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Gagnon JC, Beauregard-Tousignant S, Marcil JS, Lazar CS. Deep Isolated Aquifer Brines Harbor Atypical Halophilic Microbial Communities in Quebec, Canada. Genes (Basel) 2023; 14:1529. [PMID: 37628582 PMCID: PMC10454208 DOI: 10.3390/genes14081529] [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: 06/15/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
The deep terrestrial subsurface, hundreds of meters to kilometers below the surface, is characterized by oligotrophic conditions, dark and often anoxic settings, with fluctuating pH, salinity, and water availability. Despite this, microbial populations are detected and active, contributing to biogeochemical cycles over geological time. Because it is extremely difficult to access the deep biosphere, little is known about the identity and metabolisms of these communities, although they likely possess unknown pathways and might interfere with deep waste deposits. Therefore, we analyzed rock and groundwater microbial communities from deep, isolated brine aquifers in two regions dating back to the Ordovician and Devonian, using amplicon and whole genome sequencing. We observed significant differences in diversity and community structure between both regions, suggesting an impact of site age and composition. The deep hypersaline groundwater did not contain typical halophilic bacteria, and genomes suggested pathways involved in protein and hydrocarbon degradation, and carbon fixation. We identified mainly one strategy to cope with osmotic stress: compatible solute uptake and biosynthesis. Finally, we detected many bacteriophage families, potentially indicating that bacteria are infected. However, we also found auxiliary metabolic genes in the viral genomes, probably conferring an advantage to the infected hosts.
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Affiliation(s)
- Jean-Christophe Gagnon
- Department of Biological Sciences, University of Québec at Montréal (UQAM), C.P. 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada; (J.-C.G.); (S.B.-T.)
- Interuniversity Research Group in Limnology/Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Montréal, QC H3C 3P8, Canada
| | - Samuel Beauregard-Tousignant
- Department of Biological Sciences, University of Québec at Montréal (UQAM), C.P. 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada; (J.-C.G.); (S.B.-T.)
| | - Jean-Sébastien Marcil
- Derena Geosciences, Quebec, QC G7A 3Y5, Canada;
- Ressources Utica Inc., Quebec, QC G1V 4M7, Canada
| | - Cassandre Sara Lazar
- Department of Biological Sciences, University of Québec at Montréal (UQAM), C.P. 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada; (J.-C.G.); (S.B.-T.)
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Urata S, Kurosawa Y, Yamasaki N, Yamamoto H, Nishiwaki N, Hongo Y, Adachi M, Yamaguchi H. Utilization of phosphonic acid compounds by marine bacteria of the genera Phaeobacter, Ruegeria, and Thalassospira (α-Proteobacteria). FEMS Microbiol Lett 2022; 369:6652134. [DOI: 10.1093/femsle/fnac065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/27/2022] [Accepted: 07/27/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Phosphonic acid (phosphonate) that possesses a carbon (C)-P bond is a chemically stable form of organic phosphorus (P). Various phosphonic acids are widely distributed in oceanic waters; in particular, methylphosphonic acid (namely methylphosphonate) is believed to be responsible for global methane production. To discuss the microbial degradation of phosphonic acids, we investigated the utilization of phosphonic acid compounds by cultures of marine bacteria, Phaeobacter sp., Ruegeria sp. (Rhodobacterales), and Thalassospira sp. (Rhodospirillales). These bacterial cultures were able to grow on methylphosphonic acid as well as on the tested alkyl-, carboxy-, aminoalkyl-, and hydroxyalkyl-phosphonic acid compounds. Cell yields and growth rates of Ruegeria and Thalassospira cultures grown on methyl-, ethyl-, propyl-, and butyl-phosphonic acid compounds tended to decrease with increasing alkyl chain length. In contrast, Phaeobacter sp. grew well on such alkyl phosphonic acids. Our results suggest that these marine bacteria, which exhibit varied utilization, are involved in microbial degradation of various phosphonic acid compounds.
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Affiliation(s)
- Shinnpei Urata
- Graduate School of Integrated Arts and Sciences, Kochi University , Monobe-Otsu, Nankoku , Kochi 783–8502, Japan
| | - Yuki Kurosawa
- Graduate School of Integrated Arts and Sciences, Kochi University , Monobe-Otsu, Nankoku , Kochi 783–8502, Japan
| | - Naoto Yamasaki
- Faculty of Pharmaceutical Science, Tokushima Bunri University , Yamashiro-cho, Tokushima 770–8514, Japan
| | - Hirofumi Yamamoto
- Faculty of Pharmaceutical Science, Tokushima Bunri University , Yamashiro-cho, Tokushima 770–8514, Japan
| | - Nagatoshi Nishiwaki
- School of Environmental Science and Engineering, Kochi University of Technology , Tosayamada , Kami, Kochi 782–8502, Japan
- Research Centre of Molecular Design, Kochi University of Technology , Tosayamada , Kami, Kochi 782–8502, Japan
| | - Yuki Hongo
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency , Fukuura, Yokohama , Kanagawa 236–8648, Japan
| | - Masao Adachi
- Faculty of Agriculture and Marine Science, Kochi University , Monobe-Otsu, Nankoku , Kochi 783–8502, Japan
| | - Haruo Yamaguchi
- Faculty of Agriculture and Marine Science, Kochi University , Monobe-Otsu, Nankoku , Kochi 783–8502, Japan
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Abstract
Beneath the seafloor, microbial life subsists in isolation from the surface world under persistent energy limitation. The nature and extent of genomic evolution in subseafloor microbes have been unknown. Here, we show that the genomes of Thalassospira bacterial populations cultured from million-year-old subseafloor sediments evolve in clonal populations by point mutation, with a relatively low rate of homologous recombination and elevated numbers of pseudogenes. Ratios of nonsynonymous to synonymous substitutions correlate with the accumulation of pseudogenes, consistent with a role for genetic drift in the subseafloor strains but not in type strains of Thalassospira isolated from the surface world. Consistent with this, pangenome analysis reveals that the subseafloor bacterial genomes have a significantly lower number of singleton genes than the type strains, indicating a reduction in recent gene acquisitions. Numerous insertion-deletion events and pseudogenes were present in a flagellar operon of the subseafloor bacteria, indicating that motility is nonessential in these million-year-old subseafloor sediments. This genomic evolution in subseafloor clonal populations coincided with a phenotypic difference: all subseafloor isolates have a lower rate of growth under laboratory conditions than the Thalassospira xiamenensis type strain. Our findings demonstrate that the long-term physical isolation of Thalassospira, in the absence of recombination, has resulted in clonal populations whereby reduced access to novel genetic material from neighbors has resulted in the fixation of new mutations that accumulate in genomes over millions of years.
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Carreira C, Carvalho JPS, Talbot S, Pereira I, Lønborg C. Small-scale distribution of microbes and biogeochemistry in the Great Barrier Reef. PeerJ 2020; 8:e10049. [PMID: 33150061 PMCID: PMC7585385 DOI: 10.7717/peerj.10049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/06/2020] [Indexed: 12/17/2022] Open
Abstract
Microbial communities distribute heterogeneously at small-scales (mm-cm) due to physical, chemical and biological processes. To understand microbial processes and functions it is necessary to appreciate microbes and matter at small scales, however, few studies have determined microbial, viral, and biogeochemical distribution over space and time at these scales. In this study, the small-scale spatial and temporal distribution of microbes (bacteria and chlorophyll a), viruses, dissolved inorganic nutrients and dissolved organic carbon were determined at five locations (spatial) along the Great Barrier Reef (Australia), and over 4 consecutive days (temporal) at a coastal location. Our results show that: (1) the parameters show high small-scale heterogeneity; (2) none of the parameters measured explained the bacterial abundance distributions at these scales spatially or temporally; (3) chemical (ammonium, nitrate/nitrite, phosphate, dissolved organic carbon, and total dissolved nitrogen) and biological (chl a, and bacterial and viral abundances) measurements did not reveal significant relationships at the small scale; and (4) statistically significant differences were found between sites/days for all parameter measured but without a clear pattern.
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Affiliation(s)
- Cátia Carreira
- Department of Biology & CESAM -The Centre for Environmental and Marine Studies, University of Aveiro, Aveiro, Portugal
| | | | - Samantha Talbot
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Isabel Pereira
- Department of Mathematic & CIDMA - Center for Research and Development in Mathematics and Applications, University of Aveiro, Aveiro, Portugal
| | - Christian Lønborg
- Australian Institute of Marine Science, Townsville, Queensland, Australia.,Section for Applied Marine Ecology and Modelling, Department of Bioscience, Aarhus University, Roskilde, Denmark
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Ghosh M, Gera M, Singh J, Prasad R, Pulicherla KK. A Comprehensive Investigation of Potential Novel Marine Psychrotolerant Actinomycetes sp. Isolated from the Bay-of-Bengal. Curr Genomics 2020; 21:271-282. [PMID: 33071620 PMCID: PMC7521042 DOI: 10.2174/1389202921666200330150642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 03/05/2020] [Accepted: 03/12/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND This study was carried out to classify the diversity of the deep marine psychrotolerant actinomycetes sp. nov., in the Bay of Bengal and exploit the production of cold-active industrial and pharmaceutical biomolecules. OBJECTIVE 1) Characterization, optimum the growth conditions and classify the diversity of the novel isolated deep marine psychrotolerant actinomycetes sp from the Bay-of-Bengal. 2) Screening for industrially important biocatalysts and determine the antimicrobial activities against the five dreadful pathogens. 3) The differential expression profiling of the candidate genes to regulate the biosynthesis of selected enzymes. METHODS The cold-adapted actinomycetes were isolated from the deep marine water collections at 1200 mts below the surface in Bay-of-Bengal. The phenotypic and genotypic characterizations have been carried out to understand the persistent diversity of this novel marine psychrotolerant actinomycetes species. The production of cold-active enzymes, such as amylase, cellulase, lipase, pectinase, and L-asparaginase, were screened and the expression profiling genes were determined by using qRT PCR. The antibacterial and antifungal activities have also been investigated. RESULTS A total number of 37 novel actinomycetes were isolated and the phenotypic and genotypic characterizations identified the genus, dominated by Streptomyces (17 distinct sub-groups) as the major group, followed by Micromonospora, Actinopolyspora, Actinosynnema, Streptoverticillium, Saccharopolyspora, Nocardiopsis, and Nocardia. The optimum growth and abundant mycelium formation are observed at 15°C to 20°C and also capability for thriving at 4°C. All the isolates exhibited a significant role in the production of biocatalysts, and the antagonistic activities were also noted against five major selected pathogens. CONCLUSION The Streptomyces from the Bay-of-Bengal have high biosynthetic potential and can serve as a good resource for the exploration of bioactive natural products.
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Affiliation(s)
- Mrinmoy Ghosh
- 1Department of Biotechnology, Division of Research and Development, Lovely Professional University, Punjab-144411, India; 2Department of Animal Biotechnology, School of Life Science, Genetic Engineering and Molecular Biology Lab, Jeju National University, Jeju-Do, Republic of Korea; 3Department of Botany, Mahatma Gandhi Central University, Motihari- 845801, Bihar, India; 4Department of Science and Technology, Ministry of Science and Technology, Technology Bhavan, New Mehrauli Road, New Delhi-110016, India
| | - Meeta Gera
- 1Department of Biotechnology, Division of Research and Development, Lovely Professional University, Punjab-144411, India; 2Department of Animal Biotechnology, School of Life Science, Genetic Engineering and Molecular Biology Lab, Jeju National University, Jeju-Do, Republic of Korea; 3Department of Botany, Mahatma Gandhi Central University, Motihari- 845801, Bihar, India; 4Department of Science and Technology, Ministry of Science and Technology, Technology Bhavan, New Mehrauli Road, New Delhi-110016, India
| | - Joginder Singh
- 1Department of Biotechnology, Division of Research and Development, Lovely Professional University, Punjab-144411, India; 2Department of Animal Biotechnology, School of Life Science, Genetic Engineering and Molecular Biology Lab, Jeju National University, Jeju-Do, Republic of Korea; 3Department of Botany, Mahatma Gandhi Central University, Motihari- 845801, Bihar, India; 4Department of Science and Technology, Ministry of Science and Technology, Technology Bhavan, New Mehrauli Road, New Delhi-110016, India
| | - Ram Prasad
- 1Department of Biotechnology, Division of Research and Development, Lovely Professional University, Punjab-144411, India; 2Department of Animal Biotechnology, School of Life Science, Genetic Engineering and Molecular Biology Lab, Jeju National University, Jeju-Do, Republic of Korea; 3Department of Botany, Mahatma Gandhi Central University, Motihari- 845801, Bihar, India; 4Department of Science and Technology, Ministry of Science and Technology, Technology Bhavan, New Mehrauli Road, New Delhi-110016, India
| | - Krishna Kanth Pulicherla
- 1Department of Biotechnology, Division of Research and Development, Lovely Professional University, Punjab-144411, India; 2Department of Animal Biotechnology, School of Life Science, Genetic Engineering and Molecular Biology Lab, Jeju National University, Jeju-Do, Republic of Korea; 3Department of Botany, Mahatma Gandhi Central University, Motihari- 845801, Bihar, India; 4Department of Science and Technology, Ministry of Science and Technology, Technology Bhavan, New Mehrauli Road, New Delhi-110016, India
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Temperature and Nutrient Levels Correspond with Lineage-Specific Microdiversification in the Ubiquitous and Abundant Freshwater Genus Limnohabitans. Appl Environ Microbiol 2020; 86:AEM.00140-20. [PMID: 32169939 DOI: 10.1128/aem.00140-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 03/10/2020] [Indexed: 11/20/2022] Open
Abstract
Most freshwater bacterial communities are characterized by a few dominant taxa that are often ubiquitous across freshwater biomes worldwide. Our understanding of the genomic diversity within these taxonomic groups is limited to a subset of taxa. Here, we investigated the genomic diversity that enables Limnohabitans, a freshwater genus key in funneling carbon from primary producers to higher trophic levels, to achieve abundance and ubiquity. We reconstructed eight putative Limnohabitans metagenome-assembled genomes (MAGs) from stations located along broad environmental gradients existing in Lake Michigan, part of Earth's largest surface freshwater system. De novo strain inference analysis resolved a total of 23 strains from these MAGs, which strongly partitioned into two habitat-specific clusters with cooccurring strains from different lineages. The largest number of strains belonged to the abundant LimB lineage, for which robust in situ strain delineation had not previously been achieved. Our data show that temperature and nutrient levels may be important environmental parameters associated with microdiversification within the Limnohabitans genus. In addition, strains predominant in low- and high-phosphorus conditions had larger genomic divergence than strains abundant under different temperatures. Comparative genomics and gene expression analysis yielded evidence for the ability of LimB populations to exhibit cellular motility and chemotaxis, a phenotype not yet associated with available Limnohabitans isolates. Our findings broaden historical marker gene-based surveys of Limnohabitans microdiversification and provide in situ evidence of genome diversity and its functional implications across freshwater gradients.IMPORTANCE Limnohabitans is an important bacterial taxonomic group for cycling carbon in freshwater ecosystems worldwide. Here, we examined the genomic diversity of different Limnohabitans lineages. We focused on the LimB lineage of this genus, which is globally distributed and often abundant, and its abundance has shown to be largely invariant to environmental change. Our data show that the LimB lineage is actually comprised of multiple cooccurring populations for which the composition and genomic characteristics are associated with variations in temperature and nutrient levels. The gene expression profiles of this lineage suggest the importance of chemotaxis and motility, traits that had not yet been associated with the Limnohabitans genus, in adapting to environmental conditions.
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Sosa OA, Repeta DJ, DeLong EF, Ashkezari MD, Karl DM. Phosphate-limited ocean regions select for bacterial populations enriched in the carbon-phosphorus lyase pathway for phosphonate degradation. Environ Microbiol 2019; 21:2402-2414. [PMID: 30972938 PMCID: PMC6852614 DOI: 10.1111/1462-2920.14628] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 04/04/2019] [Accepted: 04/08/2019] [Indexed: 11/25/2022]
Abstract
In tropical and subtropical oceanic surface waters phosphate scarcity can limit microbial productivity. However, these environments also have bioavailable forms of phosphorus incorporated into dissolved organic matter (DOM) that microbes with the necessary transport and hydrolysis metabolic pathways can access to supplement their phosphorus requirements. In this study we evaluated how the environment shapes the abundance and taxonomic distribution of the bacterial carbon–phosphorus (C–P) lyase pathway, an enzyme complex evolved to extract phosphate from phosphonates. Phosphonates are organophosphorus compounds characterized by a highly stable C–P bond and are enriched in marine DOM. Similar to other known bacterial adaptions to low phosphate environments, C–P lyase was found to become more prevalent as phosphate concentrations decreased. C–P lyase was particularly enriched in the Mediterranean Sea and North Atlantic Ocean, two regions that feature sustained periods of phosphate depletion. In these regions, C–P lyase was prevalent in several lineages of Alphaproteobacteria (Pelagibacter, SAR116, Roseobacter and Rhodospirillales), Gammaproteobacteria, and Actinobacteria. The global scope of this analysis supports previous studies that infer phosphonate catabolism via C–P lyase is an important adaptive strategy implemented by bacteria to alleviate phosphate limitation and expands the known geographic extent and taxonomic affiliation of this metabolic pathway in the ocean.
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Affiliation(s)
- Oscar A Sosa
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Daniel J Repeta
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02540, USA
| | - Edward F DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | | | - David M Karl
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
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Brailo M, Schreier HJ, McDonald R, Maršić-Lučić J, Gavrilović A, Pećarević M, Jug-Dujaković J. Bacterial community analysis of marine recirculating aquaculture system bioreactors for complete nitrogen removal established from a commercial inoculum. AQUACULTURE (AMSTERDAM, NETHERLANDS) 2019; 503:198-206. [PMID: 30778266 PMCID: PMC6376983 DOI: 10.1016/j.aquaculture.2018.12.078] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
An experimental recirculating aquaculture system was constructed under ambient seawater conditions to compare microbial community diversity of nitrifying and denitrifying biofilters that were derived from a commercial inoculum used for aquarium applications. Next generation sequencing revealed distinct and diverse microbial communities in samples analyzed from the commercial inoculant and the denitrification and nitrification biofilters. In all samples, communities were represented by a few dominant operational taxonomic units (OTUs). Bacteria having the capacity to carry out ammonia and nitrite oxidation were more abundant in the nitrification biofilter. Similarly, the proportion of the bacterial taxa known to carry out heterotrophic and autotrophic denitrification and participate in sulfur cycling were found in the denitrification bioreactor, and likely originated from the ambient environmental water source. Our results indicated that environmental seawater can be a favorable enhancement to the bacterial consortium of recirculating aquaculture systems biofilters.
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Affiliation(s)
- Marina Brailo
- Department of Aquaculture, University of Dubrovnik, Ćira Carića 4, Dubrovnik 20000, Croatia
| | - Harold J. Schreier
- Department of Marine Biotechnology, Institute of Marine and Environmental Technology, University of Maryland Baltimore County, 701 E. Pratt St., Baltimore, MD 21202, USA
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Ryan McDonald
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Jasna Maršić-Lučić
- Institute of Oceanography and Fisheries, PO Box 500, Šetalište Ivana Meštrovića 63, Split 21000, Croatia
| | - Ana Gavrilović
- Department of Fisheries, Beekeeping, Game Management and Special Zoology, University of Zagreb Faculty of Agriculture, Svetošimunska cesta 25, Zagreb 10000, Croatia
| | - Marijana Pećarević
- Department of Aquaculture, University of Dubrovnik, Ćira Carića 4, Dubrovnik 20000, Croatia
| | - Jurica Jug-Dujaković
- Sustainable Aquaculture Systems Inc., 715 Pittstown Road, Frenchtown, NJ 08825, USA
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Teira E, Logares R, Gutiérrez‐Barral A, Ferrera I, Varela MM, Morán XAG, Gasol JM. Impact of grazing, resource availability and light on prokaryotic growth and diversity in the oligotrophic surface global ocean. Environ Microbiol 2019; 21:1482-1496. [DOI: 10.1111/1462-2920.14581] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 02/26/2019] [Accepted: 03/02/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Eva Teira
- Departamento de Ecoloxía e Bioloxía AnimalUniversidade de Vigo Vigo Spain
| | - Ramiro Logares
- Departamento de Biologia Marina i OceanografiaInstitut de Ciències del Mar, CSIC Barcelona Catalonia Spain
| | | | - Isabel Ferrera
- Departamento de Biologia Marina i OceanografiaInstitut de Ciències del Mar, CSIC Barcelona Catalonia Spain
- Instituto Español de OceanografíaCentro Oceanográfico de Málaga Fuengirola Spain
| | - Marta M. Varela
- Instituto Español de OceanografíaCentro Oceanográfico de A Coruña A Coruña Spain
| | - Xosé Anxelu G. Morán
- Red Sea Research Center, Division of Biological and Environmental Sciences and EngineeringKing Abdullah University of Science and Technology Thuwal Saudi Arabia
| | - Josep M. Gasol
- Departamento de Biologia Marina i OceanografiaInstitut de Ciències del Mar, CSIC Barcelona Catalonia Spain
- Centre for Marine Ecosystems ResearchEdith Cowan University Joondalup Western Australia Australia
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Computational prediction of microRNAs in marine bacteria of the genus Thalassospira. PLoS One 2019; 14:e0212996. [PMID: 30861013 PMCID: PMC6413936 DOI: 10.1371/journal.pone.0212996] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 02/13/2019] [Indexed: 01/29/2023] Open
Abstract
MicroRNAs (miRNAs) are key players in regulation of gene expression at post-transcription level in eukaryotic cells. MiRNAs have been intensively studied in plants, animals and viruses. The investigations of bacterial miRNAs have gained less attention, except for the recent studies on miRNAs derived from Streptococcus mutans ATCC 25175 and Escherichia coli DH10B. In this study, high-throughput sequencing approach was employed to investigate the miRNA population in bacteria of the genus Thalassospira using both the miRDeep2 and CID-miRNA methods. A total of 984 putative miRNAs were identified in 9 species of the genus Thalassospira using both miRDeep and CID-miRNA analyses. Fifty seven conserved putative miRNAs were found in different species of the genus Thalassospira, and up to 6 miRNAs were found to be present at different locations in the T. alkalitolerans JCM 18968T, T. lucentensis QMT2T and T. xianhensis P-4T. None of the putative miRNAs was found to share sequence to the reported miRNAs in E. coli DH10B and S. mutans ATCC 25175. The findings provide a comprehensive list of computationally identified miRNAs in 9 bacterial species of the genus Thalassospira and addressed the existing knowledge gap on the presence of miRNAs in the Thalassospira genomes.
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Kosek K, Luczkiewicz A, Kozioł K, Jankowska K, Ruman M, Polkowska Ż. Environmental characteristics of a tundra river system in Svalbard. Part 1: Bacterial abundance, community structure and nutrient levels. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 653:1571-1584. [PMID: 30545665 DOI: 10.1016/j.scitotenv.2018.11.378] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/24/2018] [Accepted: 11/25/2018] [Indexed: 06/09/2023]
Abstract
The Arctic hosts a set of unique ecosystems, characterised by extreme environmental conditions and undergoing a rapid change resulting from the average temperature rising. We present a study on an aquatic ecosystem of the Revelva catchment (Spitsbergen), based on samples collected from the lake, river and their tributaries, in the summer of 2016. The landscape variety of the study site and the seasonal change in the hydrological regime modify the availability of nutrients. In general, the upper part of the catchment consists of the mountain rocky slopes which are especially abundant in iron minerals, sulphides and phosphorus minerals. The lower part of the catchment is covered by plants - lichens, saxifrages and bryophytes, which are a different source of nutrients. In the analysed water samples, the maximum concentrations of nutrients such as iron, boron and phosphorus were 0.28 μg L-1, 4.52 μg L-1 and 1.91 μg L-1, respectively, in June, while in September, Fe and B reached the concentrations of 1.32 μg L-1 and 2.71 μg L-1, respectively. The concentration of P in September was below the detection limit of 1.00 μg L-1, which may be explained by the necessity of bacteria to consume it immediately on current needs. We noted also an increase in TOC concentration between the June and September samples, which could originate both from the biomass accumulation in the catchment and the permafrost melting contributing to the hydrological regime of the river. The bacterial community developed in this environment consisted mainly of Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes phylum, while the presence of Acidobacteria was less pronounced than in other tundra-related environments. The described catchment shows that despite the relatively small amount of bioavailable nutrients, the Revelva system is biodiverse and one of the most significant biogeochemical changes occurs there in response to seasonally switching water sources.
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Affiliation(s)
- Klaudia Kosek
- Department of Analytical Chemistry, Faculty of Chemistry, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Aneta Luczkiewicz
- Department of Water and Waste-Water Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Krystyna Kozioł
- Institute of Geography, Faculty of Geography and Biology, Pedagogical University in Cracow, Podchorążych 2 St., Cracow 30-084, Poland; Institute of Geophysics, Polish Academy of Sciences, 64 Księcia Janusza St., Warsaw 01-452, Poland
| | - Katarzyna Jankowska
- Department of Water and Waste-Water Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Marek Ruman
- Faculty of Earth Sciences, University of Silesia,60 Będzińska St., Sosnowiec 41-200, Poland
| | - Żaneta Polkowska
- Department of Analytical Chemistry, Faculty of Chemistry, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland.
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Abstract
By combining a genome-centric metagenomic approach with a culture-based approach, we investigated the genomic adaptations of prevalent populations in an engineered oligotrophic freshwater system. We found evidence for widespread positive selection on genes involved in phosphorus and carbon scavenging pathways and for gene expansions in motility and environmental sensing to be important genomic adaptations of the abundant taxon in this system. In addition, microscopic and flow cytometric analysis of the first freshwater representative of this population (Ramlibacter aquaticus LMG 30558T) demonstrated phenotypic plasticity, possibly due to the metabolic versatility granted by its larger genome, to be a strategy to cope with nutrient limitation. Our study clearly demonstrates the need for the use of a broad set of genomic tools combined with culture-based physiological characterization assays to investigate and validate genomic adaptations. We examined the genomic adaptations of prevalent bacterial taxa in a highly nutrient- and ion-depleted freshwater environment located in the secondary cooling water system of a nuclear research reactor. Using genome-centric metagenomics, we found that none of the prevalent bacterial taxa were related to typical freshwater bacterial lineages. We also did not identify strong signatures of genome streamlining, which has been shown to be one of the ecoevolutionary forces shaping the genome characteristics of bacterial taxa in nutrient-depleted environments. Instead, focusing on the dominant taxon, a novel Ramlibacter sp. which we propose to name Ramlibacter aquaticus, we detected extensive positive selection on genes involved in phosphorus and carbon scavenging pathways. These genes were involved in the high-affinity phosphate uptake and storage into polyphosphate granules, metabolism of nitrogen-rich organic matter, and carbon/energy storage into polyhydroxyalkanoate. In parallel, comparative genomics revealed a high number of paralogs and an accessory genome significantly enriched in environmental sensing pathways (i.e., chemotaxis and motility), suggesting extensive gene expansions in R. aquaticus. The type strain of R. aquaticus (LMG 30558T) displayed optimal growth kinetics and productivity at low nutrient concentrations, as well as substantial cell size plasticity. Our findings with R. aquaticus LMG 30558T demonstrate that positive selection and gene expansions may represent successful adaptive strategies to oligotrophic environments that preserve high growth rates and cellular productivity. IMPORTANCE By combining a genome-centric metagenomic approach with a culture-based approach, we investigated the genomic adaptations of prevalent populations in an engineered oligotrophic freshwater system. We found evidence for widespread positive selection on genes involved in phosphorus and carbon scavenging pathways and for gene expansions in motility and environmental sensing to be important genomic adaptations of the abundant taxon in this system. In addition, microscopic and flow cytometric analysis of the first freshwater representative of this population (Ramlibacter aquaticus LMG 30558T) demonstrated phenotypic plasticity, possibly due to the metabolic versatility granted by its larger genome, to be a strategy to cope with nutrient limitation. Our study clearly demonstrates the need for the use of a broad set of genomic tools combined with culture-based physiological characterization assays to investigate and validate genomic adaptations.
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13
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V Bondoc KG, Lembke C, Vyverman W, Pohnert G. Selective chemoattraction of the benthic diatom Seminavis robusta to phosphate but not to inorganic nitrogen sources contributes to biofilm structuring. Microbiologyopen 2018; 8:e00694. [PMID: 30033670 PMCID: PMC6460271 DOI: 10.1002/mbo3.694] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/12/2018] [Accepted: 06/20/2018] [Indexed: 11/07/2022] Open
Abstract
Diatoms frequently dominate marine and freshwater biofilms as major primary producers. Nutrient resources in these biofilms are patchily distributed and fluctuate dynamically over time. We recently reported that this spatially and temporally structured environment can be exploited by motile diatoms that use chemoattraction to dissolved silicate (dSi) under Si starvation. Here, we show that the behavioral response of diatoms is more complex and selective as cells are also responding to gradients of dissolved phosphate (dP) when starved in this nutrient. In contrast, neither nitrate nor ammonium (dN) triggers an attractive response under nitrogen limitation. Video monitoring and movement pattern analysis of the model diatom Seminavis robusta revealed that dP attraction is mediated by a combined chemokinetic and chemotactic response. After locating nutrient hotspots, the microalgae slow down and recover from the limitation. The fastest recovery in terms of growth was observed after dSi limitation. In agreement with the lack of directional response, recovery from dN limitation was slowest, indicating that no short-term benefit would be drawn by the algae from the location of transient hotspots of this resource. Our results highlight the ability of diatoms to adapt to nutrient limitation by active foraging and might explain their success in patchy benthic environments.
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Affiliation(s)
- Karen Grace V Bondoc
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Jena, Germany.,Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Christine Lembke
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Gent, Gent, Belgium
| | - Georg Pohnert
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Jena, Germany.,Max Planck Institute for Chemical Ecology, Jena, Germany
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14
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Affiliation(s)
- Jörg Overmann
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
- German Center for Infection Research, Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Birte Abt
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
- German Center for Infection Research, Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Johannes Sikorski
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
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15
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Kazamia E, Helliwell KE, Purton S, Smith AG. How mutualisms arise in phytoplankton communities: building eco-evolutionary principles for aquatic microbes. Ecol Lett 2017; 19:810-22. [PMID: 27282316 PMCID: PMC5103174 DOI: 10.1111/ele.12615] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/03/2016] [Accepted: 04/07/2016] [Indexed: 01/05/2023]
Abstract
Extensive sampling and metagenomics analyses of plankton communities across all aquatic environments are beginning to provide insights into the ecology of microbial communities. In particular, the importance of metabolic exchanges that provide a foundation for ecological interactions between microorganisms has emerged as a key factor in forging such communities. Here we show how both studies of environmental samples and physiological experimentation in the laboratory with defined microbial co‐cultures are being used to decipher the metabolic and molecular underpinnings of such exchanges. In addition, we explain how metabolic modelling may be used to conduct investigations in reverse, deducing novel molecular exchanges from analysis of large‐scale data sets, which can identify persistently co‐occurring species. Finally, we consider how knowledge of microbial community ecology can be built into evolutionary theories tailored to these species’ unique lifestyles. We propose a novel model for the evolution of metabolic auxotrophy in microorganisms that arises as a result of symbiosis, termed the Foraging‐to‐Farming hypothesis. The model has testable predictions, fits several known examples of mutualism in the aquatic world, and sheds light on how interactions, which cement dependencies within communities of microorganisms, might be initiated.
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Affiliation(s)
- Elena Kazamia
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | | | - Saul Purton
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Alison Gail Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
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16
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Lu X, Zhou B, Xu L, Liu L, Wang G, Liu X, Tang X. A marine algicidal Thalassospira and its active substance against the harmful algal bloom species Karenia mikimotoi. Appl Microbiol Biotechnol 2016; 100:5131-9. [DOI: 10.1007/s00253-016-7352-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 01/08/2016] [Accepted: 01/23/2016] [Indexed: 11/28/2022]
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17
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Bondoc KGV, Heuschele J, Gillard J, Vyverman W, Pohnert G. Selective silicate-directed motility in diatoms. Nat Commun 2016; 7:10540. [PMID: 26842428 PMCID: PMC4742965 DOI: 10.1038/ncomms10540] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 12/23/2015] [Indexed: 11/09/2022] Open
Abstract
Diatoms are highly abundant unicellular algae that often dominate pelagic as well as benthic primary production in the oceans and inland waters. Being strictly dependent on silica to build their biomineralized cell walls, marine diatoms precipitate 240 × 10(12) mol Si per year, which makes them the major sink in the global Si cycle. Dissolved silicic acid (dSi) availability frequently limits diatom productivity and influences species composition of communities. We show that benthic diatoms selectively perceive and behaviourally react to gradients of dSi. Cell speed increases under dSi-limited conditions in a chemokinetic response and, if gradients of this resource are present, increased directionality of cell movement promotes chemotaxis. The ability to exploit local and short-lived dSi hotspots using a specific search behaviour likely contributes to micro-scale patch dynamics in biofilm communities. On a global scale this behaviour might affect sediment-water dSi fluxes and biogeochemical cycling.
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Affiliation(s)
- Karen Grace V Bondoc
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Department of Chemistry and Earth Sciences, Friedrich-Schiller-Universität Jena, Lessingstrasse 8, D-07743 Jena, Germany.,Max Planck Institute for Chemical Ecology, Max Planck Fellow, Hans-Knöll-Str. 8, D-07745 Jena, Germany
| | - Jan Heuschele
- Centre for Ocean Life, National Institute of Aquatic Resources, Technical University of Denmark, Charlottenlund Slot, Jægersborg Allé, DK-2920 Charlottenlund, Denmark.,Department of Biology, Aquatic Ecology Unit, Lund University, SE-22362 Lund, Sweden
| | - Jeroen Gillard
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Gent, Krijgslaan 281, S8, 9000 Gent, Belgium.,California State University, Department of Biology, 9001 Stockdale Hwy, Bakersfield, California 93311, USA
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Gent, Krijgslaan 281, S8, 9000 Gent, Belgium
| | - Georg Pohnert
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Department of Chemistry and Earth Sciences, Friedrich-Schiller-Universität Jena, Lessingstrasse 8, D-07743 Jena, Germany.,Max Planck Institute for Chemical Ecology, Max Planck Fellow, Hans-Knöll-Str. 8, D-07745 Jena, Germany
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18
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Microbial Surface Colonization and Biofilm Development in Marine Environments. Microbiol Mol Biol Rev 2015; 80:91-138. [PMID: 26700108 DOI: 10.1128/mmbr.00037-15] [Citation(s) in RCA: 462] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.
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19
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Lever MA, Rogers KL, Lloyd KG, Overmann J, Schink B, Thauer RK, Hoehler TM, Jørgensen BB. Life under extreme energy limitation: a synthesis of laboratory- and field-based investigations. FEMS Microbiol Rev 2015; 39:688-728. [PMID: 25994609 DOI: 10.1093/femsre/fuv020] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2015] [Indexed: 11/13/2022] Open
Abstract
The ability of microorganisms to withstand long periods with extremely low energy input has gained increasing scientific attention in recent years. Starvation experiments in the laboratory have shown that a phylogenetically wide range of microorganisms evolve fitness-enhancing genetic traits within weeks of incubation under low-energy stress. Studies on natural environments that are cut off from new energy supplies over geologic time scales, such as deeply buried sediments, suggest that similar adaptations might mediate survival under energy limitation in the environment. Yet, the extent to which laboratory-based evidence of starvation survival in pure or mixed cultures can be extrapolated to sustained microbial ecosystems in nature remains unclear. In this review, we discuss past investigations on microbial energy requirements and adaptations to energy limitation, identify gaps in our current knowledge, and outline possible future foci of research on life under extreme energy limitation.
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Affiliation(s)
- Mark A Lever
- Center for Geomicrobiology, Institute of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
| | - Karyn L Rogers
- Rensselaer Polytechnic Institute, Earth and Environmental Sciences, Jonsson-Rowland Science Center, 1W19, 110 8th Street, Troy, NY 12180, USA
| | - Karen G Lloyd
- Department of Microbiology, University of Tennessee at Knoxville, M409 Walters Life Sciences, Knoxville, TN 37996-0845, USA
| | - Jörg Overmann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, D-38124 Braunschweig, Germany
| | - Bernhard Schink
- Microbial Ecology, Department of Biology, University of Konstanz, P.O. Box 55 60, D-78457 Konstanz, Germany
| | - Rudolf K Thauer
- Max Planck Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Straße, D-35043 Marburg, Germany
| | - Tori M Hoehler
- NASA Ames Research Center, Mail Stop 239-4, Moffett Field, CA 94035-1000, USA
| | - Bo Barker Jørgensen
- Center for Geomicrobiology, Institute of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
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20
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Bi S, Lai L. Bacterial chemoreceptors and chemoeffectors. Cell Mol Life Sci 2015; 72:691-708. [PMID: 25374297 PMCID: PMC11113376 DOI: 10.1007/s00018-014-1770-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/05/2014] [Accepted: 10/23/2014] [Indexed: 01/11/2023]
Abstract
Bacteria use chemotaxis signaling pathways to sense environmental changes. Escherichia coli chemotaxis system represents an ideal model that illustrates fundamental principles of biological signaling processes. Chemoreceptors are crucial signaling proteins that mediate taxis toward a wide range of chemoeffectors. Recently, in deep study of the biochemical and structural features of chemoreceptors, the organization of higher-order clusters in native cells, and the signal transduction mechanisms related to the on-off signal output provides us with general insights to understand how chemotaxis performs high sensitivity, precise adaptation, signal amplification, and wide dynamic range. Along with the increasing knowledge, bacterial chemoreceptors can be engineered to sense novel chemoeffectors, which has extensive applications in therapeutics and industry. Here we mainly review recent advances in the E. coli chemotaxis system involving structure and organization of chemoreceptors, discovery, design, and characterization of chemoeffectors, and signal recognition and transduction mechanisms. Possible strategies for changing the specificity of bacterial chemoreceptors to sense novel chemoeffectors are also discussed.
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Affiliation(s)
- Shuangyu Bi
- Center for Quantitative Biology, Peking University, Beijing, 100871 China
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Luhua Lai
- Center for Quantitative Biology, Peking University, Beijing, 100871 China
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, and Peking-Tsinghua Center for Life Sciences at College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871 China
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21
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Hao W, Gerdts G, Peplies J, Wichels A. Bacterial communities associated with four ctenophore genera from the German Bight (North Sea). FEMS Microbiol Ecol 2014; 91:1-11. [DOI: 10.1093/femsec/fiu006] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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22
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Lai Q, Liu Y, Yuan J, Du J, Wang L, Sun F, Shao Z. Multilocus sequence analysis for assessment of phylogenetic diversity and biogeography in Thalassospira bacteria from diverse marine environments. PLoS One 2014; 9:e106353. [PMID: 25198177 PMCID: PMC4157779 DOI: 10.1371/journal.pone.0106353] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 08/02/2014] [Indexed: 11/23/2022] Open
Abstract
Thalassospira bacteria are widespread and have been isolated from various marine environments. Less is known about their genetic diversity and biogeography, as well as their role in marine environments, many of them cannot be discriminated merely using the 16S rRNA gene. To address these issues, in this report, the phylogenetic analysis of 58 strains from seawater and deep sea sediments were carried out using the multilocus sequence analysis (MLSA) based on acsA, aroE, gyrB, mutL, rpoD and trpB genes, and the DNA-DNA hybridization (DDH) and average nucleotide identity (ANI) based on genome sequences. The MLSA analysis demonstrated that the 58 strains were clearly separated into 15 lineages, corresponding to seven validly described species and eight potential novel species. The DDH and ANI values further confirmed the validity of the MLSA analysis and eight potential novel species. The MLSA interspecies gap of the genus Thalassospira was determined to be 96.16–97.12% sequence identity on the basis of the combined analyses of the DDH and MLSA, while the ANIm interspecies gap was 95.76–97.20% based on the in silico DDH analysis. Meanwhile, phylogenetic analyses showed that the Thalassospira bacteria exhibited distribution pattern to a certain degree according to geographic regions. Moreover, they clustered together according to the habitats depth. For short, the phylogenetic analyses and biogeography of the Thalassospira bacteria were systematically investigated for the first time. These results will be helpful to explore further their ecological role and adaptive evolution in marine environments.
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Affiliation(s)
- Qiliang Lai
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
- Collaborative Innovation Center of Deep Sea Biology, Xiamen, China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, China
| | - Yang Liu
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
- Collaborative Innovation Center of Deep Sea Biology, Xiamen, China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, China
| | - Jun Yuan
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
- Collaborative Innovation Center of Deep Sea Biology, Xiamen, China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, China
| | - Juan Du
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
- Collaborative Innovation Center of Deep Sea Biology, Xiamen, China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, China
| | - Liping Wang
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
- Collaborative Innovation Center of Deep Sea Biology, Xiamen, China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, China
| | - Fengqin Sun
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
- Collaborative Innovation Center of Deep Sea Biology, Xiamen, China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
- Collaborative Innovation Center of Deep Sea Biology, Xiamen, China
- Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen, China
- * E-mail:
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Abstract
Intuitively, it may seem that from the perspective of an individual bacterium the ocean is a vast, dilute, and largely homogeneous environment. Microbial oceanographers have typically considered the ocean from this point of view. In reality, marine bacteria inhabit a chemical seascape that is highly heterogeneous down to the microscale, owing to ubiquitous nutrient patches, plumes, and gradients. Exudation and excretion of dissolved matter by larger organisms, lysis events, particles, animal surfaces, and fluxes from the sediment-water interface all contribute to create strong and pervasive heterogeneity, where chemotaxis may provide a significant fitness advantage to bacteria. The dynamic nature of the ocean imposes strong selective pressures on bacterial foraging strategies, and many marine bacteria indeed display adaptations that characterize their chemotactic motility as "high performance" compared to that of enteric model organisms. Fast swimming speeds, strongly directional responses, and effective turning and steering strategies ensure that marine bacteria can successfully use chemotaxis to very rapidly respond to chemical gradients in the ocean. These fast responses are advantageous in a broad range of ecological processes, including attaching to particles, exploiting particle plumes, retaining position close to phytoplankton cells, colonizing host animals, and hovering at a preferred height above the sediment-water interface. At larger scales, these responses can impact ocean biogeochemistry by increasing the rates of chemical transformation, influencing the flux of sinking material, and potentially altering the balance of biomass incorporation versus respiration. This review highlights the physical and ecological processes underpinning bacterial motility and chemotaxis in the ocean, describes the current state of knowledge of chemotaxis in marine bacteria, and summarizes our understanding of how these microscale dynamics scale up to affect ecosystem-scale processes in the sea.
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24
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Bioremediation of Southern Mediterranean oil polluted sites comes of age. N Biotechnol 2013; 30:743-8. [DOI: 10.1016/j.nbt.2013.05.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 04/21/2013] [Accepted: 05/10/2013] [Indexed: 11/21/2022]
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25
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Dennis PG, Seymour J, Kumbun K, Tyson GW. Diverse populations of lake water bacteria exhibit chemotaxis towards inorganic nutrients. ISME JOURNAL 2013; 7:1661-4. [PMID: 23514780 DOI: 10.1038/ismej.2013.47] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 02/11/2013] [Accepted: 02/12/2013] [Indexed: 11/09/2022]
Abstract
Chemotaxis allows microorganisms to rapidly respond to different environmental stimuli; however, understanding of this process is limited by conventional assays, which typically focus on the response of single axenic cultures to given compounds. In this study, we used a modified capillary assay coupled with flow cytometry and 16S rRNA gene amplicon pyrosequencing to enumerate and identify populations within a lake water microbial community that exhibited chemotaxis towards ammonium, nitrate and phosphate. All compounds elicited chemotactic responses from populations within the lake water, with members of Sphingobacteriales exhibiting the strongest responses to nitrate and phosphate, and representatives of the Variovorax, Actinobacteria ACK-M1 and Methylophilaceae exhibiting the strongest responses to ammonium. Our results suggest that chemotaxis towards inorganic substrates may influence the rates of biogeochemical processes.
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Affiliation(s)
- Paul G Dennis
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
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26
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Abstract
Marine bacteria influence Earth's environmental dynamics in fundamental ways by controlling the biogeochemistry and productivity of the oceans. These large-scale consequences result from the combined effect of countless interactions occurring at the level of the individual cells. At these small scales, the ocean is surprisingly heterogeneous, and microbes experience an environment of pervasive and dynamic chemical and physical gradients. Many species actively exploit this heterogeneity, while others rely on gradient-independent adaptations. This is an exciting time to explore this frontier of oceanography, but understanding microbial behavior and competition in the context of the water column's microarchitecture calls for new ecological frameworks, such as a microbial optimal foraging theory, to determine the relevant trade-offs and global consequences of microbial life in a sea of gradients.
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Affiliation(s)
- Roman Stocker
- Ralph M. Parsons Laboratory, Department of Civil and Environmental Engineering, 49-213, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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27
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Abstract
Bacteria play an indispensable role in marine biogeochemistry by recycling dissolved organic matter. Motile species can exploit small, ephemeral solute patches through chemotaxis and thereby gain a fitness advantage over nonmotile competitors. This competition occurs in a turbulent environment, yet turbulence is generally considered inconsequential for bacterial uptake. In contrast, we show that turbulence affects uptake by stirring nutrient patches into networks of thin filaments that motile bacteria can readily exploit. We find that chemotactic motility is subject to a trade-off between the uptake benefit due to chemotaxis and the cost of locomotion, resulting in an optimal swimming speed. A second trade-off results from the competing effects of stirring and mixing and leads to the prediction that chemotaxis is optimally favored at intermediate turbulence intensities.
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Affiliation(s)
- John R Taylor
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, UK
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28
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Ghosh M, Pulicherla KK, Rekha VPB, Raja PK, Sambasiva Rao KRS. Cold active β-galactosidase from Thalassospira sp. 3SC-21 to use in milk lactose hydrolysis: a novel source from deep waters of Bay-of-Bengal. World J Microbiol Biotechnol 2012; 28:2859-69. [PMID: 22806727 DOI: 10.1007/s11274-012-1097-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 05/31/2012] [Indexed: 11/26/2022]
Abstract
The cold active β-galactosidase from psychrophilic bacteria accelerate the possibility of outperforming the current commercial β-galactosidase production from mesophilic sources. The present study is carried out to screen and isolate a cold active β-galactosidase producing bacterium from profound marine waters of Bay-of-Bengal and to optimize the factors for lactose hydrolysis in milk. Isolated bacterium 3SC-21 was characterized as marine psychrotolerant, halophile, gram negative, rod shaped strain producing an intracellular cold active β-galactosidase enzyme. Further, based upon the 16S rRNA gene sequence, bacterium 3SC-21 was identified as Thalassospira sp. The isolated strain Thalassospira sp. 3SC-21 had shown the enzyme activity between 4 and 20 °C at pH of 6.5 and the enzyme was completely inactivated at 45 °C. The statistical method, central composite rotatable design of response surface methodology was employed to optimize the hydrolysis of lactose and to reveal the interactions between various factors behind this hydrolysis. It was found that maximum of 80.18 % of lactose in 8 ml of raw milk was hydrolysed at pH of 6.5 at 20 °C in comparison to 40 % of lactose hydrolysis at 40 °C, suggesting that the cold active β-galactosidase from Thalassospira sp. 3SC-21 would be best suited for manufacturing the lactose free dairy products at low temperature.
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Affiliation(s)
- Mrinmoy Ghosh
- Department of Biotechnology, Acharya Nagarjuna University, Nagarjuna Nagar, Guntur, India
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Daniels C, Breitbart M. Bacterial communities associated with the ctenophores Mnemiopsis leidyi and Beroe ovata. FEMS Microbiol Ecol 2012; 82:90-101. [DOI: 10.1111/j.1574-6941.2012.01409.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 05/01/2012] [Accepted: 05/06/2012] [Indexed: 01/25/2023] Open
Affiliation(s)
- Camille Daniels
- College of Marine Science, University of South Florida; St. Petersburg; FL; USA
| | - Mya Breitbart
- College of Marine Science, University of South Florida; St. Petersburg; FL; USA
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