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Zhang Q, Xiong Y, Zhang J, Liu B, Chen T, Liu S, Dang C, Xu WD, Ahmad HA, Liu T. Eutrophication impacts the distribution and functional traits of viral communities in lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174339. [PMID: 38960155 DOI: 10.1016/j.scitotenv.2024.174339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/05/2024]
Abstract
Viruses play a crucial role in aquatic ecosystems by regulating microbial composition and impacting biogeochemical cycling. While the response of viral diversity to the trophic status has been preliminarily explored in lake ecosystems, there is limited integrated exploration of the biogeography of viruses, host associations, and the auxiliary metabolic genes (AMGs), particularly for plateau lakes. Therefore, this research investigated the viral biogeography, virus-host association, and AMGs in the surface waters of 11 lakes varying in trophic levels (eutrophic and oligo-mesotrophic) in the Yunnan-Guizhou plateau region of China. A total of 73,105 viral operational taxonomic units were obtained from 11 samples, with 84.8 % remaining unannotated at the family level, indicating a predominance of novel viruses within these lakes. The most abundant viral family was Kyanoviridae (24.4 %), recognized as a common cyanophage. The vast majority of cyanobacteria and several eukaryotic algae were predicted as hosts for the viruses, with a lytic lifestyle predominating the life strategy of these cyanophages, implying the potential influence of the virus on algae. The viral community structure significantly correlated with both trophic status and the bacterial community. The structure equation model analysis revealed chlorophyll a was the primary factor affecting viral communities. Moreover, numerous AMGs linked to carbon metabolism, phosphorus metabolism, sulfur metabolism, and photosynthesis were found in these lakes, some of which showed virus preference for the trophic statuses, suggesting a vital role of the virus in driving biogeochemical cycling in the lake crossing different nutrient levels. In addition, a restricted presence of viruses was found to infect humans or harbor antibiotic resistance genes in the lakes, suggesting a subtle yet potential link to human health. Overall, these findings offer insights into the response of viral communities to eutrophication and their potential role in biogeochemical cycling and controlling algal propagation.
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Affiliation(s)
- Qiue Zhang
- Environmental Microbiome Engineering and Innovative Genomics Laboratory, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, PR China
| | - Yanxuan Xiong
- Environmental Microbiome Engineering and Innovative Genomics Laboratory, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, PR China
| | - Jinhong Zhang
- Environmental Microbiome Engineering and Innovative Genomics Laboratory, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, PR China
| | - Boya Liu
- Environmental Microbiome Engineering and Innovative Genomics Laboratory, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, PR China
| | - Tianyi Chen
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, PR China
| | - Shufeng Liu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100083, PR China
| | - Chenyuan Dang
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074, PR China
| | - Wei D Xu
- Changjiang Institute of Survey, Planning, Design and Research, Wuhan, Hubei 430010, PR China
| | - Hafiz Adeel Ahmad
- Environmental Microbiome Engineering and Innovative Genomics Laboratory, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, PR China; School of Biomedical Engineering, Shenzhen University, Shenzhen 518060, PR China.
| | - Tang Liu
- Environmental Microbiome Engineering and Innovative Genomics Laboratory, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, PR China.
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2
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Peoples LM, Dore JE, Bilbrey EM, Vick-Majors TJ, Ranieri JR, Evans KA, Ross AM, Devlin SP, Church MJ. Oxic methane production from methylphosphonate in a large oligotrophic lake: limitation by substrate and organic carbon supply. Appl Environ Microbiol 2023; 89:e0109723. [PMID: 38032216 PMCID: PMC10734540 DOI: 10.1128/aem.01097-23] [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: 06/28/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE Methane is an important greenhouse gas that is typically produced under anoxic conditions. We show that methane is supersaturated in a large oligotrophic lake despite the presence of oxygen. Metagenomic sequencing indicates that diverse, widespread microorganisms may contribute to the oxic production of methane through the cleavage of methylphosphonate. We experimentally demonstrate that these organisms, especially members of the genus Acidovorax, can produce methane through this process. However, appreciable rates of methane production only occurred when both methylphosphonate and labile sources of carbon were added, indicating that this process may be limited to specific niches and may not be completely responsible for methane concentrations in Flathead Lake. This work adds to our understanding of methane dynamics by describing the organisms and the rates at which they can produce methane through an oxic pathway in a representative oligotrophic lake.
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Affiliation(s)
- Logan M. Peoples
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - John E. Dore
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, USA
| | - Evan M. Bilbrey
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - Trista J. Vick-Majors
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan, USA
| | - John R. Ranieri
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Kate A. Evans
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Abigail M. Ross
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Shawn P. Devlin
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Matthew J. Church
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
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3
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Sagua MI, Nuozzi G, Sánchez ML, Huber P, Perdomo S, Schiaffino MR. Unraveling the effect of land use on the bacterioplankton community composition from highly impacted shallow lakes at a regional scale. FEMS Microbiol Ecol 2023; 99:fiad109. [PMID: 37715304 DOI: 10.1093/femsec/fiad109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 09/06/2023] [Accepted: 09/14/2023] [Indexed: 09/17/2023] Open
Abstract
Bacterioplankton communities play a crucial role in global biogeochemical processes and are highly sensitive to changes induced by natural and anthropogenic stressors in aquatic ecosystems. We assessed the influence of Land Use Land Cover (LULC), environmental, and geographic changes on the bacterioplankton structure in highly connected and impacted shallow lakes within the Salado River basin, Buenos Aires, Argentina. Additionally, we investigated how changes in LULC affected the limnological characteristics of these lakes at a regional scale. Our analysis revealed that the lakes were ordinated by sub-basins (upper and lower) depending on their LULC characteristics and limnological properties. In coincidence, the same ordination was observed when considering the Bacterioplankton Community Composition (BCC). Spatial and environmental predictors significantly explained the variation in BCC, although when combined with LULC the effect was also important. While the pure LULC effect did not explain a significant percentage of BCC variation, the presence of atrazine in water, an anthropogenic variable linked to LULC, directly influenced both the BCC and some Amplicon Sequence Variants (ASVs) in particular. Our regional-scale approach contributes to understanding the complexity of factors driving bacterioplankton structure and how LULC pervasively affect these communities in highly impacted shallow lake ecosystems from the understudied Southern Hemisphere.
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Affiliation(s)
- Mara I Sagua
- Departamento de Ciencias Básicas y Experimentales, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Roque Saez Pena 456 (6000), Junín, Buenos Aires, Argentina
- Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CIT NOBA) - UNNOBA-UNSAdA-CONICET, Monteagudo 2772 (2700), Pergamino, Buenos Aires, Argentina
| | - Guillermina Nuozzi
- Departamento de Ciencias Básicas y Experimentales, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Roque Saez Pena 456 (6000), Junín, Buenos Aires, Argentina
- Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CIT NOBA) - UNNOBA-UNSAdA-CONICET, Monteagudo 2772 (2700), Pergamino, Buenos Aires, Argentina
| | - María L Sánchez
- CONICET - Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA), Universidad de Buenos Aires, Intendente Guiraldes 2160 (C1428EGA), Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Universidad de Buenos Aires, Intendente Guiraldes 2160 (C1428EGA), Ciudad Autónoma de Buenos Aires, Argentina
| | - Paula Huber
- Instituto Nacional de Limnología (INALI, CONICET-UNL). Colectora RN 168 Km 0 (3000), Paraje El Pozo, Santa Fe, Argentina
- Departamento de Hydrobiologia, Universidade Federal de São Carlos (UFSCar). Rodovia Washington Luis S/N - Monjolinho (13565-905), São Carlos, São Paulo, Brazil
| | - Santiago Perdomo
- Departamento de Ciencias Básicas y Experimentales, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Roque Saez Pena 456 (6000), Junín, Buenos Aires, Argentina
- Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CIT NOBA) - UNNOBA-UNSAdA-CONICET, Monteagudo 2772 (2700), Pergamino, Buenos Aires, Argentina
| | - María R Schiaffino
- Departamento de Ciencias Básicas y Experimentales, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Roque Saez Pena 456 (6000), Junín, Buenos Aires, Argentina
- Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CIT NOBA) - UNNOBA-UNSAdA-CONICET, Monteagudo 2772 (2700), Pergamino, Buenos Aires, Argentina
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4
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Lanclos VC, Rasmussen AN, Kojima CY, Cheng C, Henson MW, Faircloth BC, Francis CA, Thrash JC. Ecophysiology and genomics of the brackish water adapted SAR11 subclade IIIa. THE ISME JOURNAL 2023; 17:620-629. [PMID: 36739346 PMCID: PMC10030771 DOI: 10.1038/s41396-023-01376-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/06/2023] [Accepted: 01/20/2023] [Indexed: 02/05/2023]
Abstract
The Order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacterioplankton in global oceans and comprises multiple subclades with unique spatiotemporal distributions. Subclade IIIa is the primary SAR11 group in brackish waters and shares a common ancestor with the dominant freshwater IIIb (LD12) subclade. Despite its dominance in brackish environments, subclade IIIa lacks systematic genomic or ecological studies. Here, we combine closed genomes from new IIIa isolates, new IIIa MAGS from San Francisco Bay (SFB), and 460 highly complete publicly available SAR11 genomes for the most comprehensive pangenomic study of subclade IIIa to date. Subclade IIIa represents a taxonomic family containing three genera (denoted as subgroups IIIa.1, IIIa.2, and IIIa.3) that had distinct ecological distributions related to salinity. The expansion of taxon selection within subclade IIIa also established previously noted metabolic differentiation in subclade IIIa compared to other SAR11 subclades such as glycine/serine prototrophy, mosaic glyoxylate shunt presence, and polyhydroxyalkanoate synthesis potential. Our analysis further shows metabolic flexibility among subgroups within IIIa. Additionally, we find that subclade IIIa.3 bridges the marine and freshwater clades based on its potential for compatible solute transport, iron utilization, and bicarbonate management potential. Pure culture experimentation validated differential salinity ranges in IIIa.1 and IIIa.3 and provided detailed IIIa cell size and volume data. This study is an important step forward for understanding the genomic, ecological, and physiological differentiation of subclade IIIa and the overall evolutionary history of SAR11.
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Affiliation(s)
- V Celeste Lanclos
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Anna N Rasmussen
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Conner Y Kojima
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Chuankai Cheng
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Michael W Henson
- Department of Geophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA
| | | | - J Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
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5
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Chiriac MC, Haber M, Salcher MM. Adaptive genetic traits in pelagic freshwater microbes. Environ Microbiol 2023; 25:606-641. [PMID: 36513610 DOI: 10.1111/1462-2920.16313] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022]
Abstract
Pelagic microbes have adopted distinct strategies to inhabit the pelagial of lakes and oceans and can be broadly categorized in two groups: free-living, specialized oligotrophs and patch-associated generalists or copiotrophs. In this review, we aim to identify genomic traits that enable pelagic freshwater microbes to thrive in their habitat. To do so, we discuss the main genetic differences of pelagic marine and freshwater microbes that are both dominated by specialized oligotrophs and the difference to freshwater sediment microbes, where copiotrophs are more prevalent. We phylogenomically analysed a collection of >7700 metagenome-assembled genomes, classified habitat preferences on different taxonomic levels, and compared the metabolic traits of pelagic freshwater, marine, and freshwater sediment microbes. Metabolic differences are mainly associated with transport functions, environmental information processing, components of the electron transport chain, osmoregulation and the isoelectric point of proteins. Several lineages with known habitat transitions (Nitrososphaeria, SAR11, Methylophilaceae, Synechococcales, Flavobacteriaceae, Planctomycetota) and the underlying mechanisms in this process are discussed in this review. Additionally, the distribution, ecology and genomic make-up of the most abundant freshwater prokaryotes are described in details in separate chapters for Actinobacteriota, Bacteroidota, Burkholderiales, Verrucomicrobiota, Chloroflexota, and 'Ca. Patescibacteria'.
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Affiliation(s)
| | - Markus Haber
- Institute of Hydrobiology, Biology Centre CAS, Ceske Budejovice, Czechia
| | - Michaela M Salcher
- Institute of Hydrobiology, Biology Centre CAS, Ceske Budejovice, Czechia
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6
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Villena‐Alemany C, Mujakić I, Porcal P, Koblížek M, Piwosz K. Diversity dynamics of aerobic anoxygenic phototrophic bacteria in a freshwater lake. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:60-71. [PMID: 36507772 PMCID: PMC10103773 DOI: 10.1111/1758-2229.13131] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 09/19/2022] [Indexed: 05/20/2023]
Abstract
Aerobic anoxygenic photoheterotrophic (AAP) bacteria represent a functional group of prokaryotic organisms that harvests light energy using bacteriochlorophyll-containing photosynthetic reaction centers. They represent an active and rapidly growing component of freshwater bacterioplankton, with the highest numbers observed usually in summer. Species diversity of freshwater AAP bacteria has been studied before in lakes, but its seasonal dynamics remain unknown. In this report, we analysed temporal changes in the composition of the phototrophic community in an oligo-mesotrophic freshwater lake using amplicon sequencing of the pufM marker gene. The AAP community was dominated by phototrophic Gammaproteobacteria and Alphaproteobacteria, with smaller contribution of phototrophic Chloroflexota and Gemmatimonadota. Phototrophic Eremiobacteriota or members of Myxococcota were not detected. Interestingly, some AAP taxa, such as Limnohabitans, Rhodoferax, Rhodobacterales or Rhizobiales, were permanently present over the sampling period, while others, such as Sphingomonadales, Rhodospirillales or Caulobacterales appeared only transiently. The environmental factors that best explain the seasonal changes in AAP community were temperature, concentrations of oxygen and dissolved organic matter.
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Affiliation(s)
- Cristian Villena‐Alemany
- Laboratory of Anoxygenic PhototrophsInstitute of Microbiology of the Czech Academy of SciencesTřeboňCzechia
- Department of Ecosystem Biology, Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzechia
| | - Izabela Mujakić
- Laboratory of Anoxygenic PhototrophsInstitute of Microbiology of the Czech Academy of SciencesTřeboňCzechia
- Department of Ecosystem Biology, Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzechia
| | - Petr Porcal
- Department of Ecosystem Biology, Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzechia
- Department of Hydrochemistry and Ecosystem Modelling, Biology Centre of the Czech Academy of SciencesInstitute of HydrobiologyČeské BudějoviceCzechia
| | - Michal Koblížek
- Laboratory of Anoxygenic PhototrophsInstitute of Microbiology of the Czech Academy of SciencesTřeboňCzechia
- Department of Ecosystem Biology, Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzechia
| | - Kasia Piwosz
- Department of Fisheries Oceanography and Marine EcologyNational Marine Fisheries Research InstituteGdyniaPoland
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7
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Brenes-Guillén L, Vidaurre-Barahona D, Avilés-Vargas L, Castro-Gutierrez V, Gómez-Ramírez E, González-Sánchez K, Mora-López M, Umaña-Villalobos G, Uribe-Lorío L, Hassard F. First insights into the prokaryotic community structure of Lake Cote, Costa Rica: Influence on nutrient cycling. Front Microbiol 2022; 13:941897. [PMID: 36262328 PMCID: PMC9574093 DOI: 10.3389/fmicb.2022.941897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Prokaryotic diversity in lakes has been studied for many years mainly focusing on community structure and how the bacterial assemblages are driven by physicochemical conditions such as temperature, oxygen, and nutrients. However, little is known about how the composition and function of the prokaryotic community changes upon lake stratification. To elucidate this, we studied Lake Cote in Costa Rica determining prokaryotic diversity and community structure in conjunction with physicochemistry along vertical gradients during stratification and mixing periods. Of the parameters measured, ammonium, oxygen, and temperature, in that order, were the main determinants driving the variability in the prokaryotic community structure of the lake. Distinct stratification of Lake Cote occurred (March 2018) and the community diversity was compared to a period of complete mixing (March 2019). The microbial community analysis indicated that stratification significantly altered the bacterial composition in the epi-meta- and hypolimnion. During stratification, the Deltaproteobacteria, Chloroflexi, Bacteroidetes, Nitrospirae, and Euryarchaeota were dominant in the hypolimnion yet largely absent in surface layers. Among these taxa, strict or facultative anaerobic bacteria were likely contributing to the lake nitrogen biogeochemical cycling, consistent with measurements of inorganic nitrogen measurements and microbial functional abundance predictions. In general, during both sampling events, a higher abundance of Alphaproteobacteria, Betaproteobacteria, Actinobacteria, and Cyanobacteria was found in the oxygenated layers. Lake Cote had a unique bacterial diversity, with 80% of Amplicon Sequence Variant (ASV) recovered similar to unclassified/uncultured strains and exhibits archetypal shallow lake physicochemical but not microbial fluctuations worthy of further investigation. This study provides an example of lake hydrodynamics impacts to microbial community and their function in Central American lakes with implications for other shallow, upland, and oligotrophic lake systems.
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Affiliation(s)
- Laura Brenes-Guillén
- Cellular and Molecular Biology Research Center, University of Costa Rica, San José, Costa Rica
| | | | - Lidia Avilés-Vargas
- Research Center in Sciences of the Sea and Limnology, University of Costa Rica, San José, Costa Rica
| | | | - Eddy Gómez-Ramírez
- Research Center in Sciences of the Sea and Limnology, University of Costa Rica, San José, Costa Rica
| | - Kaylen González-Sánchez
- Research Center in Sciences of the Sea and Limnology, University of Costa Rica, San José, Costa Rica
| | - Marielos Mora-López
- Cellular and Molecular Biology Research Center, University of Costa Rica, San José, Costa Rica
| | - Gerardo Umaña-Villalobos
- Research Center in Sciences of the Sea and Limnology, University of Costa Rica, San José, Costa Rica
| | - Lorena Uribe-Lorío
- Cellular and Molecular Biology Research Center, University of Costa Rica, San José, Costa Rica
| | - Francis Hassard
- Cranfield Water Science Institute, Cranfield University, Cranfield, United Kingdom
- Institute for Nanotechnology and Water Sustainability, University of South Africa, Johannesburg, South Africa
- *Correspondence: Francis Hassard,
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8
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Tucker SJ, Freel KC, Monaghan EA, Sullivan CES, Ramfelt O, Rii YM, Rappé MS. Spatial and temporal dynamics of SAR11 marine bacteria across a nearshore to offshore transect in the tropical Pacific Ocean. PeerJ 2021; 9:e12274. [PMID: 34760357 PMCID: PMC8572523 DOI: 10.7717/peerj.12274] [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: 03/22/2021] [Accepted: 09/19/2021] [Indexed: 01/04/2023] Open
Abstract
Surveys of microbial communities across transitions coupled with contextual measures of the environment provide a useful approach to dissect the factors determining distributions of microorganisms across ecological niches. Here, monthly time-series samples of surface seawater along a transect spanning the nearshore coastal environment within Kāneʻohe Bay on the island of Oʻahu, Hawaiʻi, and the adjacent offshore environment were collected to investigate the diversity and abundance of SAR11 marine bacteria (order Pelagibacterales) over a 2-year time period. Using 16S ribosomal RNA gene amplicon sequencing, the spatiotemporal distributions of major SAR11 subclades and exact amplicon sequence variants (ASVs) were evaluated. Seven of eight SAR11 subclades detected in this study showed distinct subclade distributions across the coastal to offshore environments. The SAR11 community was dominated by seven (of 106 total) SAR11 ASVs that made up an average of 77% of total SAR11. These seven ASVs spanned five different SAR11 subclades (Ia, Ib, IIa, IV, and Va), and were recovered from all samples collected from either the coastal environment, the offshore, or both. SAR11 ASVs were more often restricted spatially to coastal or offshore environments (64 of 106 ASVs) than they were shared among coastal, transition, and offshore environments (39 of 106 ASVs). Overall, offshore SAR11 communities contained a higher diversity of SAR11 ASVs than their nearshore counterparts, with the highest diversity within the little-studied subclade IIa. This study reveals ecological differentiation of SAR11 marine bacteria across a short physiochemical gradient, further increasing our understanding of how SAR11 genetic diversity partitions into distinct ecological units.
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Affiliation(s)
- Sarah J Tucker
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States.,Marine Biology Graduate Program, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States
| | - Kelle C Freel
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States
| | - Elizabeth A Monaghan
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States.,Marine Biology Graduate Program, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States
| | - Clarisse E S Sullivan
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States
| | - Oscar Ramfelt
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States
| | - Yoshimi M Rii
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States.,He'eia National Estuarine Research Reserve, Kāne'ohe, Hawai'i, United States
| | - Michael S Rappé
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States
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9
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Rodriguez-R LM, Jain C, Conrad RE, Aluru S, Konstantinidis KT. Reply to: "Re-evaluating the evidence for a universal genetic boundary among microbial species". Nat Commun 2021; 12:4060. [PMID: 34234115 PMCID: PMC8263725 DOI: 10.1038/s41467-021-24129-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 05/20/2021] [Indexed: 11/18/2022] Open
Affiliation(s)
- Luis M Rodriguez-R
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Microbiology, and Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Tyrol, Austria
| | - Chirag Jain
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, India
| | - Roth E Conrad
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Srinivas Aluru
- School of Computational Science and Engineering, and Institute for Data Engineering and Science, Georgia Institute of Technology, Atlanta, GA, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
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10
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Kuznetsova EV, Sukhanova EV, Kosolapov DB. Taxonomic Diversity and Size-Morphological Structure of Bacterioplankton of the Rybinsk Reservoir. Microbiology (Reading) 2021. [DOI: 10.1134/s002626172103005x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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11
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Oren A, Garrity GM. Candidatus List No. 2. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2021; 71. [PMID: 33881984 DOI: 10.1099/ijsem.0.004671] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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12
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Ionescu D, Zoccarato L, Zaduryan A, Schorn S, Bizic M, Pinnow S, Cypionka H, Grossart HP. Heterozygous, Polyploid, Giant Bacterium, Achromatium, Possesses an Identical Functional Inventory Worldwide across Drastically Different Ecosystems. Mol Biol Evol 2021; 38:1040-1059. [PMID: 33169788 PMCID: PMC7947748 DOI: 10.1093/molbev/msaa273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Achromatium is large, hyperpolyploid and the only known heterozygous bacterium. Single cells contain approximately 300 different chromosomes with allelic diversity far exceeding that typically harbored by single bacteria genera. Surveying all publicly available sediment sequence archives, we show that Achromatium is common worldwide, spanning temperature, salinity, pH, and depth ranges normally resulting in bacterial speciation. Although saline and freshwater Achromatium spp. appear phylogenetically separated, the genus Achromatium contains a globally identical, complete functional inventory regardless of habitat. Achromatium spp. cells from differing ecosystems (e.g., from freshwater to saline) are, unexpectedly, equally functionally equipped but differ in gene expression patterns by transcribing only relevant genes. We suggest that environmental adaptation occurs by increasing the copy number of relevant genes across the cell's hundreds of chromosomes, without losing irrelevant ones, thus maintaining the ability to survive in any ecosystem type. The functional versatility of Achromatium and its genomic features reveal alternative genetic and evolutionary mechanisms, expanding our understanding of the role and evolution of polyploidy in bacteria while challenging the bacterial species concept and drivers of bacterial speciation.
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Affiliation(s)
- Danny Ionescu
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
- Berlin Brandenburg Institute of Biodiversity, Berlin, Germany
| | - Luca Zoccarato
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
| | - Artur Zaduryan
- Department of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Sina Schorn
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Mina Bizic
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
- Berlin Brandenburg Institute of Biodiversity, Berlin, Germany
| | - Solvig Pinnow
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
| | - Heribert Cypionka
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany
| | - Hans-Peter Grossart
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
- Berlin Brandenburg Institute of Biodiversity, Berlin, Germany
- Institute of Biochemistry and Biology, Potsdam University, Potsdam, Germany
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Ruiz-Perez CA, Bertagnolli AD, Tsementzi D, Woyke T, Stewart FJ, Konstantinidis KT. Description of Candidatus Mesopelagibacter carboxydoxydans and Candidatus Anoxipelagibacter denitrificans: Nitrate-reducing SAR11 genera that dominate mesopelagic and anoxic marine zones. Syst Appl Microbiol 2021; 44:126185. [PMID: 33676264 DOI: 10.1016/j.syapm.2021.126185] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 11/25/2020] [Accepted: 12/09/2020] [Indexed: 11/29/2022]
Abstract
The diverse and ubiquitous members of the SAR11 lineage (Alphaproteobacteria) represent up to 30-40% of the surface and mesopelagic oceanic microbial communities. However, the molecular and ecological mechanisms that differentiate closely related, yet distinct, SAR11 members that often co-occur under similar environmental conditions remain speculative. Recently, two mesopelagic and oxygen minimum zone (OMZ)-associated subclades of SAR11 (Ic and IIa.A) were described using single-cell amplified genomes (SAGs) linked to nitrate reduction in OMZs. In this current study, the collection of genomes belonging to these two subclades was expanded with thirteen new metagenome-assembled genomes (MAGs), thus providing a more detailed phylogenetic and functional characterization of these subclades. Gene content-based predictions of metabolic functions revealed similarities in central carbon metabolism between subclades Ic and IIa.A and surface SAR11 clades, with small variations in central pathways. These variations included more versatile sulfur assimilation pathways, as well as a previously predicted capacity for nitrate reduction that conferred unique versatility on mesopelagic-adapted clades compared to their surface counterparts. Finally, consistent with previously reported abundances of carbon monoxide (CO) in surface and mesopelagic waters, subclades Ia (surface) and Ic (mesopelagic) have the genetic potential to oxidize carbon monoxide (CO), presumably taking advantage of this abundant compound as an electron donor. Based on genomic analyses, environmental distribution and metabolic reconstruction, we propose two new SAR11 genera, Ca. Mesopelagibacter carboxydoxydans (subclade Ic) and Ca. Anoxipelagibacter denitrificans (subclade IIa.A), which represent members of the mesopelagic and OMZ-adapted SAR11 clades.
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Affiliation(s)
- Carlos A Ruiz-Perez
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Anthony D Bertagnolli
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Despina Tsementzi
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, One Cyclotron Road, Mail Stop 91R0183, Berkeley, CA 94720, USA
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, USA; Department of Microbiology & Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Konstantinos T Konstantinidis
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA; School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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Abstract
This study examines evolutionary and ecological relationships of three of the most ubiquitous and abundant freshwater bacterial genera: “Ca. Planktophila” (acI-A), “Ca. Nanopelagicus” (acI-B), and “Ca. Fonsibacter” (LD12). Due to high abundance, these genera might have a significant influence on nutrient cycling in freshwaters worldwide, and this study adds a layer of understanding to how seemingly competing clades of bacteria can coexist by having different cooperation strategies. Our synthesis ties together network and ecological theory with empirical evidence and lays out a framework for how the functioning of populations within complex microbial communities can be studied. While fastidious microbes can be abundant and ubiquitous in their natural communities, many fail to grow axenically in laboratories due to auxotrophies or other dependencies. To overcome auxotrophies, these microbes rely on their surrounding cohort. A cohort may consist of kin (ecotypes) or more distantly related organisms (community) with the cooperation being reciprocal or nonreciprocal and expensive (Black Queen hypothesis) or costless (by-product). These metabolic partnerships (whether at single species population or community level) enable dominance by and coexistence of these lineages in nature. Here we examine the relevance of these cooperation models to explain the abundance and ubiquity of the dominant fastidious bacterioplankton of a dimictic mesotrophic freshwater lake. Using both culture-dependent (dilution mixed cultures) and culture-independent (small subunit [SSU] rRNA gene time series and environmental metagenomics) methods, we independently identified the primary cohorts of actinobacterial genera “Candidatus Planktophila” (acI-A) and “Candidatus Nanopelagicus” (acI-B) and the proteobacterial genus “Candidatus Fonsibacter” (LD12). While “Ca. Planktophila” and “Ca. Fonsibacter” had no correlation in their natural habitat, they have the potential to be complementary in laboratory settings. We also investigated the bifunctional catalase-peroxidase enzyme KatG (a common good which “Ca. Planktophila” is dependent upon) and its most likely providers in the lake. Further, we found that while ecotype and community cooperation combined may explain “Ca. Planktophila” population abundance, the success of “Ca. Nanopelagicus” and “Ca. Fonsibacter” is better explained as a community by-product. Ecotype differentiation of “Ca. Fonsibacter” as a means of escaping predation was supported but not for overcoming auxotrophies. IMPORTANCE This study examines evolutionary and ecological relationships of three of the most ubiquitous and abundant freshwater bacterial genera: “Ca. Planktophila” (acI-A), “Ca. Nanopelagicus” (acI-B), and “Ca. Fonsibacter” (LD12). Due to high abundance, these genera might have a significant influence on nutrient cycling in freshwaters worldwide, and this study adds a layer of understanding to how seemingly competing clades of bacteria can coexist by having different cooperation strategies. Our synthesis ties together network and ecological theory with empirical evidence and lays out a framework for how the functioning of populations within complex microbial communities can be studied.
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15
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Environmental stability impacts the differential sensitivity of marine microbiomes to increases in temperature and acidity. ISME JOURNAL 2020; 15:19-28. [PMID: 32887943 DOI: 10.1038/s41396-020-00748-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 07/31/2020] [Accepted: 08/12/2020] [Indexed: 11/08/2022]
Abstract
Ambient conditions shape microbiome responses to both short- and long-duration environment changes through processes including physiological acclimation, compositional shifts, and evolution. Thus, we predict that microbial communities inhabiting locations with larger diel, episodic, and annual variability in temperature and pH should be less sensitive to shifts in these climate-change factors. To test this hypothesis, we compared responses of surface ocean microbes from more variable (nearshore) and more constant (offshore) sites to short-term factorial warming (+3 °C) and/or acidification (pH -0.3). In all cases, warming alone significantly altered microbial community composition, while acidification had a minor influence. Compared with nearshore microbes, warmed offshore microbiomes exhibited larger changes in community composition, phylotype abundances, respiration rates, and metatranscriptomes, suggesting increased sensitivity of microbes from the less-variable environment. Moreover, while warming increased respiration rates, offshore metatranscriptomes yielded evidence of thermal stress responses in protein synthesis, heat shock proteins, and regulation. Future oceans with warmer waters may enhance overall metabolic and biogeochemical rates, but they will host altered microbial communities, especially in relatively thermally stable regions of the oceans.
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Karthikeyan S, Kim M, Heritier-Robbins P, Hatt JK, Spain JC, Overholt WA, Huettel M, Kostka JE, Konstantinidis KT. Integrated Omics Elucidate the Mechanisms Driving the Rapid Biodegradation of Deepwater Horizon Oil in Intertidal Sediments Undergoing Oxic-Anoxic Cycles. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:10088-10099. [PMID: 32667785 DOI: 10.1021/acs.est.0c02834] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Crude oil buried in intertidal sands may be exposed to alternating oxic and anoxic conditions but the effect of this tidally induced biogeochemical oscillation remains poorly understood, limiting the effectiveness of remediation and managing efforts after oil spills. Here, we used a combination of metatranscriptomics and genome-resolved metagenomics to study microbial activities in oil-contaminated sediments during oxic-anoxic cycles in laboratory chambers that closely emulated in situ conditions. Approximately 5-fold higher reductions in the total petroleum hydrocarbons were observed in the oxic as compared to the anoxic phases with a relatively constant ratio between aerobic and anaerobic oil decomposition rates even after prolonged anoxic conditions. Metatranscriptomics analysis indicated that the oxic phases promoted oil biodegradation in subsequent anoxic phases by microbially mediated reoxidation of alternative electron acceptors like sulfide and by providing degradation-limiting nitrogen through biological nitrogen fixation. Most population genomes reconstructed from the mesocosm samples represented uncultured taxa and were present typically as members of the rare biosphere in metagenomic data from uncontaminated field samples, implying that the intertidal communities are adapted to changes in redox conditions. Collectively, these results have important implications for enhancing oil spill remediation efforts in beach sands and coastal sediments and underscore the role of uncultured taxa in such efforts.
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Affiliation(s)
- Smruthi Karthikeyan
- Department of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta 30332-0002, Georgia, United States
| | - Minjae Kim
- Department of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta 30332-0002, Georgia, United States
| | - Patrick Heritier-Robbins
- Department of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta 30332-0002, Georgia, United States
| | - Janet K Hatt
- Department of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta 30332-0002, Georgia, United States
| | - Jim C Spain
- Center for Environmental Diagnostics & Bioremediation, University of West Florida, 11000 University Parkway, Pensacola 32514, Florida, United States
| | - Will A Overholt
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332-0002, Georgia, United States
| | - Markus Huettel
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University, Tallahassee 32306-4320, Florida, United States
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332-0002, Georgia, United States
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta 30332-0002, Georgia, United States
| | - Konstantinos T Konstantinidis
- Department of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta 30332-0002, Georgia, United States
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332-0002, Georgia, United States
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17
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Rodriguez-R LM, Tsementzi D, Luo C, Konstantinidis KT. Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences. Environ Microbiol 2020; 22:3394-3412. [PMID: 32495495 DOI: 10.1111/1462-2920.15112] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 04/26/2020] [Accepted: 05/31/2020] [Indexed: 01/22/2023]
Abstract
Recent advances in sequencing technology and bioinformatic pipelines have allowed unprecedented access to the genomes of yet-uncultivated microorganisms from diverse environments. However, the catalogue of freshwater genomes remains limited, and most genome recovery attempts in freshwater ecosystems have only targeted specific taxa. Here, we present a genome recovery pipeline incorporating iterative subtractive binning, and apply it to a time series of 100 metagenomic datasets from seven connected lakes and estuaries along the Chattahoochee River (Southeastern USA). Our set of metagenome-assembled genomes (MAGs) represents >400 yet-unnamed genomospecies, substantially increasing the number of high-quality MAGs from freshwater lakes. We propose names for two novel species: 'Candidatus Elulimicrobium humile' ('Ca. Elulimicrobiota', 'Patescibacteria') and 'Candidatus Aquidulcis frankliniae' ('Chloroflexi'). Collectively, our MAGs represented about half of the total microbial community at any sampling point. To evaluate the prevalence of these genomospecies in the chronoseries, we introduce methodologies to estimate relative abundance and habitat preference that control for uneven genome quality and sample representation. We demonstrate high degrees of habitat-specialization and endemicity for most genomospecies in the Chattahoochee lakes. Wider ecological ranges characterized smaller genomes with higher coding densities, indicating an overall advantage of smaller, more compact genomes for cosmopolitan distributions.
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Affiliation(s)
- Luis M Rodriguez-R
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Dr NW, Atlanta, GA, 30332, USA
| | - Despina Tsementzi
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Dr NW, Atlanta, GA, 30332, USA
| | - Chengwei Luo
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Dr NW, Atlanta, GA, 30332, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Dr NW, Atlanta, GA, 30332, USA
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18
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Karthikeyan S, Rodriguez-R LM, Heritier-Robbins P, Hatt JK, Huettel M, Kostka JE, Konstantinidis KT. Genome repository of oil systems: An interactive and searchable database that expands the catalogued diversity of crude oil-associated microbes. Environ Microbiol 2020; 22:2094-2106. [PMID: 32114693 DOI: 10.1111/1462-2920.14966] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/26/2020] [Accepted: 02/27/2020] [Indexed: 12/17/2022]
Abstract
Microbial communities ultimately control the fate of petroleum hydrocarbons (PHCs) that enter the natural environment, but the interactions of microbes with PHCs and the environment are highly complex and poorly understood. Genome-resolved metagenomics can help unravel these complex interactions. However, the lack of a comprehensive database that integrates existing genomic/metagenomic data from oil environments with physicochemical parameters known to regulate the fate of PHCs currently limits data analysis and interpretations. Here, we curated a comprehensive, searchable database that documents microbial populations in natural oil ecosystems and oil spills, along with available underlying physicochemical data, geocoded via geographic information system to reveal their geographic distribution patterns. Analysis of the ~2000 metagenome-assembled genomes (MAGs) available in the database revealed strong ecological niche specialization within habitats. Over 95% of the recovered MAGs represented novel taxa underscoring the limited representation of cultured organisms from oil-contaminated and oil reservoir ecosystems. The majority of MAGs linked to oil-contaminated ecosystems were detectable in non-oiled samples from the Gulf of Mexico but not in comparable samples from elsewhere, indicating that the Gulf is primed for oil biodegradation. The repository should facilitate future work toward a predictive understanding of the microbial taxa and their activities that control the fate of oil spills.
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Affiliation(s)
- Smruthi Karthikeyan
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, ES&T Building, Room 3321, Atlanta, GA 30332, USA
| | - Luis M Rodriguez-R
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, ES&T Building, Room 3321, Atlanta, GA 30332, USA
| | - Patrick Heritier-Robbins
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, ES&T Building, Room 3321, Atlanta, GA 30332, USA
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, ES&T Building, Room 3321, Atlanta, GA 30332, USA
| | - Markus Huettel
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University, Tallahassee, FL, USA
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, ES&T Building, Room 3321, Atlanta, GA 30332, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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19
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Goh KM, Shahar S, Chan KG, Chong CS, Amran SI, Sani MH, Zakaria II, Kahar UM. Current Status and Potential Applications of Underexplored Prokaryotes. Microorganisms 2019; 7:E468. [PMID: 31635256 PMCID: PMC6843859 DOI: 10.3390/microorganisms7100468] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/05/2019] [Accepted: 10/08/2019] [Indexed: 12/20/2022] Open
Abstract
Thousands of prokaryotic genera have been published, but methodological bias in the study of prokaryotes is noted. Prokaryotes that are relatively easy to isolate have been well-studied from multiple aspects. Massive quantities of experimental findings and knowledge generated from the well-known prokaryotic strains are inundating scientific publications. However, researchers may neglect or pay little attention to the uncommon prokaryotes and hard-to-cultivate microorganisms. In this review, we provide a systematic update on the discovery of underexplored culturable and unculturable prokaryotes and discuss the insights accumulated from various research efforts. Examining these neglected prokaryotes may elucidate their novelties and functions and pave the way for their industrial applications. In addition, we hope that this review will prompt the scientific community to reconsider these untapped pragmatic resources.
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Affiliation(s)
- Kian Mau Goh
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Saleha Shahar
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Science, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia.
- International Genome Centre, Jiangsu University, ZhenJiang 212013, China.
| | - Chun Shiong Chong
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Syazwani Itri Amran
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Mohd Helmi Sani
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Iffah Izzati Zakaria
- Malaysia Genome Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, Kajang 43000, Selangor, Malaysia.
| | - Ummirul Mukminin Kahar
- Malaysia Genome Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, Kajang 43000, Selangor, Malaysia.
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Ruiz-Perez CA, Tsementzi D, Hatt JK, Sullivan MB, Konstantinidis KT. Prevalence of viral photosynthesis genes along a freshwater to saltwater transect in Southeast USA. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:672-689. [PMID: 31265211 DOI: 10.1111/1758-2229.12780] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 06/29/2019] [Indexed: 05/28/2023]
Abstract
Bacteriophages encode host-acquired functional genes known as auxiliary metabolic genes (AMGs). Photosynthesis AMGs are commonly found in marine cyanobacteria-infecting Myoviridae and Podoviridae cyanophages, but their ecology remains understudied in freshwater environments. To advance knowledge of this issue, we analysed viral metagenomes collected in the summertime for four years from five lakes and two estuarine locations interconnected by the Chattahoochee River, Southeast USA. Sequences representing ten different AMGs were recovered and found to be prevalent in all sites. Most freshwater AMGs were 10-fold less abundant than estuarine and marine AMGs and were encoded by novel Myoviridae and Podoviridae cyanophage genera. Notably, several of the corresponding viral genomes showed endemism to a specific province along the river. This translated into psbA gene phylogenetic clustering patterns that matched a marine vs. freshwater origin indicating that psbA may serve as a robust classification and source-tracking biomarker. Genomes classified in a novel viral lineage represented by isolate S-EIVl contained psbA, which is unprecedented for this lineage. Collectively, our findings indicated that the acquisition of photosynthesis AMGs is a widespread strategy used by cyanophages in aquatic ecosystems, and further indicated the existence of viral provinces in which certain viral species and/or genotypes are locally abundant.
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Affiliation(s)
- Carlos A Ruiz-Perez
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Despina Tsementzi
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, USA
| | - Konstantinos T Konstantinidis
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta, GA, USA
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