenotypes in a limited number of genomes. In this work, we describe the results of a whole-genome comparative analysis of 254 surveillance isolates of Acinetobacter species, 203 of which were A. baumannii, isolated from perianal swabs and sputum samples collected as part of an infection control active surveillance program at the University of Maryland Medical Center. The collection of surveillance isolates includes both carbapenem-susceptible and -resistant isolates. Based on the whole-genome phylogeny, the A. baumannii isolates collected belong to two major phylogenomic lineages. Results from multilocus sequence typing indicated that one of the major phylogenetic groups of A. baumannii was comprised solely of strains from the international clonal lineage 2. The genomic content of the A. baumannii isolates was examined using large-scale BLAST score ratio analysis to identify genes that are associated with carbapenem-susceptible and -resistant isolates, as well as genes potentially associated with the source of isolation. This analysis revealed a number of genes that were exclusive or at greater frequency in each of these classifications. This study is the most comprehensive genomic comparison of Acinetobacter isolates from a surveillance study to date and provides important information that will contribute to our understanding of the success of A. baumannii as a human pathogen.
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27
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Warden JG, Casaburi G, Omelon CR, Bennett PC, Breecker DO, Foster JS. Characterization of Microbial Mat Microbiomes in the Modern Thrombolite Ecosystem of Lake Clifton, Western Australia Using Shotgun Metagenomics. Front Microbiol 2016; 7:1064. [PMID: 27458453 PMCID: PMC4933708 DOI: 10.3389/fmicb.2016.01064] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/24/2016] [Indexed: 12/02/2022] Open
Abstract
Microbialite-forming communities interact with the environment and influence the precipitation of calcium carbonate through their metabolic activity. The functional genes associated with these metabolic processes and their environmental interactions are therefore critical to microbialite formation. The microbiomes associated with microbialite-forming ecosystems are just now being elucidated and the extent of shared pathways and taxa across different environments is not fully known. In this study, we profiled the microbiome of microbial communities associated with lacustrine thrombolites located in Lake Clifton, Western Australia using metagenomic sequencing and compared it to the non-lithifying mats associated with surrounding sediments to determine whether differences in the mat microbiomes, particularly with respect to metabolic pathways and environmental interactions, may potentially contribute to thrombolite formation. Additionally, we used stable isotope biosignatures to delineate the dominant metabolism associated with calcium carbonate precipitation in the thrombolite build-ups. Results indicated that the microbial community associated with the Lake Clifton thrombolites was predominantly bacterial (98.4%) with Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria comprising the majority of annotated reads. Thrombolite-associated mats were enriched in photoautotrophic taxa and functional genes associated with photosynthesis. Observed δ13C values of thrombolite CaCO3 were enriched by at least 3.5‰ compared to theoretical values in equilibrium with lake water DIC, which is consistent with the occurrence of photoautotrophic activity in thrombolite-associated microbial mats. In contrast, the microbiomes of microbial communities found on the sandy non-lithifying sediments of Lake Clifton represented distinct microbial communities that varied in taxa and functional capability and were enriched in heterotrophic taxa compared to the thrombolite-associated mats. This study provides new insight into the taxa and functional capabilities that differentiate potentially lithifying mats from other non-lithifying types and suggests that thrombolites are actively accreting and growing in limited areas of Lake Clifton.
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Affiliation(s)
- John G Warden
- Department of Geological Sciences, University of Texas at Austin, AustinTX, USA; Space Life Science Lab, Department of Microbiology and Cell Science, University of Florida, Merritt IslandFL, USA
| | - Giorgio Casaburi
- Space Life Science Lab, Department of Microbiology and Cell Science, University of Florida, Merritt Island FL, USA
| | - Christopher R Omelon
- Department of Geological Sciences, University of Texas at Austin, Austin TX, USA
| | - Philip C Bennett
- Department of Geological Sciences, University of Texas at Austin, Austin TX, USA
| | - Daniel O Breecker
- Department of Geological Sciences, University of Texas at Austin, Austin TX, USA
| | - Jamie S Foster
- Space Life Science Lab, Department of Microbiology and Cell Science, University of Florida, Merritt Island FL, USA
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28
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Røder HL, Sørensen SJ, Burmølle M. Studying Bacterial Multispecies Biofilms: Where to Start? Trends Microbiol 2016; 24:503-513. [DOI: 10.1016/j.tim.2016.02.019] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 02/18/2016] [Accepted: 02/29/2016] [Indexed: 11/26/2022]
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29
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Wong HL, Ahmed-Cox A, Burns BP. Molecular Ecology of Hypersaline Microbial Mats: Current Insights and New Directions. Microorganisms 2016; 4:microorganisms4010006. [PMID: 27681900 PMCID: PMC5029511 DOI: 10.3390/microorganisms4010006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 12/08/2015] [Accepted: 12/15/2015] [Indexed: 11/17/2022] Open
Abstract
Microbial mats are unique geobiological ecosystems that form as a result of complex communities of microorganisms interacting with each other and their physical environment. Both the microorganisms present and the network of metabolic interactions govern ecosystem function therein. These systems are often found in a range of extreme environments, and those found in elevated salinity have been particularly well studied. The purpose of this review is to briefly describe the molecular ecology of select model hypersaline mat systems (Guerrero Negro, Shark Bay, S’Avall, and Kiritimati Atoll), and any potentially modulating effects caused by salinity to community structure. In addition, we discuss several emerging issues in the field (linking function to newly discovered phyla and microbial dark matter), which illustrate the changing paradigm that is seen as technology has rapidly advanced in the study of these extreme and evolutionally significant ecosystems.
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Affiliation(s)
- Hon Lun Wong
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia.
- Australian Centre for Astrobiology, University of New South Wales, Sydney 2052, Australia.
| | - Aria Ahmed-Cox
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia.
| | - Brendan Paul Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia.
- Australian Centre for Astrobiology, University of New South Wales, Sydney 2052, Australia.
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30
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Oren A. Life in Hypersaline Environments. THEIR WORLD: A DIVERSITY OF MICROBIAL ENVIRONMENTS 2016. [DOI: 10.1007/978-3-319-28071-4_8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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31
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Koskella B, Vos M. Adaptation in Natural Microbial Populations. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2015. [DOI: 10.1146/annurev-ecolsys-112414-054458] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, California 94720;
- Department of Biosciences, University of Exeter, Penryn Campus, Cornwall TR10 9FE, United Kingdom
| | - Michiel Vos
- European Centre for Environment and Human Health, University of Exeter Medical School, Penryn Campus, Cornwall TR10 9FE, United Kingdom;
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32
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Riquelme C, Rigal F, Hathaway JJM, Northup DE, Spilde MN, Borges PAV, Gabriel R, Amorim IR, Dapkevicius MDLNE. Cave microbial community composition in oceanic islands: disentangling the effect of different colored mats in diversity patterns of Azorean lava caves. FEMS Microbiol Ecol 2015; 91:fiv141. [PMID: 26564959 DOI: 10.1093/femsec/fiv141] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2015] [Indexed: 11/14/2022] Open
Abstract
Processes determining diversity and composition of bacterial communities in island volcanic caves are still poorly understood. Here, we characterized colored microbial mats in 14 volcanic caves from two oceanic islands of the Azores using 16S rRNA gene sequences. Factors determining community diversity (α) and composition (β) were explored, namely colored mats, caves and islands, as well as environmental and chemical characteristics of caves. Additive partitioning of diversity using OTU occurrence showed a greater influence of β-diversity between islands and caves that may relate to differences in rare OTUs (singletons and doubletons) across scales. In contrast, Shannon diversity partitioning revealed the importance of the lowest hierarchical level (α diversity, colored mat), suggesting a dominance of cosmopolitan OTUs (>1%) in most samples. Cosmopolitan OTUs included members involved in nitrogen cycling, supporting the importance of this process in Azorean caves. Environmental and chemical conditions in caves did not show any significant relationship to OTU diversity and composition. The absence of clear differences between mat colors and across scales may be explained by (1) the geological youth of the cave system (cave communities have not had enough time to diverge) or/and (2) community convergence, as the result of selection pressure in extreme environments.
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Affiliation(s)
- Cristina Riquelme
- Food Science and Health Group (CITA-A), Universidade dos Açores, Departamento de Ciências Agrárias, Rua Capitão João d'Ávila, São Pedro, 9700-042 Angra do Heroísmo, Terceira, Azores, Portugal
| | - François Rigal
- cE3c - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos Açores - Departamento de Ciências Agrárias, Rua Capitão João d'Ávila, São Pedro, 9700-042 Angra do Heroísmo, Terceira, Azores, Portugal Environment and Microbiology Team, MELODY group, Université of Pau et des Pays de l'Adour, IPREM UMR CNRS 5254, BP 1155, 64013 Pau Cedex, France
| | - Jennifer J M Hathaway
- Department of Biology, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | - Diana E Northup
- Department of Biology, MSC03 2020, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | - Michael N Spilde
- Institute of Meteoritics, MSC03 2050, University of New Mexico, Albuquerque, NM 87131, USA
| | - Paulo A V Borges
- cE3c - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos Açores - Departamento de Ciências Agrárias, Rua Capitão João d'Ávila, São Pedro, 9700-042 Angra do Heroísmo, Terceira, Azores, Portugal
| | - Rosalina Gabriel
- cE3c - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos Açores - Departamento de Ciências Agrárias, Rua Capitão João d'Ávila, São Pedro, 9700-042 Angra do Heroísmo, Terceira, Azores, Portugal
| | - Isabel R Amorim
- cE3c - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos Açores - Departamento de Ciências Agrárias, Rua Capitão João d'Ávila, São Pedro, 9700-042 Angra do Heroísmo, Terceira, Azores, Portugal
| | - Maria de Lurdes N E Dapkevicius
- Food Science and Health Group (CITA-A), Universidade dos Açores, Departamento de Ciências Agrárias, Rua Capitão João d'Ávila, São Pedro, 9700-042 Angra do Heroísmo, Terceira, Azores, Portugal
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33
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Hemme CL, Tu Q, Shi Z, Qin Y, Gao W, Deng Y, Nostrand JDV, Wu L, He Z, Chain PSG, Tringe SG, Fields MW, Rubin EM, Tiedje JM, Hazen TC, Arkin AP, Zhou J. Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. Front Microbiol 2015; 6:1205. [PMID: 26583008 PMCID: PMC4628106 DOI: 10.3389/fmicb.2015.01205] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/16/2015] [Indexed: 11/15/2022] Open
Abstract
To understand patterns of geochemical cycling in pristine versus contaminated groundwater ecosystems, pristine shallow groundwater (FW301) and contaminated groundwater (FW106) samples from the Oak Ridge Integrated Field Research Center (OR-IFRC) were sequenced and compared to each other to determine phylogenetic and metabolic difference between the communities. Proteobacteria (e.g., Burkholderia, Pseudomonas) are the most abundant lineages in the pristine community, though a significant proportion ( >55%) of the community is composed of poorly characterized low abundance (individually <1%) lineages. The phylogenetic diversity of the pristine community contributed to a broader diversity of metabolic networks than the contaminated community. In addition, the pristine community encodes redundant and mostly complete geochemical cycles distributed over multiple lineages and appears capable of a wide range of metabolic activities. In contrast, many geochemical cycles in the contaminated community appear truncated or minimized due to decreased biodiversity and dominance by Rhodanobacter populations capable of surviving the combination of stresses at the site. These results indicate that the pristine site contains more robust and encodes more functional redundancy than the stressed community, which contributes to more efficient nutrient cycling and adaptability than the stressed community.
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Affiliation(s)
- Christopher L Hemme
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Qichao Tu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Zhou Shi
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Yujia Qin
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Weimin Gao
- The Biodesign Institute, Arizona State University, Tempe AZ, USA
| | - Ye Deng
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA ; CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences Beijing, China
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Liyou Wu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Zhili He
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos NM, USA
| | - Susannah G Tringe
- United States Department of Energy, Joint Genome Institute, Walnut Creek CA, USA
| | - Matthew W Fields
- Department of Microbiology, Montana State University, Bozeman MT, USA
| | - Edward M Rubin
- United States Department of Energy, Joint Genome Institute, Walnut Creek CA, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing MI, USA
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee-Knoxville, Knoxville TN, USA ; Department of Earth and Planetary Sciences, University of Tennessee-Knoxville, Knoxville TN, USA ; Department of Microbiology, University of Tennessee-Knoxville, Knoxville TN, USA ; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN, USA
| | - Adam P Arkin
- Department of Bioengineering, Lawrence Berkeley National Laboratory, Berkeley CA, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA ; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley CA, USA ; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University Beijing, China
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34
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Wong HL, Smith DL, Visscher PT, Burns BP. Niche differentiation of bacterial communities at a millimeter scale in Shark Bay microbial mats. Sci Rep 2015; 5:15607. [PMID: 26499760 PMCID: PMC4620479 DOI: 10.1038/srep15607] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 09/28/2015] [Indexed: 02/01/2023] Open
Abstract
Modern microbial mats can provide key insights into early Earth ecosystems, and Shark Bay, Australia, holds one of the best examples of these systems. Identifying the spatial distribution of microorganisms with mat depth facilitates a greater understanding of specific niches and potentially novel microbial interactions. High throughput sequencing coupled with elemental analyses and biogeochemical measurements of two distinct mat types (smooth and pustular) at a millimeter scale were undertaken in the present study. A total of 8,263,982 16S rRNA gene sequences were obtained, which were affiliated to 58 bacterial and candidate phyla. The surface of both mats were dominated by Cyanobacteria, accompanied with known or putative members of Alphaproteobacteria and Bacteroidetes. The deeper anoxic layers of smooth mats were dominated by Chloroflexi, while Alphaproteobacteria dominated the lower layers of pustular mats. In situ microelectrode measurements revealed smooth mats have a steeper profile of O2 and H2S concentrations, as well as higher oxygen production, consumption, and sulfate reduction rates. Specific elements (Mo, Mg, Mn, Fe, V, P) could be correlated with specific mat types and putative phylogenetic groups. Models are proposed for these systems suggesting putative surface anoxic niches, differential nitrogen fixing niches, and those coupled with methane metabolism.
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Affiliation(s)
- Hon Lun Wong
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
- Australian Centre for Astrobiology, University of New South Wales Sydney, Australia
| | - Daniela-Lee Smith
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
- Australian Centre for Astrobiology, University of New South Wales Sydney, Australia
| | - Pieter T. Visscher
- Department of Marine Sciences, University of Connecticut, USA
- Australian Centre for Astrobiology, University of New South Wales Sydney, Australia
| | - Brendan P. Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
- Australian Centre for Astrobiology, University of New South Wales Sydney, Australia
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Mirete S, Mora-Ruiz MR, Lamprecht-Grandío M, de Figueras CG, Rosselló-Móra R, González-Pastor JE. Salt resistance genes revealed by functional metagenomics from brines and moderate-salinity rhizosphere within a hypersaline environment. Front Microbiol 2015; 6:1121. [PMID: 26528268 PMCID: PMC4602150 DOI: 10.3389/fmicb.2015.01121] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 09/28/2015] [Indexed: 11/13/2022] Open
Abstract
Hypersaline environments are considered one of the most extreme habitats on earth and microorganisms have developed diverse molecular mechanisms of adaptation to withstand these conditions. The present study was aimed at identifying novel genes from the microbial communities of a moderate-salinity rhizosphere and brine from the Es Trenc saltern (Mallorca, Spain), which could confer increased salt resistance to Escherichia coli. The microbial diversity assessed by pyrosequencing of 16S rRNA gene libraries revealed the presence of communities that are typical in such environments and the remarkable presence of three bacterial groups never revealed as major components of salt brines. Metagenomic libraries from brine and rhizosphere samples, were transferred to the osmosensitive strain E. coli MKH13, and screened for salt resistance. Eleven genes that conferred salt resistance were identified, some encoding for well-known proteins previously related to osmoadaptation such as a glycerol transporter and a proton pump, whereas others encoded proteins not previously related to this function in microorganisms such as DNA/RNA helicases, an endonuclease III (Nth) and hypothetical proteins of unknown function. Furthermore, four of the retrieved genes were cloned and expressed in Bacillus subtilis and they also conferred salt resistance to this bacterium, broadening the spectrum of bacterial species in which these genes can function. This is the first report of salt resistance genes recovered from metagenomes of a hypersaline environment.
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Affiliation(s)
- Salvador Mirete
- Laboratory of Molecular Adaptation, Department of Molecular Evolution, Centro de Astrobiología, Consejo Superior de Investigaciones Científicas - Instituto Nacional de Técnica Aeroespacial, Madrid Spain
| | - Merit R Mora-Ruiz
- Marine Microbiology Group, Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies, Consejo Superior de Investigaciones Científicas - Universidad de las Islas Baleares, Esporles Spain
| | - María Lamprecht-Grandío
- Laboratory of Molecular Adaptation, Department of Molecular Evolution, Centro de Astrobiología, Consejo Superior de Investigaciones Científicas - Instituto Nacional de Técnica Aeroespacial, Madrid Spain
| | - Carolina G de Figueras
- Laboratory of Molecular Adaptation, Department of Molecular Evolution, Centro de Astrobiología, Consejo Superior de Investigaciones Científicas - Instituto Nacional de Técnica Aeroespacial, Madrid Spain
| | - Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies, Consejo Superior de Investigaciones Científicas - Universidad de las Islas Baleares, Esporles Spain
| | - José E González-Pastor
- Laboratory of Molecular Adaptation, Department of Molecular Evolution, Centro de Astrobiología, Consejo Superior de Investigaciones Científicas - Instituto Nacional de Técnica Aeroespacial, Madrid Spain
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36
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Mobberley JM, Khodadad CLM, Visscher PT, Reid RP, Hagan P, Foster JS. Inner workings of thrombolites: spatial gradients of metabolic activity as revealed by metatranscriptome profiling. Sci Rep 2015. [PMID: 26213359 PMCID: PMC4515876 DOI: 10.1038/srep12601] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Microbialites are sedimentary deposits formed by the metabolic interactions of microbes and their environment. These lithifying microbial communities represent one of the oldest ecosystems on Earth, yet the molecular mechanisms underlying the function of these communities are poorly understood. In this study, we used comparative metagenomic and metatranscriptomic analyses to characterize the spatial organization of the thrombolites of Highborne Cay, The Bahamas, an actively forming microbialite system. At midday, there were differences in gene expression throughout the spatial profile of the thrombolitic mat with a high abundance of transcripts encoding genes required for photosynthesis, nitrogen fixation and exopolymeric substance production in the upper three mm of the mat. Transcripts associated with denitrification and sulfate reduction were in low abundance throughout the depth profile, suggesting these metabolisms were less active during midday. Comparative metagenomics of the Bahamian thrombolites with other known microbialite ecosystems from across the globe revealed that, despite many shared core pathways, the thrombolites represented genetically distinct communities. This study represents the first time the metatranscriptome of living microbialite has been characterized and offers a new molecular perspective on those microbial metabolisms, and their underlying genetic pathways, that influence the mechanisms of carbonate precipitation in lithifying microbial mat ecosystems.
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Affiliation(s)
- J M Mobberley
- Department of Microbiology and Cell Science, University of Florida, Space Life Science Lab-Exploration Park, Merritt Island, FL 32953
| | - C L M Khodadad
- Department of Microbiology and Cell Science, University of Florida, Space Life Science Lab-Exploration Park, Merritt Island, FL 32953
| | - P T Visscher
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340
| | - R P Reid
- Rosenstiel School of Marine Sciences, University of Miami, Miami, FL, 33149
| | - P Hagan
- Rosenstiel School of Marine Sciences, University of Miami, Miami, FL, 33149
| | - J S Foster
- Department of Microbiology and Cell Science, University of Florida, Space Life Science Lab-Exploration Park, Merritt Island, FL 32953
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Aßhauer KP, Wemheuer B, Daniel R, Meinicke P. Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data. Bioinformatics 2015; 31:2882-4. [PMID: 25957349 PMCID: PMC4547618 DOI: 10.1093/bioinformatics/btv287] [Citation(s) in RCA: 866] [Impact Index Per Article: 96.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 05/03/2015] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION The characterization of phylogenetic and functional diversity is a key element in the analysis of microbial communities. Amplicon-based sequencing of marker genes, such as 16S rRNA, is a powerful tool for assessing and comparing the structure of microbial communities at a high phylogenetic resolution. Because 16S rRNA sequencing is more cost-effective than whole metagenome shotgun sequencing, marker gene analysis is frequently used for broad studies that involve a large number of different samples. However, in comparison to shotgun sequencing approaches, insights into the functional capabilities of the community get lost when restricting the analysis to taxonomic assignment of 16S rRNA data. RESULTS Tax4Fun is a software package that predicts the functional capabilities of microbial communities based on 16S rRNA datasets. We evaluated Tax4Fun on a range of paired metagenome/16S rRNA datasets to assess its performance. Our results indicate that Tax4Fun provides a good approximation to functional profiles obtained from metagenomic shotgun sequencing approaches. AVAILABILITY AND IMPLEMENTATION Tax4Fun is an open-source R package and applicable to output as obtained from the SILVAngs web server or the application of QIIME with a SILVA database extension. Tax4Fun is freely available for download at http://tax4fun.gobics.de/. CONTACT kasshau@gwdg.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Bernd Wemheuer
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, 37077 Göttingen, Germany
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Insights from the metagenome of an acid salt lake: the role of biology in an extreme depositional environment. PLoS One 2015; 10:e0122869. [PMID: 25923206 PMCID: PMC4414474 DOI: 10.1371/journal.pone.0122869] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 02/24/2015] [Indexed: 12/31/2022] Open
Abstract
The extremely acidic brine lakes of the Yilgarn Craton of Western Australia are home to some of the most biologically challenging waters on Earth. In this study, we employed metagenomic shotgun sequencing to generate a microbial profile of the depositional environment associated with the sulfur-rich sediments of one such lake. Of the 1.5 M high-quality reads generated, 0.25 M were mapped to protein features, which in turn provide new insights into the metabolic function of this community. In particular, 45 diverse genes associated with sulfur metabolism were identified, the majority of which were linked to either the conversion of sulfate to adenylylsulfate and the subsequent production of sulfide from sulfite or the oxidation of sulfide, elemental sulfur, and thiosulfate via the sulfur oxidation (Sox) system. This is the first metagenomic study of an acidic, hypersaline depositional environment, and we present evidence for a surprisingly high level of microbial diversity. Our findings also illuminate the possibility that we may be meaningfully underestimating the effects of biology on the chemistry of these sulfur-rich sediments, thereby influencing our understanding of past geobiological conditions that may have been present on Earth as well as early Mars.
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Reichenberger ER, Rosen G, Hershberg U, Hershberg R. Prokaryotic nucleotide composition is shaped by both phylogeny and the environment. Genome Biol Evol 2015; 7:1380-9. [PMID: 25861819 PMCID: PMC4453058 DOI: 10.1093/gbe/evv063] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2015] [Indexed: 02/07/2023] Open
Abstract
The causes of the great variation in nucleotide composition of prokaryotic genomes have long been disputed. Here, we use extensive metagenomic and whole-genome data to demonstrate that both phylogeny and the environment shape prokaryotic nucleotide content. We show that across environments, various phyla are characterized by different mean guanine and cytosine (GC) values as well as by the extent of variation on that mean value. At the same time, we show that GC-content varies greatly as a function of environment, in a manner that cannot be entirely explained by disparities in phylogenetic composition. We find environmentally driven differences in nucleotide content not only between highly diverged environments (e.g., soil, vs. aquatic vs. human gut) but also within a single type of environment. More specifically, we demonstrate that some human guts are associated with a microbiome that is consistently more GC-rich across phyla, whereas others are associated with a more AT-rich microbiome. These differences appear to be driven both by variations in phylogenetic composition and by environmental differences-which are independent of these phylogenetic composition differences. Combined, our results demonstrate that both phylogeny and the environment significantly affect nucleotide composition and that the environmental differences affecting nucleotide composition are far subtler than previously appreciated.
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Affiliation(s)
- Erin R Reichenberger
- Department of Biomedical Engineering, Science & Health Systems, Drexel University
| | - Gail Rosen
- Department of Computer and Electrical Engineering, Drexel University
| | - Uri Hershberg
- Department of Biomedical Engineering, Science & Health Systems, Drexel University Department of Microbiology and Immunology, Drexel University College of Medicine
| | - Ruth Hershberg
- Rachel and Menachem Mendelovitch Evolutionary Processes of Mutation and Natural Selection Research Laboratory, Department of Genetics and Developmental Biology, The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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Oren A. Halophilic microbial communities and their environments. Curr Opin Biotechnol 2015; 33:119-24. [PMID: 25727188 DOI: 10.1016/j.copbio.2015.02.005] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 01/04/2015] [Accepted: 02/13/2015] [Indexed: 10/23/2022]
Abstract
Use of culture-independent studies have greatly increased our understanding of the microbiology of hypersaline lakes (the Dead Sea, Great Salt Lake) and saltern ponds in recent years. Exciting new information has become available on the microbial processes in Antarctic lakes and in deep-sea brines. These studies led to the recognition of many new lineages of microorganisms not yet available for study in culture, and their cultivation in the laboratory is now a major challenge. Studies of the metabolic potentials of different halophilic microorganisms, Archaea as well as Bacteria, shed light on the possibilities and the limitations of life at high salt concentrations, and also show their potential for applications in bioremediation.
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Affiliation(s)
- Aharon Oren
- Department of Plant & Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat-Ram, Jerusalem 91904, Israel.
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Meinicke P. UProC: tools for ultra-fast protein domain classification. ACTA ACUST UNITED AC 2014; 31:1382-8. [PMID: 25540185 PMCID: PMC4410661 DOI: 10.1093/bioinformatics/btu843] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 12/17/2014] [Indexed: 01/20/2023]
Abstract
Motivation: With rapidly increasing volumes of biological sequence data the functional analysis of new sequences in terms of similarities to known protein families challenges classical bioinformatics. Results: The ultrafast protein classification (UProC) toolbox implements a novel algorithm (‘Mosaic Matching’) for large-scale sequence analysis. UProC is by three orders of magnitude faster than profile-based methods and in a metagenome simulation study achieved up to 80% higher sensitivity on unassembled 100 bp reads. Availability and implementation: UProC is available as an open-source software at https://github.com/gobics/uproc. Precompiled databases (Pfam) are linked on the UProC homepage: http://uproc.gobics.de/. Contact:peter@gobics.de. Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Peter Meinicke
- Department of Bioinformatics, Institute for Microbiology and Genetics, University of Göttingen, Germany
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Alsop EB, Boyd ES, Raymond J. Merging metagenomics and geochemistry reveals environmental controls on biological diversity and evolution. BMC Ecol 2014; 14:16. [PMID: 24886397 PMCID: PMC4047435 DOI: 10.1186/1472-6785-14-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 05/16/2014] [Indexed: 11/13/2022] Open
Abstract
Background The metabolic strategies employed by microbes inhabiting natural systems are, in large part, dictated by the physical and geochemical properties of the environment. This study sheds light onto the complex relationship between biology and environmental geochemistry using forty-three metagenomes collected from geochemically diverse and globally distributed natural systems. It is widely hypothesized that many uncommonly measured geochemical parameters affect community dynamics and this study leverages the development and application of multidimensional biogeochemical metrics to study correlations between geochemistry and microbial ecology. Analysis techniques such as a Markov cluster-based measure of the evolutionary distance between whole communities and a principal component analysis (PCA) of the geochemical gradients between environments allows for the determination of correlations between microbial community dynamics and environmental geochemistry and provides insight into which geochemical parameters most strongly influence microbial biodiversity. Results By progressively building from samples taken along well defined geochemical gradients to samples widely dispersed in geochemical space this study reveals strong links between the extent of taxonomic and functional diversification of resident communities and environmental geochemistry and reveals temperature and pH as the primary factors that have shaped the evolution of these communities. Moreover, the inclusion of extensive geochemical data into analyses reveals new links between geochemical parameters (e.g. oxygen and trace element availability) and the distribution and taxonomic diversification of communities at the functional level. Further, an overall geochemical gradient (from multivariate analyses) between natural systems provides one of the most complete predictions of microbial taxonomic and functional composition. Conclusions Clustering based on the frequency in which orthologous proteins occur among metagenomes facilitated accurate prediction of the ordering of community functional composition along geochemical gradients, despite a lack of geochemical input. The consistency in the results obtained from the application of Markov clustering and multivariate methods to distinct natural systems underscore their utility in predicting the functional potential of microbial communities within a natural system based on system geochemistry alone, allowing geochemical measurements to be used to predict purely biological metrics such as microbial community composition and metabolism.
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Affiliation(s)
| | | | - Jason Raymond
- School of Earth and Space Exploration, Arizona State University, ISTB4, Room 795, 781 E, Terrace Rd, Tempe, AZ 85287, USA.
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43
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Fernández AB, Ghai R, Martin-Cuadrado AB, Sánchez-Porro C, Rodriguez-Valera F, Ventosa A. Prokaryotic taxonomic and metabolic diversity of an intermediate salinity hypersaline habitat assessed by metagenomics. FEMS Microbiol Ecol 2014; 88:623-35. [PMID: 24661078 DOI: 10.1111/1574-6941.12329] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 03/11/2014] [Accepted: 03/12/2014] [Indexed: 11/28/2022] Open
Abstract
A metagenome was obtained by pyrosequencing the total prokaryotic DNA from the water of a pond with intermediate salinity (13% salts) from a saltern located in Santa Pola, Spain. We analyzed and compared the phylogenomic and metabolic diversity of this saltern pond with respect to other two metagenomes obtained previously from the same saltern (ponds with 19% and 37% salts, respectively) and two reference metagenomes from marine and coastal lagoon habitats. A large microbial diversity, representing seven major higher taxa (Euryarchaeota, Gammaproteobacteria, Alphaproteobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia and Betaproteobacteria), was found. However, most sequences (57%) were not assigned to any previously described genus. Principal component analysis of tetranucleotide frequencies of assembled contigs showed the presence of new groups of Euryarchaeota, different from those previously described but related to Haloquadratum walsbyi and other members of the Halobacteriaceae. Besides, some new Gammaproteobacteria, several closely related to the recently isolated bacterium 'Spiribacter salinus' were observed. Metabolically, the nitrogen and carbon cycles appear to be very simplified in this extreme habitat. Light is extensively used as energy source by bacteriorhodopsins and other rhodopsins. Microorganisms known to use the 'salt-in' strategy are probably able to combine the accumulation of potassium ions and of compatible solutes.
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Affiliation(s)
- Ana B Fernández
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
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44
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Sahl JW, Caporaso JG, Rasko DA, Keim P. The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes. PeerJ 2014; 2:e332. [PMID: 24749011 PMCID: PMC3976120 DOI: 10.7717/peerj.332] [Citation(s) in RCA: 181] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 03/14/2014] [Indexed: 12/30/2022] Open
Abstract
Background. As whole genome sequence data from bacterial isolates becomes cheaper to generate, computational methods are needed to correlate sequence data with biological observations. Here we present the large-scale BLAST score ratio (LS-BSR) pipeline, which rapidly compares the genetic content of hundreds to thousands of bacterial genomes, and returns a matrix that describes the relatedness of all coding sequences (CDSs) in all genomes surveyed. This matrix can be easily parsed in order to identify genetic relationships between bacterial genomes. Although pipelines have been published that group peptides by sequence similarity, no other software performs the rapid, large-scale, full-genome comparative analyses carried out by LS-BSR. Results. To demonstrate the utility of the method, the LS-BSR pipeline was tested on 96 Escherichia coli and Shigella genomes; the pipeline ran in 163 min using 16 processors, which is a greater than 7-fold speedup compared to using a single processor. The BSR values for each CDS, which indicate a relative level of relatedness, were then mapped to each genome on an independent core genome single nucleotide polymorphism (SNP) based phylogeny. Comparisons were then used to identify clade specific CDS markers and validate the LS-BSR pipeline based on molecular markers that delineate between classical E. coli pathogenic variant (pathovar) designations. Scalability tests demonstrated that the LS-BSR pipeline can process 1,000 E. coli genomes in 27-57 h, depending upon the alignment method, using 16 processors. Conclusions. LS-BSR is an open-source, parallel implementation of the BSR algorithm, enabling rapid comparison of the genetic content of large numbers of genomes. The results of the pipeline can be used to identify specific markers between user-defined phylogenetic groups, and to identify the loss and/or acquisition of genetic information between bacterial isolates. Taxa-specific genetic markers can then be translated into clinical diagnostics, or can be used to identify broadly conserved putative therapeutic candidates.
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Affiliation(s)
- Jason W Sahl
- Division of Pathogen Genomics, Translational Genomics Research Institute , Flagstaff, AZ , USA ; Department of Biological Sciences, Northern Arizona University , Flagstaff, AZ , USA ; Center for Microbial Genetics and Genomics, Northern Arizona University , Flagstaff, AZ , USA
| | - J Gregory Caporaso
- Department of Biological Sciences, Northern Arizona University , Flagstaff, AZ , USA
| | - David A Rasko
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine , Baltimore, MD , USA
| | - Paul Keim
- Division of Pathogen Genomics, Translational Genomics Research Institute , Flagstaff, AZ , USA ; Department of Biological Sciences, Northern Arizona University , Flagstaff, AZ , USA ; Center for Microbial Genetics and Genomics, Northern Arizona University , Flagstaff, AZ , USA
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Dillon JG, Carlin M, Gutierrez A, Nguyen V, McLain N. Patterns of microbial diversity along a salinity gradient in the Guerrero Negro solar saltern, Baja CA Sur, Mexico. Front Microbiol 2013; 4:399. [PMID: 24391633 PMCID: PMC3868825 DOI: 10.3389/fmicb.2013.00399] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 12/04/2013] [Indexed: 01/28/2023] Open
Abstract
The goal of this study was to use environmental sequencing of 16S rRNA and bop genes to compare the diversity of planktonic bacteria and archaea across ponds with increasing salinity in the Exportadora de Sal (ESSA) evaporative saltern in Guerrero Negro, Baja CA S., Mexico. We hypothesized that diverse communities of heterotrophic bacteria and archaea would be found in the ESSA ponds, but that bacterial diversity would decrease relative to archaea at the highest salinities. Archaeal 16S rRNA diversity was higher in Ponds 11 and 12 (370 and 380 g l(-1) total salts, respectively) compared to Pond 9 (180 g l(-1) total salts). Both Pond 11 and 12 communities had high representation (47 and 45% of clones, respectively) by Haloquadratum walsbyi-like (99% similarity) lineages. The archaeal community in Pond 9 was dominated (79%) by a single uncultured phylotype with 99% similarity to sequences recovered from the Sfax saltern in Tunisia. This pattern was mirrored in bop gene diversity with greater numbers of highly supported phylotypes including many Haloquadratum-like sequences from the two highest salinity ponds. In Pond 9, most bop sequences, were not closely related to sequences in databases. Bacterial 16S rRNA diversity was higher than archaeal in both Pond 9 and Pond 12 samples, but not Pond 11, where a non-Salinibacter lineage within the Bacteroidetes >98% similar to environmental clones recovered from Lake Tuz in Turkey and a saltern in Chula Vista, CA was most abundant (69% of community). This OTU was also the most abundant in Pond 12, but only represented 14% of clones in the more diverse pond. The most abundant OTU in Pond 9 (33% of community) was 99% similar to an uncultured gammaproteobacterial clone from the Salton Sea. Results suggest that the communities of saltern bacteria and archaea vary even in ponds with similar salinity and further investigation into the ecology of diverse, uncultured halophile communities is warranted.
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Affiliation(s)
- Jesse G Dillon
- Department of Biological Sciences, California State University Long Beach, CA, USA
| | - Mark Carlin
- Department of Biological Sciences, California State University Long Beach, CA, USA
| | - Abraham Gutierrez
- Department of Biological Sciences, California State University Long Beach, CA, USA
| | - Vivian Nguyen
- Department of Biological Sciences, California State University Long Beach, CA, USA
| | - Nathan McLain
- Department of Biological Sciences, California State University Long Beach, CA, USA
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Eiler A, Zaremba-Niedzwiedzka K, Martínez-García M, McMahon KD, Stepanauskas R, Andersson SGE, Bertilsson S. Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics. Environ Microbiol 2013; 16:2682-98. [PMID: 24118837 PMCID: PMC4253090 DOI: 10.1111/1462-2920.12301] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 09/27/2013] [Indexed: 01/17/2023]
Abstract
Little is known about the diversity and structuring of freshwater microbial communities beyond
the patterns revealed by tracing their distribution in the landscape with common taxonomic markers
such as the ribosomal RNA. To address this gap in knowledge, metagenomes from temperate lakes were
compared to selected marine metagenomes. Taxonomic analyses of rRNA genes in these freshwater
metagenomes confirm the previously reported dominance of a limited subset of uncultured lineages of
freshwater bacteria, whereas Archaea were rare. Diversification into marine and freshwater microbial
lineages was also reflected in phylogenies of functional genes, and there were also significant
differences in functional beta-diversity. The pathways and functions that accounted for these
differences are involved in osmoregulation, active transport, carbohydrate and amino acid
metabolism. Moreover, predicted genes orthologous to active transporters and recalcitrant organic
matter degradation were more common in microbial genomes from oligotrophic versus eutrophic lakes.
This comparative metagenomic analysis allowed us to formulate a general hypothesis that oceanic-
compared with freshwater-dwelling microorganisms, invest more in metabolism of amino acids and that
strategies of carbohydrate metabolism differ significantly between marine and freshwater microbial
communities.
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Affiliation(s)
- Alexander Eiler
- Department of Ecology and Genetics, Limnology, Uppsala University, Uppsala, Sweden
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Oren A. Life at high salt concentrations, intracellular KCl concentrations, and acidic proteomes. Front Microbiol 2013; 4:315. [PMID: 24204364 PMCID: PMC3817357 DOI: 10.3389/fmicb.2013.00315] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 10/06/2013] [Indexed: 11/23/2022] Open
Abstract
Extremely halophilic microorganisms that accumulate KCl for osmotic balance (the Halobacteriaceae, Salinibacter) have a large excess of acidic amino acids in their proteins. This minireview explores the occurrence of acidic proteomes in halophiles of different physiology and phylogenetic affiliation. For fermentative bacteria of the order Halanaerobiales, known to accumulate KCl, an acidic proteome was predicted. However, this is not confirmed by genome analysis. The reported excess of acidic amino acids is due to a high content of Gln and Asn, which yield Glu and Asp upon acid hydrolysis. The closely related Halorhodospira halophila and Halorhodospira halochloris use different strategies to cope with high salt. The first has an acidic proteome and accumulates high KCl concentrations at high salt concentrations; the second does not accumulate KCl and lacks an acidic proteome. Acidic proteomes can be predicted from the genomes of some moderately halophilic aerobes that accumulate organic osmotic solutes (Halomonas elongata, Chromohalobacter salexigens) and some marine bacteria. Based on the information on cultured species it is possible to understand the pI profiles predicted from metagenomic data from hypersaline environments.
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Affiliation(s)
- Aharon Oren
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem Jerusalem, Israel
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48
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Mobberley JM, Khodadad CLM, Foster JS. Metabolic potential of lithifying cyanobacteria-dominated thrombolitic mats. PHOTOSYNTHESIS RESEARCH 2013; 118:125-140. [PMID: 23868401 PMCID: PMC5766932 DOI: 10.1007/s11120-013-9890-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 07/09/2013] [Indexed: 06/02/2023]
Abstract
Thrombolites are unlaminated carbonate deposits formed by the metabolic activities of microbial mats and can serve as potential models for understanding the molecular mechanisms underlying the formation of lithifying communities. To assess the metabolic complexity of these ecosystems, high throughput DNA sequencing of a thrombolitic mat metagenome was coupled with phenotypic microarray analysis. Functional protein analysis of the thrombolite community metagenome delineated several of the major metabolic pathways that influence carbonate mineralization including cyanobacterial photosynthesis, sulfate reduction, sulfide oxidation, and aerobic heterotrophy. Spatial profiling of metabolite utilization within the thrombolite-forming microbial mats suggested that the top 5 mm contained a more metabolically diverse and active community than the deeper within the mat. This study provides evidence that despite the lack of mineral layering within the clotted thrombolite structure there is a vertical gradient of metabolic activity within the thrombolitic mat community. This metagenomic profiling also serves as a foundation for examining the active role individual functional groups of microbes play in coordinating metabolisms that lead to mineralization.
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Affiliation(s)
- Jennifer M Mobberley
- Department of Microbiology and Cell Science, University of Florida, Space Life Sciences Lab, Kennedy Space Center, FL, 32899, USA
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Lanzén A, Simachew A, Gessesse A, Chmolowska D, Jonassen I, Øvreås L. Surprising prokaryotic and eukaryotic diversity, community structure and biogeography of Ethiopian soda lakes. PLoS One 2013; 8:e72577. [PMID: 24023625 PMCID: PMC3758324 DOI: 10.1371/journal.pone.0072577] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 07/11/2013] [Indexed: 11/18/2022] Open
Abstract
Soda lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. This makes them valuable model systems for studying the connection between community structure and abiotic parameters such as pH and salinity. For the first time, we apply high-throughput sequencing to accurately estimate phylogenetic richness and composition in five soda lakes, located in the Ethiopian Rift Valley. The lakes were selected for their contrasting pH, salinities and stratification and several depths or spatial positions were covered in each lake. DNA was extracted and analyzed from all lakes at various depths and RNA extracted from two of the lakes, analyzed using both amplicon- and shotgun sequencing. We reveal a surprisingly high biodiversity in all of the studied lakes, similar to that of freshwater lakes. Interestingly, diversity appeared uncorrelated or positively correlated to pH and salinity, with the most “extreme” lakes showing the highest richness. Together, pH, dissolved oxygen, sodium- and potassium concentration explained approximately 30% of the compositional variation between samples. A diversity of prokaryotic and eukaryotic taxa could be identified, including several putatively involved in carbon-, sulfur- or nitrogen cycling. Key processes like methane oxidation, ammonia oxidation and ‘nitrifier denitrification’ were also confirmed by mRNA transcript analyses.
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Affiliation(s)
- Anders Lanzén
- Department of Biology and Centre for Geobiology, University of Bergen, Bergen, Norway
- Computational Biology Unit, Uni Computing, Uni Research AS, Bergen, Norway
- * E-mail:
| | - Addis Simachew
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Amare Gessesse
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Dominika Chmolowska
- Institute of Environmental Sciences, Jagiellonian University, Krakow, Poland
| | - Inge Jonassen
- Computational Biology Unit, Uni Computing, Uni Research AS, Bergen, Norway
- Department of Informatics, University of Bergen, Bergen, Norway
| | - Lise Øvreås
- Department of Biology and Centre for Geobiology, University of Bergen, Bergen, Norway
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Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 2013; 31:814-21. [PMID: 23975157 PMCID: PMC3819121 DOI: 10.1038/nbt.2676] [Citation(s) in RCA: 5903] [Impact Index Per Article: 536.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Accepted: 07/29/2013] [Indexed: 12/12/2022]
Abstract
Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community’s functional capabilities. Here we describe PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States), a computational approach to predict the functional composition of a metagenome using marker gene data and a database of reference genomes. PICRUSt uses an extended ancestral-state reconstruction algorithm to predict which gene families are present and then combines gene families to estimate the composite metagenome. Using 16S information, PICRUSt recaptures key findings from the Human Microbiome Project and accurately predicts the abundance of gene families in host-associated and environmental communities, with quantifiable uncertainty. Our results demonstrate that phylogeny and function are sufficiently linked that this ‘predictive metagenomic’ approach should provide useful insights into the thousands of uncultivated microbial communities for which only marker gene surveys are currently available.
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Affiliation(s)
- Morgan G I Langille
- 1] Faculty of Computer Science, Dalhousie University, Halifax, NS, Canada. [2]
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