1
|
Brauner M, Briggs BR. Microbial iron acquisition is influenced by spatial and temporal conditions in a glacial influenced river and estuary system. Environ Microbiol 2023; 25:3450-3465. [PMID: 37956696 PMCID: PMC10872409 DOI: 10.1111/1462-2920.16541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023]
Abstract
In Arctic regions, glaciers are major sources of iron to rivers and streams; however, estuaries are considered iron sinks due to the coagulation and flocculation processes that occur at higher salinities. It is unknown how iron dynamics in a glacial influenced river and estuary environment affect microbial mechanisms for iron acquisition. Microbial taxonomic and functional sequencing was performed on samples taken throughout the year from the Kenai River and the estuary, Alaska. Despite distinct iron, sodium, and other nutrient concentrations, the river and estuary did not have statistically different microbial communities nor was time of sampling significant. However, ferrous iron transport (Feo) system genes were more abundant in river environments, while siderophore genes were more abundant and diverse in estuary environments. Siderophore transport and iron storage genes were found in all samples, but gene abundance and distribution were potentially influenced by physical drivers such as discharge rates and nutrient distributions. Differences in iron metabolism between river and estuary ecosystems indicate environmental conditions drive microbial mechanisms to sequester iron. This could have implications for iron transport as the Arctic continues to warm.
Collapse
Affiliation(s)
- Megan Brauner
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Dr CPSB 101, Anchorage, Alaska
| | - Brandon R. Briggs
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Dr CPSB 101, Anchorage, Alaska
| |
Collapse
|
2
|
Biogeographic and Evolutionary Patterns of Trace Element Utilization in Marine Microbial World. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:958-972. [PMID: 33631428 PMCID: PMC9402790 DOI: 10.1016/j.gpb.2021.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 01/23/2019] [Accepted: 06/06/2019] [Indexed: 12/01/2022]
Abstract
Trace elements are required by all organisms, which are key components of many enzymes catalyzing important biological reactions. Many trace element-dependent proteins have been characterized; however, little is known about their occurrence in microbial communities in diverse environments, especially the global marine ecosystem. Moreover, the relationships between trace element utilization and different types of environmental stressors are unclear. In this study, we used metagenomic data from the Global Ocean Sampling expedition project to identify the biogeographic distribution of genes encoding trace element-dependent proteins (for copper, molybdenum, cobalt, nickel, and selenium) in a variety of marine and non-marine aquatic samples. More than 56,000 metalloprotein and selenoprotein genes corresponding to nearly 100 families were predicted, becoming the largest dataset of marine metalloprotein and selenoprotein genes reported to date. In addition, samples with enriched or depleted metalloprotein/selenoprotein genes were identified, suggesting an active or inactive usage of these micronutrients in various sites. Further analysis of interactions among the elements showed significant correlations between some of them, especially those between nickel and selenium/copper. Finally, investigation of the relationships between environmental conditions and metalloprotein/selenoprotein families revealed that many environmental factors might contribute to the evolution of different metalloprotein and/or selenoprotein genes in the marine microbial world. Our data provide new insights into the utilization and biological roles of these trace elements in extant marine microbes, and might also be helpful for the understanding of how these organisms have adapted to their local environments.
Collapse
|
3
|
Sinha S, Lynn AM, Desai DK. Implementation of homology based and non-homology based computational methods for the identification and annotation of orphan enzymes: using Mycobacterium tuberculosis H37Rv as a case study. BMC Bioinformatics 2020; 21:466. [PMID: 33076816 PMCID: PMC7574302 DOI: 10.1186/s12859-020-03794-x] [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: 07/23/2019] [Accepted: 10/01/2020] [Indexed: 02/06/2023] Open
Abstract
Background Homology based methods are one of the most important and widely used approaches for functional annotation of high-throughput microbial genome data. A major limitation of these methods is the absence of well-characterized sequences for certain functions. The non-homology methods based on the context and the interactions of a protein are very useful for identifying missing metabolic activities and functional annotation in the absence of significant sequence similarity. In the current work, we employ both homology and context-based methods, incrementally, to identify local holes and chokepoints, whose presence in the Mycobacterium tuberculosis genome is indicated based on its interaction with known proteins in a metabolic network context, but have not been annotated. We have developed two computational procedures using network theory to identify orphan enzymes (‘Hole finding protocol’) coupled with the identification of candidate proteins for the predicted orphan enzyme (‘Hole filling protocol’). We propose an integrated interaction score based on scores from the STRING database to identify candidate protein sequences for the orphan enzymes from M. tuberculosis, as a case study, which are most likely to perform the missing function. Results The application of an automated homology-based enzyme identification protocol, ModEnzA, on M. tuberculosis genome yielded 56 novel enzyme predictions. We further predicted 74 putative local holes, 6 choke points, and 3 high confidence local holes in the genome using ‘Hole finding protocol’. The ‘Hole-filling protocol’ was validated on the E. coli genome using artificial in-silico enzyme knockouts where our method showed 25% increased accuracy, compared to other methods, in assigning the correct sequence for the knocked-out enzyme amongst the top 10 ranks. The method was further validated on 8 additional genomes. Conclusions We have developed methods that can be generalized to augment homology-based annotation to identify missing enzyme coding genes and to predict a candidate protein for them. For pathogens such as M. tuberculosis, this work holds significance in terms of increasing the protein repertoire and thereby, the potential for identifying novel drug targets.
Collapse
Affiliation(s)
- Swati Sinha
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*Star), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Republic of Singapore
| | - Andrew M Lynn
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Dhwani K Desai
- Department of Biology and Department of Pharmacology, Dalhousie University, Halifax, NS, B3H4R2, Canada. .,School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
| |
Collapse
|
4
|
Haas S, Desai DK, LaRoche J, Pawlowicz R, Wallace DWR. Geomicrobiology of the carbon, nitrogen and sulphur cycles in Powell Lake: a permanently stratified water column containing ancient seawater. Environ Microbiol 2019; 21:3927-3952. [PMID: 31314947 DOI: 10.1111/1462-2920.14743] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 07/12/2019] [Accepted: 07/13/2019] [Indexed: 11/30/2022]
Abstract
We present the first geomicrobiological characterization of the meromictic water column of Powell Lake (British Columbia, Canada), a former fjord, which has been stably stratified since the last glacial period. Its deepest layers (300-350 m) retain isolated, relict seawater from that period. Fine-scale vertical profiling of the water chemistry and microbial communities allowed subdivision of the water column into distinct geomicrobiological zones. These zones were further characterized by phylogenetic and functional marker genes from amplicon and shotgun metagenome sequencing. Binning of metagenomic reads allowed the linkage of function to specific taxonomic groups. Statistical analyses (analysis of similarities, Bray-Curtis similarity) confirmed that the microbial community structure followed closely the geochemical zonation. Yet, our characterization of the genetic potential relevant to carbon, nitrogen and sulphur cycling of each zone revealed unexpected features, including potential for facultative anaerobic methylotrophy, nitrogen fixation despite high ammonium concentrations and potential micro-aerobic nitrifiers within the chemocline. At the oxic-suboxic interface, facultative anaerobic potential was found in the widespread freshwater lineage acI (Actinobacteria), suggesting intriguing ecophysiological similarities to the marine SAR11. Evolutionary divergent lineages among diverse phyla were identified in the ancient seawater zone and may indicate novel adaptations to this unusual environment.
Collapse
Affiliation(s)
- Sebastian Haas
- Department of Oceanography, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, Canada
| | - Dhwani K Desai
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, Canada
| | - Julie LaRoche
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, Canada
| | - Rich Pawlowicz
- Department of Earth and Ocean Sciences, University of British Columbia, 6339 Stores Road, Vancouver, British Columbia, Canada
| | - Douglas W R Wallace
- Department of Oceanography, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, Canada
| |
Collapse
|
5
|
Debeljak P, Toulza E, Beier S, Blain S, Obernosterer I. Microbial iron metabolism as revealed by gene expression profiles in contrasted Southern Ocean regimes. Environ Microbiol 2019; 21:2360-2374. [PMID: 30958628 PMCID: PMC6618146 DOI: 10.1111/1462-2920.14621] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/18/2019] [Accepted: 04/01/2019] [Indexed: 11/28/2022]
Abstract
Iron (Fe) is a limiting nutrient in large regions of the ocean, but the strategies of prokaryotes to cope with this micronutrient are poorly known. Using a gene-specific approach from metatranscriptomics data, we investigated seven Fe-related metabolic pathways in microbial communities from high nutrient low chlorophyll and naturally Fe-fertilized waters in the Southern Ocean. We observed major differences in the contribution of prokaryotic groups at different taxonomic levels to transcripts encoding Fe-uptake mechanisms, intracellular Fe storage and replacement and Fe-related pathways in the tricarboxylic acid (TCA) cycle. The composition of the prokaryotic communities contributing to the transcripts of a given Fe-related pathway was overall independent of the in situ Fe supply, indicating that microbial taxa utilize distinct Fe-related metabolic processes. Only a few prokaryotic groups contributed to the transcripts of more than one Fe-uptake mechanism, suggesting limited metabolic versatility. Taxa-specific expression of individual genes varied among prokaryotic groups and was substantially higher for all inspected genes in Fe-limited as compared to naturally fertilized waters, indicating the link between transcriptional state and Fe regime. Different metabolic strategies regarding low Fe concentrations in the Southern Ocean are discussed for two abundant prokaryotic groups, Pelagibacteraceae and Flavobacteriaceae.
Collapse
Affiliation(s)
- Pavla Debeljak
- Sorbonne UniversitéCNRS, Laboratoire d'Océanographie Microbienne, LOMICF‐66650 Banyuls/merFrance
- Department of Limnology and Bio‐OceanographyUniversity of Vienna, A‐1090ViennaAustria
| | - Eve Toulza
- Université Perpignan Via DomitiaIHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, F‐66860PerpignanFrance
| | - Sara Beier
- Leibniz Institute for Baltic Sea ResearchWarnemündeGermany
| | - Stephane Blain
- Sorbonne UniversitéCNRS, Laboratoire d'Océanographie Microbienne, LOMICF‐66650 Banyuls/merFrance
| | - Ingrid Obernosterer
- Sorbonne UniversitéCNRS, Laboratoire d'Océanographie Microbienne, LOMICF‐66650 Banyuls/merFrance
| |
Collapse
|
6
|
Zhang Y, Ying H, Xu Y. Comparative genomics and metagenomics of the metallomes. Metallomics 2019; 11:1026-1043. [DOI: 10.1039/c9mt00023b] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent achievements and advances in comparative genomic and metagenomic analyses of trace metals were reviewed and discussed.
Collapse
Affiliation(s)
- Yan Zhang
- Shenzhen Key Laboratory of Marine Bioresources and Ecology
- College of Life Sciences and Oceanography
- Shenzhen University
- Shenzhen
- P. R. China
| | - Huimin Ying
- Department of Endocrinology
- Hangzhou Xixi Hospital
- Hangzhou
- P. R. China
| | - Yinzhen Xu
- Shenzhen Key Laboratory of Marine Bioresources and Ecology
- College of Life Sciences and Oceanography
- Shenzhen University
- Shenzhen
- P. R. China
| |
Collapse
|
7
|
Pierella Karlusich JJ, Ceccoli RD, Graña M, Romero H, Carrillo N. Environmental selection pressures related to iron utilization are involved in the loss of the flavodoxin gene from the plant genome. Genome Biol Evol 2015; 7:750-67. [PMID: 25688107 PMCID: PMC5322553 DOI: 10.1093/gbe/evv031] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Oxidative stress and iron limitation represent the grim side of life in an oxygen-rich atmosphere. The versatile electron transfer shuttle ferredoxin, an iron-sulfur protein, is particularly sensitive to these hardships, and its downregulation under adverse conditions severely compromises survival of phototrophs. Replacement of ferredoxin by a stress-resistant isofunctional carrier, flavin-containing flavodoxin, is a widespread strategy employed by photosynthetic microorganisms to overcome environmental adversities. The flavodoxin gene was lost in the course of plant evolution, but its reintroduction in transgenic plants confers increased tolerance to environmental stress and iron starvation, raising the question as to why a genetic asset with obvious adaptive value was not kept by natural selection. Phylogenetic analyses reveal that the evolutionary history of flavodoxin is intricate, with several horizontal gene transfer events between distant organisms, including Eukarya, Bacteria, and Archaea. The flavodoxin gene is unevenly distributed in most algal lineages, with flavodoxin-containing species being overrepresented in iron-limited regions and scarce or absent in iron-rich environments. Evaluation of cyanobacterial genomic and metagenomic data yielded essentially the same results, indicating that there was little selection pressure to retain flavodoxin in iron-rich coastal/freshwater phototrophs. Our results show a highly dynamic evolution pattern of flavodoxin tightly connected to the bioavailability of iron. Evidence presented here also indicates that the high concentration of iron in coastal and freshwater habitats may have facilitated the loss of flavodoxin in the freshwater ancestor of modern plants during the transition of photosynthetic organisms from the open oceans to the firm land.
Collapse
Affiliation(s)
- Juan J Pierella Karlusich
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-Universidad Nacional de Rosario, Ocampo y Esmeralda, Rosario, Argentina
| | - Romina D Ceccoli
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-Universidad Nacional de Rosario, Ocampo y Esmeralda, Rosario, Argentina Present address: Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario; CONICET, Rosario, Argentina
| | - Martín Graña
- Unidad de Bioinformática, Institut Pasteur Montevideo, Uruguay
| | - Héctor Romero
- Departamento de Ecología y Evolución, Facultad de Ciencias/CURE, Universidad de la República, Montevideo, Uruguay
| | - Néstor Carrillo
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-Universidad Nacional de Rosario, Ocampo y Esmeralda, Rosario, Argentina
| |
Collapse
|
8
|
Hogle SL, Barbeau KA, Gledhill M. Heme in the marine environment: from cells to the iron cycle. Metallomics 2015; 6:1107-20. [PMID: 24811388 DOI: 10.1039/c4mt00031e] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Hemes are iron containing heterocyclic molecules important in many cellular processes. In the marine environment, hemes participate as enzymatic cofactors in biogeochemically significant processes like photosynthesis, respiration, and nitrate assimilation. Further, hemoproteins, hemes, and their analogs appear to be iron sources for some marine bacterioplankton under certain conditions. Current oceanographic analytical methodologies allow for the extraction and measurement of heme b from marine material, and a handful of studies have begun to examine the distribution of heme b in ocean basins. The study of heme in the marine environment is still in its infancy, but some trends can be gleaned from the work that has been published so far. In this review, we summarize what is known or might be inferred about the roles of heme in marine microbes as well as the few studies on heme in the marine environment that have been conducted to date. We conclude by presenting some future questions and challenges for the field.
Collapse
Affiliation(s)
- Shane L Hogle
- Geoscience Research Division, Scripps Institution of Oceanography, La Jolla, California, USA.
| | | | | |
Collapse
|
9
|
Boiteau RM, Repeta DJ. An extended siderophore suite from Synechococcus sp. PCC 7002 revealed by LC-ICPMS-ESIMS. Metallomics 2015; 7:877-84. [DOI: 10.1039/c5mt00005j] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
New members of the synechobactin siderophore suite with variable hydroxamate chain length were discovered using an LCMS based pipeline for the sensitive characterization of iron complexes.
Collapse
Affiliation(s)
- Rene M. Boiteau
- Department of Marine Chemistry and Geochemistry
- Woods Hole Oceanographic Institution
- Woods Hole, USA
- Department of Earth
- Atmospheric and Planetary Sciences
| | - Daniel J. Repeta
- Department of Marine Chemistry and Geochemistry
- Woods Hole Oceanographic Institution
- Woods Hole, USA
| |
Collapse
|
10
|
Kranzler C, Lis H, Finkel OM, Schmetterer G, Shaked Y, Keren N. Coordinated transporter activity shapes high-affinity iron acquisition in cyanobacteria. THE ISME JOURNAL 2014; 8:409-17. [PMID: 24088625 PMCID: PMC3906821 DOI: 10.1038/ismej.2013.161] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 08/01/2013] [Accepted: 08/17/2013] [Indexed: 11/08/2022]
Abstract
Iron bioavailability limits biological activity in many aquatic and terrestrial environments. Broad scale genomic meta-analyses indicated that within a single organism, multiple iron transporters may contribute to iron acquisition. Here, we present a functional characterization of a cyanobacterial iron transport pathway that utilizes concerted transporter activities. Cyanobacteria are significant contributors to global primary productivity with high iron demands. Certain cyanobacterial species employ a siderophore-mediated uptake strategy; however, many strains possess neither siderophore biosynthesis nor siderophore transport genes. The unicellular, planktonic, freshwater cyanobacterium, Synechocystis sp. PCC 6803, employs an alternative to siderophore-based uptake-reduction of Fe(III) species before transport through the plasma membrane. In this study, we combine short-term radioactive iron uptake and reduction assays with a range of disruption mutants to generate a working model for iron reduction and uptake in Synechocystis sp. PCC 6803. We found that the Fe(II) transporter, FeoB, is the major iron transporter in this organism. In addition, we uncovered a link between a respiratory terminal oxidase (Alternate Respiratory Terminal Oxidase) and iron reduction - suggesting a coupling between these two electron transfer reactions. Furthermore, quantitative RNA transcript analysis identified a function for subunits of the Fe(III) transporter, FutABC, in modulating reductive iron uptake. Collectively, our results provide a molecular basis for a tightly coordinated, high-affinity iron transport system.
Collapse
Affiliation(s)
- Chana Kranzler
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
- Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
| | - Hagar Lis
- Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
- The Freddy and Nadine Herrmann Institute of Earth Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Omri M Finkel
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Georg Schmetterer
- Institute of Physical Chemistry, University of Vienna, Vienna, Austria
| | - Yeala Shaked
- Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
- The Freddy and Nadine Herrmann Institute of Earth Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nir Keren
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| |
Collapse
|
11
|
Gledhill M, Hassler CS, Schoemann V. The environmental bioinorganic chemistry of aquatic microbial organisms. Front Microbiol 2013; 4:100. [PMID: 23630522 PMCID: PMC3635032 DOI: 10.3389/fmicb.2013.00100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 04/08/2013] [Indexed: 11/13/2022] Open
Affiliation(s)
- Martha Gledhill
- National Oceanography Centre, School of Ocean and Earth Science, University of Southampton Southampton, UK
| | | | | |
Collapse
|