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Mrnjavac N, Degli Esposti M, Mizrahi I, Martin WF, Allen JF. Three enzymes governed the rise of O 2 on Earth. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149495. [PMID: 39004113 PMCID: PMC7616410 DOI: 10.1016/j.bbabio.2024.149495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024]
Abstract
Current views of O2 accumulation in Earth history depict three phases: The onset of O2 production by ∼2.4 billion years ago; 2 billion years of stasis at ∼1 % of modern atmospheric levels; and a rising phase, starting about 500 million years ago, in which oxygen eventually reached modern values. Purely geochemical mechanisms have been proposed to account for this tripartite time course of Earth oxygenation. In particular the second phase, the long period of stasis between the advent of O2 and the late rise to modern levels, has posed a puzzle. Proposed solutions involve Earth processes (geochemical, ecosystem, day length). Here we suggest that Earth oxygenation was not determined by geochemical processes. Rather it resulted from emergent biological innovations associated with photosynthesis and the activity of only three enzymes: 1) The oxygen evolving complex of cyanobacteria that makes O2; 2) Nitrogenase, with its inhibition by O2 causing two billion years of oxygen level stasis; 3) Cellulose synthase of land plants, which caused mass deposition and burial of carbon, thus removing an oxygen sink and therefore increasing atmospheric O2. These three enzymes are endogenously produced by, and contained within, cells that have the capacity for exponential growth. The catalytic properties of these three enzymes paved the path of Earth's atmospheric oxygenation, requiring no help from Earth other than the provision of water, CO2, salts, colonizable habitats, and sunlight.
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Affiliation(s)
- Natalia Mrnjavac
- Department of Biology, Institute for Molecular Evolution, Heinrich Heine University of Duesseldorf, Duesseldorf, Germany
| | | | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Marcus Family Campus, Be'er-Sheva, Israel
| | - William F Martin
- Department of Biology, Institute for Molecular Evolution, Heinrich Heine University of Duesseldorf, Duesseldorf, Germany
| | - John F Allen
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London, UK.
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2
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Paltsev A, Bergström AK, Vuorio K, Creed IF, Hessen DO, Kortelainen P, Vuorenmaa J, de Wit HA, Lau DCP, Vrede T, Isles PDF, Jonsson A, Geibrink E, Kahilainen KK, Drakare S. Phytoplankton biomass in northern lakes reveals a complex response to global change. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 940:173570. [PMID: 38825201 DOI: 10.1016/j.scitotenv.2024.173570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/25/2024] [Accepted: 05/25/2024] [Indexed: 06/04/2024]
Abstract
Global change may introduce fundamental alterations in phytoplankton biomass and community structure that can alter the productivity of northern lakes. In this study, we utilized Swedish and Finnish monitoring data from lakes that are spatially (135 lakes) and temporally (1995-2019, 110 lakes) extensive to assess how phytoplankton biomass (PB) of dominant phytoplankton groups related to changes in water temperature, pH and key nutrients [total phosphorus (TP), total nitrogen (TN), total organic carbon (TOC), iron (Fe)] along spatial (Fennoscandia) and temporal (25 years) gradients. Using a machine learning approach, we found that TP was the most important determinant of total PB and biomass of a specific species of Raphidophyceae - Gonyostomum semen - and Cyanobacteria (both typically with adverse impacts on food-webs and water quality) in spatial analyses, while Fe and pH were second in importance for G. semen and TN and pH were second and third in importance for Cyanobacteria. However, in temporal analyses, decreasing Fe and increasing pH and TOC were associated with a decrease in G. semen and an increase in Cyanobacteria. In addition, in many lakes increasing TOC seemed to have generated browning to an extent that significantly reduced PB. The identified discrepancy between the spatial and temporal results suggests that substitutions of data for space-for-time may not be adequate to characterize long-term effects of global change on phytoplankton. Further, we found that total PB exhibited contrasting temporal trends (increasing in northern- and decreasing in southern Fennoscandia), with the decline in total PB being more pronounced than the increase. Among phytoplankton, G. semen biomass showed the strongest decline, while cyanobacterial biomass showed the strongest increase over 25 years. Our findings suggest that progressing browning and changes in Fe and pH promote significant temporal changes in PB and shifts in phytoplankton community structures in northern lakes.
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Affiliation(s)
- Aleksey Paltsev
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden.
| | | | | | - Irena F Creed
- Department of Physical and Environmental Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Dag Olav Hessen
- Centre of Biogeochemistry in the Anthropocene and Department of Bioscience, University of Oslo, Oslo, Norway
| | | | | | - Heleen A de Wit
- Centre of Biogeochemistry in the Anthropocene and Department of Bioscience, University of Oslo, Oslo, Norway; Norwegian Institute for Water Research, Oslo, Norway
| | - Danny C P Lau
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Tobias Vrede
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Peter D F Isles
- Watershed Management Division, Vermont Department of Environmental Conservation, Montpelier, VT, USA
| | - Anders Jonsson
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
| | - Erik Geibrink
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
| | | | - Stina Drakare
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
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3
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Guo Y, Cheng S, Fang H, Geng J, Li Y, Shi F, Wang H, Chen L, Zhou Y. Copper and cadmium co-contamination increases the risk of nitrogen loss in red paddy soils. JOURNAL OF HAZARDOUS MATERIALS 2024; 479:135626. [PMID: 39197279 DOI: 10.1016/j.jhazmat.2024.135626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/27/2024] [Accepted: 08/21/2024] [Indexed: 09/01/2024]
Abstract
The microbiome plays a crucial role in soil nitrogen (N) cycling and in regulating its bioavailability. However, the functional and genomic information of microorganisms encoding N cycling in response to copper (Cu) and cadmium (Cd) contamination is largely unknown. Here, metagenomics and genome binning were used to examine microbial N cycling in Cu and Cd co-contaminated red paddy soils collected from a polluted watershed in southern China. The results showed that soil Cu and Cd concentrations induced more drastic changes in microbial N functional and taxonomic traits than soil general properties. Soil Cu and Cd co-contamination stimulated microbial nitrification, denitrification, and dissimilatory nitrate reduction processes mainly by increasing the abundance of Nitrospira (phylum Nitrospirota), while inhibiting N fixation by decreasing the abundance of Desulfobacca. These contrasting changes in microbial N cycling processes suggested a potential risk of N loss in paddy soils. A high-quality genome was identified as belonging to Nitrospirota with the highest abundance in heavily contaminated soils. This novel Nitrospirota strain possessed metabolic capacities for N transformation and metal resistance. These findings elucidate the genetic mechanisms underlying soil N bioavailability under long-term Cu and Cd contamination, which is essential for maintaining agricultural productivity and controlling heavy metal pollution.
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Affiliation(s)
- Yifan Guo
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shulan Cheng
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Huajun Fang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; The Zhongke-Ji'an Institute for Eco-Environmental Sciences, Ji'an 343000, China.
| | - Jing Geng
- School of Geospatial Engineering and Science, Sun Yat-sen University, Zhuhai 519082, China
| | - Yuna Li
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangying Shi
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Wang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Long Chen
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Zhou
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
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4
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Panda P, Giri SJ, Sherman LA, Kihara D, Aryal UK. Proteomic changes orchestrate metabolic acclimation of a unicellular diazotrophic cyanobacterium during light-dark cycle and nitrogen fixation states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.30.605809. [PMID: 39131303 PMCID: PMC11312527 DOI: 10.1101/2024.07.30.605809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Cyanobacteria have developed an impressive array of proteins and pathways, each tailored for specific metabolic attributes, to execute photosynthesis and biological nitrogen (N2)-fixation. An understanding of these biologically incompatible processes provides important insights into how they can be optimized for renewable energy. To expand upon our current knowledge, we performed label-free quantitative proteomic analysis of the unicellular diazotrophic cyanobacterium Crocosphaera subtropica ATCC 51142 grown with and without nitrate under 12-hour light-dark cycles. Results showed significant shift in metabolic activities including photosynthesis, respiration, biological nitrogen fixation (BNF), and proteostasis to different growth conditions. We identified 14 nitrogenase enzymes which were among the most highly expressed proteins in the dark under nitrogen-fixing conditions, emphasizing their importance in BNF. Nitrogenase enzymes were not expressed under non nitrogen fixing conditions, suggesting a regulatory mechanism based on nitrogen availability. The synthesis of key respiratory enzymes and uptake hydrogenase (HupSL) synchronized with the synthesis of nitrogenase indicating a coordinated regulation of processes involved in energy production and BNF. Data suggests alternative pathways that cells utilize, such as oxidative pentose phosphate (OPP) and 2-oxoglutarate (2-OG) pathways, to produce ATP and support bioenergetic BNF. Data also indicates the important role of uptake hydrogenase for the removal of O2 to support BNF. Overall, this study expands upon our knowledge regarding molecular responses of Crocosphaera 51142 to nitrogen and light-dark phases, shedding light on potential applications and optimization for renewable energy.
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Affiliation(s)
- Punyatoya Panda
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907
| | - Swagarika J Giri
- Department of Computer Science, Purdue University, West Lafayette, IN 47907
| | - Louis A Sherman
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN 47907
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
| | - Uma K Aryal
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907
- Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907
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5
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Liu X, Tang K, Hu J. Application of Cyanobacteria as Chassis Cells in Synthetic Biology. Microorganisms 2024; 12:1375. [PMID: 39065143 PMCID: PMC11278661 DOI: 10.3390/microorganisms12071375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
Synthetic biology is an exciting new area of research that combines science and engineering to design and build new biological functions and systems. Predictably, with the development of synthetic biology, more efficient and economical photosynthetic microalgae chassis will be successfully constructed, making it possible to break through laboratory research into large-scale industrial applications. The synthesis of a range of biochemicals has been demonstrated in cyanobacteria; however, low product titers are the biggest barrier to the commercialization of cyanobacterial biotechnology. This review summarizes the applied improvement strategies from the perspectives of cyanobacteria chassis cells and synthetic biology. The harvest advantages of cyanobacterial products and the latest progress in improving production strategies are discussed according to the product status. As cyanobacteria synthetic biology is still in its infancy, apart from the achievements made, the difficulties and challenges in the application and development of cyanobacteria genetic tool kits in biochemical synthesis, environmental monitoring, and remediation were assessed.
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Affiliation(s)
| | | | - Jinlu Hu
- School of Life Sciences, Northwestern Polytechnical University, Xi’an 710072, China; (X.L.); (K.T.)
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6
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Amin N, Sinha RP, Kannaujiya VK. Effects of ultraviolet and photosynthetically active radiation on morphogenesis, antioxidants and photoprotective defense mechanism in a hot-spring cyanobacterium Nostoc sp. strain VKB02. Res Microbiol 2024; 175:104180. [PMID: 38199600 DOI: 10.1016/j.resmic.2024.104180] [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: 03/25/2023] [Revised: 11/26/2023] [Accepted: 01/03/2024] [Indexed: 01/12/2024]
Abstract
The continuous increase in global temperature and ultraviolet radiation (UVR) causes profound impacts on the growth and physiology of photosynthetic microorganisms. The hot-spring cyanobacteria have a wide range of mitigation mechanisms to cope up against current unsustainable environmental conditions. In the present investigation, we have explored the indispensable mitigation strategies of an isolated hot-spring cyanobacterium Nostoc sp. strain VKB02 under simulated ultraviolet (UV-A, UV-B) and photosynthetically active radiation (PAR). The adaptive morphological changes were more significantly observed under PAB (PAR, UV-A, and UV-B) exposure as compared to P and PA (PAR and UV-A) irradiations. PAB exposure also exhibited a marked decline in pigment composition and photosynthetic efficiency by multi-fold increment of free radicals. To counteract the oxidative stress, enzymatic and non-enzymatic antioxidants defense were significantly enhanced many folds under PAB exposure as compared to the control. In addition, the cyanobacterium has also produced shinorine as a strong free radicals scavenger and excellent UV absorber for effective photoprotection against UV radiation. Therefore, the hot-spring cyanobacterium Nostoc sp. strain VKB02 has unique defense strategies for survival under prolonged lethal UVR conditions. This study will help in the understanding of environment-induced defense strategies and production of highly value-added green photo-protectants for commercial applications.
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Affiliation(s)
- Nasreen Amin
- Department of Botany, MMV, Banaras Hindu University, Varanasi-221005, India
| | - Rajeshwar P Sinha
- Laboratory of Photobiology and Molecular Microbiology, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi-221005, India
| | - Vinod K Kannaujiya
- Department of Botany, MMV, Banaras Hindu University, Varanasi-221005, India.
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7
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Samantaray A, Chattaraj S, Mitra D, Ganguly A, Kumar R, Gaur A, Mohapatra PK, Santos-Villalobos SDL, Rani A, Thatoi H. Advances in microbial based bio-inoculum for amelioration of soil health and sustainable crop production. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 7:100251. [PMID: 39165409 PMCID: PMC11334944 DOI: 10.1016/j.crmicr.2024.100251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2024] Open
Abstract
The adoption of sustainable agricultural practices is increasingly imperative in addressing global food security and environmental concerns, with microbial based bio-inoculums emerging as a promising approach for nurturing soil health and fostering sustainable crop production.This review article explores the potential of microbial based bio-inoculumsor biofertilizers as a transformative approach toenhance plant disease resistance and growth. It explores the commercial prospects of biofertilizers, highlighting their role in addressing environmental concerns associated with conventional fertilizers while meeting the growing demand for eco-friendly agricultural practices. Additionally, this review discusses the future prospects of biofertilizers, emphasizing the ongoing advancements in biotechnology and formulation techniques that are expected to enhance their efficacy and applicability. Furthermore, this article provides insights into strategies for the successful acceptance of biofertilizers among farmers, including the importance of quality control, assurance, and education initiatives to raise awareness about their benefits and overcome barriers to adoption. By synthesizing the current research findings and industrial developments, this review offers valuable guidance for stakeholders seeking to exploit the potential of biofertilizers or beneficial microbes to promote soil health, ensure sustainable crop production, and addressing the challenges of modern agriculture.
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Affiliation(s)
- Aurodeepa Samantaray
- Centre for Industrial Biotechnology Research, School of Pharmaceutical Sciences, Siksha ‘O’ Anusandhan, Deemed to be University, Kalinga Nagar, Bhubaneswar, Odisha 751003, India
| | - Sourav Chattaraj
- Centre for Industrial Biotechnology Research, School of Pharmaceutical Sciences, Siksha ‘O’ Anusandhan, Deemed to be University, Kalinga Nagar, Bhubaneswar, Odisha 751003, India
| | - Debasis Mitra
- Department of Microbiology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand 248002, India
| | - Arindam Ganguly
- Department of Microbiology, Bankura Sammilani College, Bankura, West Bengal 722102, India
| | - Rahul Kumar
- Department of Microbiology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand 248002, India
| | - Ashish Gaur
- Department of Biotechnology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand 248002, India
| | - Pradeep K.Das Mohapatra
- Department of Microbiology, Raiganj University, Uttar Dinajpur, Raiganj, West Bengal 733134, India
| | | | - Anju Rani
- Department of Microbiology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand 248002, India
| | - Hrudayanath Thatoi
- Centre for Industrial Biotechnology Research, School of Pharmaceutical Sciences, Siksha ‘O’ Anusandhan, Deemed to be University, Kalinga Nagar, Bhubaneswar, Odisha 751003, India
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8
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He H, Zheng W, Xiao S, Gong L, Li H, Zhou K, Zhang L, Tu Q, Zhu YZ, Zhang Y. Deciphering the Nitrogen Fixation Gene Cluster in Vibrio natriegens: A Study on Optimized Expression and Application of Nitrogenase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:12618-12629. [PMID: 38778776 DOI: 10.1021/acs.jafc.4c01232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Microbial nitrogen fixation presents a viable alternative to chemical fertilizers, yet the limited colonization and specificity of naturally occurring nitrogen-fixing microorganisms present significant challenges to their widespread application. In this study, we identified a nitrogen fixation gene cluster (VNnif) in Vibrio natriegens (VN) and tested its nitrogenase activity through the acetylene reduction assay. We investigated the potential utilization of nitrogenase by incorporating the nitrogenase gene cluster from VN into plant growth-promoting rhizosphere bacteria Pseudomonas protegens CHA0 and enhancing its activity to 48.16 nmol C2H2/mg/h through promoter replacement and cluster rearrangement. The engineered strain CHA0-PVNnif was found to positively impact the growth of Arabidopsis thaliana col-0 and Triticum aestivum L. (wheat). This study expanded the role of plant growth-promoting rhizobacteria (PGPR) and provided a research foundation for enhancing nitrogenase activity.
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Affiliation(s)
- Haocheng He
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Weijin Zheng
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- College of Life and Geographic Sciences, Kashi University, Kashi 844099, China
| | - Shuai Xiao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Liang Gong
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - He Li
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau SAR 999078, China
| | - Kexuan Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau SAR 999078, China
| | - Letian Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- State Key Lab of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Qiang Tu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yi Zhun Zhu
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau SAR 999078, China
- State Key Lab of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Youming Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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9
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Guden RM, Haegeman A, Ruttink T, Moens T, Derycke S. Nematodes alter the taxonomic and functional profiles of benthic bacterial communities: A metatranscriptomic approach. Mol Ecol 2024; 33:e17331. [PMID: 38533629 DOI: 10.1111/mec.17331] [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: 06/21/2023] [Revised: 02/25/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024]
Abstract
Marine sediments cover 70% of the Earth's surface, and harbour diverse bacterial communities critical for marine biogeochemical processes, which affect climate change, biodiversity and ecosystem functioning. Nematodes, the most abundant and species-rich metazoan organisms in marine sediments, in turn, affect benthic bacterial communities and bacterial-mediated ecological processes, but the underlying mechanisms by which they affect biogeochemical cycles remain poorly understood. Here, we demonstrate using a metatranscriptomic approach that nematodes alter the taxonomic and functional profiles of benthic bacterial communities. We found particularly strong stimulation of nitrogen-fixing and methane-oxidizing bacteria in the presence of nematodes, as well as increased functional activity associated with methane metabolism and degradation of various carbon compounds. This study provides empirical evidence that the presence of nematodes results in taxonomic and functional shifts in active bacterial communities, indicating that nematodes may play an important role in benthic ecosystem processes.
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Affiliation(s)
- Rodgee Mae Guden
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Annelies Haegeman
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Tom Moens
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Sofie Derycke
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium
- Aquatic Environment and Quality, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Oostende, Belgium
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10
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Addison H, Glatter T, K. A. Hochberg G, Rebelein JG. Two distinct ferredoxins are essential for nitrogen fixation by the iron nitrogenase in Rhodobacter capsulatus. mBio 2024; 15:e0331423. [PMID: 38377621 PMCID: PMC10936413 DOI: 10.1128/mbio.03314-23] [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: 12/07/2023] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Abstract
Nitrogenases are the only enzymes able to fix gaseous nitrogen into bioavailable ammonia and hence are essential for sustaining life. Catalysis by nitrogenases requires both a large amount of ATP and electrons donated by strongly reducing ferredoxins or flavodoxins. Our knowledge about the mechanisms of electron transfer to nitrogenase enzymes is limited: The electron transport to the iron (Fe)-nitrogenase has hardly been investigated. Here, we characterized the electron transfer pathway to the Fe-nitrogenase in Rhodobacter capsulatus via proteome analyses, genetic deletions, complementation studies, and phylogenetics. Proteome analyses revealed an upregulation of four ferredoxins under nitrogen-fixing conditions reliant on the Fe-nitrogenase in a molybdenum nitrogenase knockout strain, compared to non-nitrogen-fixing conditions. Based on these findings, R. capsulatus strains with deletions of ferredoxin (fdx) and flavodoxin (fld, nifF) genes were constructed to investigate their roles in nitrogen fixation by the Fe-nitrogenase. R. capsulatus deletion strains were characterized by monitoring diazotrophic growth and Fe-nitrogenase activity in vivo. Only deletions of fdxC or fdxN resulted in slower growth and reduced Fe-nitrogenase activity, whereas the double deletion of both fdxC and fdxN abolished diazotrophic growth. Differences in the proteomes of ∆fdxC and ∆fdxN strains, in conjunction with differing plasmid complementation behaviors of fdxC and fdxN, indicate that the two Fds likely possess different roles and functions. These findings will guide future engineering of the electron transport systems to nitrogenase enzymes, with the aim of increased electron flux and product formation.IMPORTANCENitrogenases are essential for biological nitrogen fixation, converting atmospheric nitrogen gas to bioavailable ammonia. The production of ammonia by diazotrophic organisms, harboring nitrogenases, is essential for sustaining plant growth. Hence, there is a large scientific interest in understanding the cellular mechanisms for nitrogen fixation via nitrogenases. Nitrogenases rely on highly reduced electrons to power catalysis, although we lack knowledge as to which proteins shuttle the electrons to nitrogenases within cells. Here, we characterized the electron transport to the iron (Fe)-nitrogenase in the model diazotroph Rhodobacter capsulatus, showing that two distinct ferredoxins are very important for nitrogen fixation despite having different redox centers. In addition, our research expands upon the debate on whether ferredoxins have functional redundancy or perform distinct roles within cells. Here, we observe that both essential ferredoxins likely have distinct roles based on differential proteome shifts of deletion strains and different complementation behaviors.
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Affiliation(s)
- Holly Addison
- Microbial Metalloenzymes Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Timo Glatter
- Core Facility for Mass Spectrometry & Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Georg K. A. Hochberg
- Evolutionary Biochemistry Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg, Germany
| | - Johannes G. Rebelein
- Microbial Metalloenzymes Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg, Germany
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11
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Guo J, Wang X, Cao X, Qi W, Peng J, Liu H, Qu J. The influence of wet-to-dry season shifts on the microbial community stability and nitrogen cycle in the Poyang Lake sediment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166036. [PMID: 37544457 DOI: 10.1016/j.scitotenv.2023.166036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/10/2023] [Accepted: 08/02/2023] [Indexed: 08/08/2023]
Abstract
In lake environments, seasonal changes can cause exposure of the lake sediment, leading to soil formation. Although previous studies have explored how environmental changes influence microbial functioning in the water-level-fluctuating zone, few studies have investigated how wholescale habitat changes affect microbial composition, community stability and ecological functions in lake environments. To address this issue, our study investigated the effects of sediment-to-soil conversion on microbial composition, community stability and subsequent ecological functioning in Poyang Lake, China. Our results revealed that, during sediment-to-soil conversion, the number of total and unique operational taxonomic units (OTUs) decreased by 40 % and 55 %, respectively. Moreover, sediment-to-soil conversion decreased the microbial community connectivity and complexity while significantly increasing its stability, as evidenced by increased absolute values of negative/positive cohesion. In sediment and soil, the abundance of dominant bacteria, and bacterial diversity strongly affected microbial community stability, although this phenomenon was not true in water. Furthermore, the specific microbial phyla and genes involved in the nitrogen cycle changed significantly following sediment-to-soil conversion, with the major nitrogen cycling processes altering from denitrification and dissimilatory nitrate reduction to ammonium to nitrification and assimilatory nitrate reduction to ammonia. Moreover, a compensation mechanism was observed in the functional genes related to the nitrogen cycle, such that all the processes in the nitrogen cycle were maintained following sediment-to-soil conversion. The oxidation-reduction potential strongly affected network complexity, microbial stability, and nitrogen cycling in the sediment and soil. These results aid in the understanding of responses of microorganisms to climate change and extreme drought. Our findings have considerable implications for predicting the ecological consequences of habitat conversion and for ecosystem management.
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Affiliation(s)
- Jiaxun Guo
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xu Wang
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xiaofeng Cao
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Weixiao Qi
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| | - Jianfeng Peng
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Huijuan Liu
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jiuhui Qu
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
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12
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Tang K, Liang Y, Yuan B, Meng J, Feng F. Spatial distribution and core community of diazotrophs in Biological soil crusts and subsoils in temperate semi-arid and arid deserts of China. Front Microbiol 2023; 14:1074855. [PMID: 37608942 PMCID: PMC10440438 DOI: 10.3389/fmicb.2023.1074855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 07/25/2023] [Indexed: 08/24/2023] Open
Abstract
Introduction Biological soil crusts (BSCs) are distributed in arid and semiarid regions, and they function as important microhabitats for nitrogen fixation. The diazotroph community is critical for nitrogen fixation in BSCs and their subsoils. However, little is known about the key groups in different types of BSCs and subsoils in temperate semi-arid or arid deserts. Methods Here, we sampled three types of BSCs and their subsoils from the Inner Mongolian plateau, investigated the distribution characteristics of the diazotroph community by high-throughput sequencing, predicted keystone species using the molecular ecological network analyses pipeline (MENAP), and verified their close relationship with the available nitrogen (AN) content. Results The results showed that available nitrogen content in BSCs was higher than that in subsoils in three different types of BSCs, and there were differences among seasons and according to the mean annual precipitation. The abundance of diazotrophs was higher in Cyano-BSCs, while diversity had no significant difference among BSCs and subsoils. Cyanobacteria and Proteobacteria, Nostocaceae and Scytonemataceae, Skermanella, Scytonema, Azohydromonas, Nostoc and Trichormus were the dominant phyla, families, and genera, respectively. The dominant groups belong to Skermanella, Scytonema, and Nostoc formed the core diazotroph community in the three types of BSCs and subsoils, and each had a close relationship with AN. Discussion These results indicate that diazotrophs in BSCs and subsoils had high diversity, and the core diazotroph communities have a close relationship with nitrogen fixation and that they may be the main contributor to nitrogen fixing in BSCs and subsoils in temperate deserts.
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Affiliation(s)
- Kai Tang
- Laboratory for Environmental Microbiology and Biotechnology in Arid and Cold Regions, College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Yungang Liang
- Laboratory for Environmental Microbiology and Biotechnology in Arid and Cold Regions, College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Bo Yuan
- Laboratory for Environmental Microbiology and Biotechnology in Arid and Cold Regions, College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
- College of Life Science, Inner Mongolia Normal University, Hohhot, China
| | - Jianyu Meng
- Laboratory for Environmental Microbiology and Biotechnology in Arid and Cold Regions, College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Fuying Feng
- Laboratory for Environmental Microbiology and Biotechnology in Arid and Cold Regions, College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
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13
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Chen L, Shi Y, Wang S, Sun M, Wang M, Ren X, Gao Z, Zhou Y, Zhang J, Zhuang W, Su X, Fu Y, Wu M. Temperature and phosphorus: the main environmental factors affecting the seasonal variation of soil bacterial diversity in Nansi Lake Wetland. Front Microbiol 2023; 14:1169444. [PMID: 37455734 PMCID: PMC10348425 DOI: 10.3389/fmicb.2023.1169444] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/01/2023] [Indexed: 07/18/2023] Open
Abstract
Introduction The soil bacteria promote the circulation conversion of lake nutrients and play an important role in maintaining the balance of the lake ecosystem. Few studies have investigated the association of seasonal variation in bacteria and environmental factors in inland freshwater lake wetlands. Nansi Lake is a large shallow freshwater lake in northern China. It is an important hub of the eastern route of the South-to-North Water Diversion Project. Methods In this study, bacterial 16S rRNA genes were used to analyze the variation of soil bacterial community diversity in Nansi Lake Wetland and its influencing factors in different seasons. Results It is showed that the phylum, family, and genus with the largest relative abundance in the soil of Nansi Lake Wetland are Proteobacteria, Nitrosomonadaceae, and MND1, respectively. There were significant seasonal differences in soil bacterial diversity in Nansi Lake Wetland, which was significantly higher in summer than in winter. Seasonal variation in environmental factors was significantly correlated with the variation in bacterial communities. Temperature and the content of available phosphorus may be the key factors influencing seasonal variation in bacterial diversity. Discussion The results of this study further enhance our understanding of the relationship between bacterial community diversity and environmental factors in the lake wetland ecosystem, which can provide scientific data for the conservation of Nansi Lake Wetland.
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Affiliation(s)
- Lei Chen
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Yuying Shi
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Shen Wang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Mengyao Sun
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Meng Wang
- Lunan Geo-Engineering Exploration Institute of Shandong Province, Yanzhou, Shandong, China
| | - Xiaoyue Ren
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Zenghao Gao
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Yiping Zhou
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Jie Zhang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Weijing Zhuang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Xinyue Su
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Yongchao Fu
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Mengmeng Wu
- Shandong Freshwater Fisheries Research Institute, Jinan, Shandong, China
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14
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Fuchs W, Rachbauer L, Rittmann SKMR, Bochmann G, Ribitsch D, Steger F. Eight Up-Coming Biotech Tools to Combat Climate Crisis. Microorganisms 2023; 11:1514. [PMID: 37375016 DOI: 10.3390/microorganisms11061514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Biotechnology has a high potential to substantially contribute to a low-carbon society. Several green processes are already well established, utilizing the unique capacity of living cells or their instruments. Beyond that, the authors believe that there are new biotechnological procedures in the pipeline which have the momentum to add to this ongoing change in our economy. Eight promising biotechnology tools were selected by the authors as potentially impactful game changers: (i) the Wood-Ljungdahl pathway, (ii) carbonic anhydrase, (iii) cutinase, (iv) methanogens, (v) electro-microbiology, (vi) hydrogenase, (vii) cellulosome and, (viii) nitrogenase. Some of them are fairly new and are explored predominantly in science labs. Others have been around for decades, however, with new scientific groundwork that may rigorously expand their roles. In the current paper, the authors summarize the latest state of research on these eight selected tools and the status of their practical implementation. We bring forward our arguments on why we consider these processes real game changers.
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Affiliation(s)
- Werner Fuchs
- Department IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria
| | - Lydia Rachbauer
- Lawrence Berkeley National Laboratory, Deconstruction Division at the Joint Bioenergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA
| | - Simon K-M R Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Djerassiplatz 1, 1030 Wien, Austria
| | - Günther Bochmann
- Department IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria
| | - Doris Ribitsch
- ACIB-Austrian Centre of Industrial Biotechnology, Krenngasse 37, 8010 Graz, Austria
| | - Franziska Steger
- Department IFA-Tulln, Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences, Vienna, Konrad-Lorenz-Strasse 20, 3430 Tulln, Austria
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15
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Gonzalez-Nayeck AC, Grim SL, Waldbauer J, Dick GJ, Pearson A. Isotopic Signatures of Carbon Transfer in a Proterozoic Analogue Microbial Mat. Appl Environ Microbiol 2023; 89:e0187022. [PMID: 37093010 PMCID: PMC10231192 DOI: 10.1128/aem.01870-22] [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: 11/04/2022] [Accepted: 03/24/2023] [Indexed: 04/25/2023] Open
Abstract
Modern microbial mats are potential analogues for Proterozoic ecosystems, yet only a few studies have characterized mats under low-oxygen conditions that are relevant to Proterozoic environments. Here, we use protein-stable isotope fingerprinting (P-SIF) to determine the protein carbon isotope (δ13C) values of autotrophic, heterotrophic, and mixotrophic organisms in a benthic microbial mat from the low-oxygen Middle Island Sinkhole, Lake Huron, USA (MIS). We also measure the δ13C values of the sugar moieties of exopolysaccharides (EPS) within the mat to explore the relationships between cyanobacterial exudates and heterotrophic anabolic carbon uptake. Our results show that Cyanobacteria (autotrophs) are 13C-depleted, relative to sulfate-reducing bacteria (heterotrophs), and 13C-enriched, relative to sulfur oxidizing bacteria (autotrophs or mixotrophs). We also find that the pentose moieties of EPS are systematically enriched in 13C, relative to the hexose moieties of EPS. We hypothesize that these isotopic patterns reflect cyanobacterial metabolic pathways, particularly phosphoketolase, that are relatively more active in low-oxygen mat environments, rather than oxygenated mat environments. This results in isotopically more heterogeneous C sources in low-oxygen mats. While this might partially explain the isotopic variability observed in Proterozoic mat facies, further work is necessary to systematically characterize the isotopic fractionations that are associated with the synthesis of cyanobacterial exudates. IMPORTANCE The δ13C compositions of heterotrophic microorganisms are dictated by the δ13C compositions of their organic carbon sources. In both modern and ancient photosynthetic microbial mats, photosynthetic exudates are the most likely source of organic carbon for heterotrophs. We measured the δ13C values of autotrophic, heterotrophic, and mixotrophic bacteria as well as the δ13C value of the most abundant photosynthetic exudate (exopolysaccharide) in a modern analogue for a Proterozoic environment. Given these data, future studies will be better equipped to estimate the most likely carbon source for heterotrophs in both modern environments as well as in Proterozoic environments preserved in the rock record.
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Affiliation(s)
- Ana C. Gonzalez-Nayeck
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Sharon L. Grim
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Jacob Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - Gregory J. Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
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16
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Tarasashvili MV, Elbakidze K, Doborjginidze ND, Gharibashvili ND. Carbonate precipitation and nitrogen fixation in AMG (Artificial Martian Ground) by cyanobacteria. LIFE SCIENCES IN SPACE RESEARCH 2023; 37:65-77. [PMID: 37087180 DOI: 10.1016/j.lssr.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/22/2023] [Accepted: 03/06/2023] [Indexed: 05/03/2023]
Abstract
This article describes experiments performed to study the survival, growth, specific adaptations and bioremediation potential of certain extreme cyanobacteria strains within a simulation of the atmospheric composition, temperature and pressure expected in a future Martian greenhouse. Initial species have been obtained from Mars-analogue sites in Georgia. The results clearly demonstrate that specific biochemical adaptations allow these autotrophs to metabolize within AMG (Artificial Martian Ground) and accumulate biogenic carbon and nitrogen. These findings may thus contribute to the development of future Martian agriculture, as well as other aspects of the life-support systems at habitable Mars stations. The study shows that carbonate precipitation and nitrogen fixation, performed by cyanobacterial communities thriving within the simulated Martian greenhouse conditions, are cross-linked biological processes. At the same time, the presence of the perchlorates (at low concentrations) in the Martian ground may serve as the initial source of oxygen and, indirectly, hydrogen via photo-Fenton reactions. Various carbonates, ammonium and nitrate salts were obtained as the result of these experiments. These affect the pH, salinity and solubility of the AMG and its components, and so the AMG's scanty biogenic properties improved, which is essential for the sustainable growth of the agricultural crops. Therefore, the use of microorganisms for the biological remediation and continuous in situ fertilization of Artificial Martian Ground is possible.
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Affiliation(s)
- M V Tarasashvili
- BTU - Business and Technology University, 82 Ilia Chavchavadze Avenue, 0179, Tbilisi, Georgia.
| | - Kh Elbakidze
- BTU - Business and Technology University, 82 Ilia Chavchavadze Avenue, 0179, Tbilisi, Georgia
| | - N D Doborjginidze
- GSRA - Georgian Space Research Agency, 4 Vasil Petriashvili Street, 0179, Tbilisi, Georgia
| | - N D Gharibashvili
- GSRA - Georgian Space Research Agency, 4 Vasil Petriashvili Street, 0179, Tbilisi, Georgia; SpaceFarms Ltd, 14 Kostava Street, 0108, Tbilisi, Georgia
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17
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Saleem F, Jiang JL, Atrache R, Paschos A, Edge TA, Schellhorn HE. Cyanobacterial Algal Bloom Monitoring: Molecular Methods and Technologies for Freshwater Ecosystems. Microorganisms 2023; 11:microorganisms11040851. [PMID: 37110273 PMCID: PMC10144707 DOI: 10.3390/microorganisms11040851] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Cyanobacteria (blue-green algae) can accumulate to form harmful algal blooms (HABs) on the surface of freshwater ecosystems under eutrophic conditions. Extensive HAB events can threaten local wildlife, public health, and the utilization of recreational waters. For the detection/quantification of cyanobacteria and cyanotoxins, both the United States Environmental Protection Agency (USEPA) and Health Canada increasingly indicate that molecular methods can be useful. However, each molecular detection method has specific advantages and limitations for monitoring HABs in recreational water ecosystems. Rapidly developing modern technologies, including satellite imaging, biosensors, and machine learning/artificial intelligence, can be integrated with standard/conventional methods to overcome the limitations associated with traditional cyanobacterial detection methodology. We examine advances in cyanobacterial cell lysis methodology and conventional/modern molecular detection methods, including imaging techniques, polymerase chain reaction (PCR)/DNA sequencing, enzyme-linked immunosorbent assays (ELISA), mass spectrometry, remote sensing, and machine learning/AI-based prediction models. This review focuses specifically on methodologies likely to be employed for recreational water ecosystems, especially in the Great Lakes region of North America.
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18
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Sidabras JW, Stripp ST. A personal account on 25 years of scientific literature on [FeFe]-hydrogenase. J Biol Inorg Chem 2023; 28:355-378. [PMID: 36856864 DOI: 10.1007/s00775-023-01992-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 01/25/2023] [Indexed: 03/02/2023]
Abstract
[FeFe]-hydrogenases are gas-processing metalloenzymes that catalyze H2 oxidation and proton reduction (H2 release) in microorganisms. Their high turnover frequencies and lack of electrical overpotential in the hydrogen conversion reaction has inspired generations of biologists, chemists, and physicists to explore the inner workings of [FeFe]-hydrogenase. Here, we revisit 25 years of scientific literature on [FeFe]-hydrogenase and propose a personal account on 'must-read' research papers and review article that will allow interested scientists to follow the recent discussions on catalytic mechanism, O2 sensitivity, and the in vivo synthesis of the active site cofactor with its biologically uncommon ligands carbon monoxide and cyanide. Focused on-but not restricted to-structural biology and molecular biophysics, we highlight future directions that may inspire young investigators to pursue a career in the exciting and competitive field of [FeFe]-hydrogenase research.
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Affiliation(s)
- Jason W Sidabras
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI, USA, 53226.
| | - Sven T Stripp
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany.
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19
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Trebuch LM, Schoofs K, Vaessen SMF, Neu TR, Janssen M, Wijffels RH, Vet LEM, Fernandes TV. N 2 -fixation can sustain wastewater treatment performance of photogranules under nitrogen-limiting conditions. Biotechnol Bioeng 2023; 120:1303-1315. [PMID: 36779371 DOI: 10.1002/bit.28349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/23/2022] [Accepted: 02/09/2023] [Indexed: 02/14/2023]
Abstract
Wastewater characteristics can vary significantly, and in some municipal wastewaters the N:P ratio is as low as 5 resulting in nitrogen-limiting conditions. In this study, the microbial community, function, and morphology of photogranules under nitrogen-replete (N+) and limiting (N-) conditions was assessed in sequencing batch reactors. Photogranules under N- condition were nitrogen deprived 2/3 of a batch cycle duration. Surprisingly, this nitrogen limitation had no adverse effect on biomass productivity. Moreover, phosphorus and chemical oxygen demand removal were similar to their removal under N+ conditions. Although performance was similar, the difference in granule morphology was obvious. While N+ photogranules were dense and structurally confined, N- photogranules showed loose structures with occasional voids. Microbial community analysis revealed high abundance of cyanobacteria capable of N2 -fixation. These were higher at N- (38%) than N+ (29%) treatments, showing that photogranules could adjust and maintain treatment performance and high biomass productivity by means of N2 -fixation.
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Affiliation(s)
- Lukas M Trebuch
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Bioprocess Engineering, AlgaePARC Wageningen University, Wageningen, The Netherlands
| | - Kobe Schoofs
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Bioprocess Engineering, AlgaePARC Wageningen University, Wageningen, The Netherlands
| | - Stijn M F Vaessen
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Bioprocess Engineering, AlgaePARC Wageningen University, Wageningen, The Netherlands
| | - Thomas R Neu
- Microbiology of Interfaces, Department River Ecology, Helmholtz Centre for Environmental Research - UFZ, Magdeburg, Germany
| | - Marcel Janssen
- Bioprocess Engineering, AlgaePARC Wageningen University, Wageningen, The Netherlands
| | - René H Wijffels
- Bioprocess Engineering, AlgaePARC Wageningen University, Wageningen, The Netherlands.,Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Louise E M Vet
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Tânia V Fernandes
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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20
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Molecular hydrogen in seawater supports growth of diverse marine bacteria. Nat Microbiol 2023; 8:581-595. [PMID: 36747116 DOI: 10.1038/s41564-023-01322-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/05/2023] [Indexed: 02/08/2023]
Abstract
Molecular hydrogen (H2) is an abundant and readily accessible energy source in marine systems, but it remains unknown whether marine microbial communities consume this gas. Here we use a suite of approaches to show that marine bacteria consume H2 to support growth. Genes for H2-uptake hydrogenases are prevalent in global ocean metagenomes, highly expressed in metatranscriptomes and found across eight bacterial phyla. Capacity for H2 oxidation increases with depth and decreases with oxygen concentration, suggesting that H2 is important in environments with low primary production. Biogeochemical measurements of tropical, temperate and subantarctic waters, and axenic cultures show that marine microbes consume H2 supplied at environmentally relevant concentrations, yielding enough cell-specific power to support growth in bacteria with low energy requirements. Conversely, our results indicate that oxidation of carbon monoxide (CO) primarily supports survival. Altogether, H2 is a notable energy source for marine bacteria and may influence oceanic ecology and biogeochemistry.
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21
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Chinchusak N, Incharoensakdi A, Phunpruch S. Dark fermentative hydrogen production and transcriptional analysis of genes involved in the unicellular halotolerant cyanobacterium Aphanothece halophytica under nitrogen and potassium deprivation. Front Bioeng Biotechnol 2023; 10:1028151. [PMID: 36686224 PMCID: PMC9852855 DOI: 10.3389/fbioe.2022.1028151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 12/19/2022] [Indexed: 01/09/2023] Open
Abstract
The unicellular halotolerant cyanobacterium Aphanothece halophytica is known as a potential hydrogen (H2) producer. This study aimed to investigate the enhancement of H2 production under nutrient deprivation. The results showed that nitrogen and potassium deprivation induced dark fermentative H2 production by A. halophytica, while no differences in H2 production were found under sulfur and phosphorus deprivation. In addition, deprivation of nitrogen and potassium resulted in the highest H2 production in A. halophytica due to the stimulation of hydrogenase activity. The effect of adaptation time under nitrogen and potassium deprivation on H2 production was investigated. The results showed that the highest H2 accumulation of 1,261.96 ± 96.99 µmol H2 g dry wt-1 and maximum hydrogenase activity of 179.39 ± 8.18 µmol H2 g dry wt-1 min-1 were obtained from A. halophytica cells adapted in the nitrogen- and potassium-deprived BG11 medium supplemented with Turk Island salt solution (BG110-K) for 48 h. An increase in hydrogenase activity was attributed to the decreased O2 concentration in the system, due to a reduction of photosynthetic O2 evolution rate and a promotion of dark respiration rate. Moreover, nitrogen and potassium deprivation stimulated glycogen accumulation and decreased specific activity of pyruvate kinase. Transcriptional analysis of genes involved in H2 metabolism using RNA-seq confirmed the above results. Several genes involved in glycogen biosynthesis (glgA, glgB, and glgP) were upregulated under both nitrogen and potassium deprivation, but genes regulating enzymes in the glycolytic pathway were downregulated, especially pyk encoding pyruvate kinase. Interestingly, genes involved in the oxidative pentose phosphate pathway (OPP) were upregulated. Thus, OPP became the favored pathway for glycogen catabolism and the generation of reduced nicotinamide adenine dinucleotide phosphate (NADPH), which resulted in an increase in H2 production under dark anaerobic condition in both nitrogen- and potassium-deprived cells.
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Affiliation(s)
- Nattanon Chinchusak
- Department of Biology, School of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Aran Incharoensakdi
- Laboratory of Cyanobacterial Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand,Academy of Science, Royal Society of Thailand, Bangkok, Thailand
| | - Saranya Phunpruch
- Department of Biology, School of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok, Thailand,Bioenergy Research Unit, School of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok, Thailand,*Correspondence: Saranya Phunpruch,
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22
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Ferrari M, Muto A, Bruno L, Cozza R. DNA Methylation in Algae and Its Impact on Abiotic Stress Responses. PLANTS (BASEL, SWITZERLAND) 2023; 12:241. [PMID: 36678953 PMCID: PMC9861306 DOI: 10.3390/plants12020241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Epigenetics, referring to heritable gene regulatory information that is independent of changes in DNA sequences, is an important mechanism involved both in organism development and in the response to environmental events. About the epigenetic marks, DNA methylation is one of the most conserved mechanisms, playing a pivotal role in organism response to several biotic and abiotic stressors. Indeed, stress can induce changes in gene expression through hypo- or hyper-methylation of DNA at specific loci and/or in DNA methylation at the genome-wide level, which has an adaptive significance and can direct genome evolution. Exploring DNA methylation in responses to abiotic stress could have important implications for improving stress tolerance in algae. This article summarises the DNA methylation pattern in algae and its impact on abiotic stress, such as heavy metals, nutrients and temperature. Our discussion provides information for further research in algae for a better comprehension of the epigenetic response under abiotic stress, which could favour important implications to sustain algae growth under abiotic stress conditions, often related to high biosynthesis of interesting metabolites.
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Kireev NV, Filippov OA, Epstein LM, Shubina ES, Belkova NV. Activation of dinitrogen by group 6 metal complexes. Russ Chem Bull 2023. [DOI: 10.1007/s11172-023-3716-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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Khetkorn W, Raksajit W, Maneeruttanarungroj C, Lindblad P. Photobiohydrogen Production and Strategies for H 2 Yield Improvements in Cyanobacteria. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 183:253-279. [PMID: 37009974 DOI: 10.1007/10_2023_216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
Hydrogen gas (H2) is one of the potential future sustainable and clean energy carriers that may substitute the use of fossil resources including fuels since it has a high energy content (heating value of 141.65 MJ/kg) when compared to traditional hydrocarbon fuels [1]. Water is a primary product of combustion being a most significant advantage of H2 being environmentally friendly with the capacity to reduce global greenhouse gas emissions. H2 is used in various applications. It generates electricity in fuel cells, including applications in transportation, and can be applied as fuel in rocket engines [2]. Moreover, H2 is an important gas and raw material in many industrial applications. However, the high cost of the H2 production processes requiring the use of other energy sources is a significant disadvantage. At present, H2 can be prepared in many conventional ways, such as steam reforming, electrolysis, and biohydrogen production processes. Steam reforming uses high-temperature steam to produce hydrogen gas from fossil resources including natural gas. Electrolysis is an electrolytic process to decompose water molecules into O2 and H2. However, both these two methods are energy-intensive and producing hydrogen from natural gas, which is mostly methane (CH4) and in steam reforming generates CO2 and pollutants as by-products. On the other hand, biological hydrogen production is more environmentally sustainable and less energy intensive than thermochemical and electrochemical processes [3], but most concepts are not yet developed to production scale.
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Affiliation(s)
- Wanthanee Khetkorn
- Division of Biology, Faculty of Science and Technology, Rajamangala University of Technology, Thanyaburi, Pathum Thani, Thailand
| | - Wuttinun Raksajit
- Faculty of Veterinary Technology, Program of Animal Health Technology, Kasetsart University, Bangkok, Thailand
| | - Cherdsak Maneeruttanarungroj
- Department of Biology, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
- Bioenergy Research Unit, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Uppsala, Sweden.
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Santana‐Sánchez A, Nikkanen L, Werner E, Tóth G, Ermakova M, Kosourov S, Walter J, He M, Aro E, Allahverdiyeva Y. Flv3A facilitates O 2 photoreduction and affects H 2 photoproduction independently of Flv1A in diazotrophic Anabaena filaments. THE NEW PHYTOLOGIST 2023; 237:126-139. [PMID: 36128660 PMCID: PMC10092803 DOI: 10.1111/nph.18506] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 09/10/2022] [Indexed: 05/23/2023]
Abstract
The model heterocyst-forming filamentous cyanobacterium Anabaena sp. PCC 7120 (Anabaena) is a typical example of a multicellular organism capable of simultaneously performing oxygenic photosynthesis in vegetative cells and O2 -sensitive N2 -fixation inside heterocysts. The flavodiiron proteins have been shown to participate in photoprotection of photosynthesis by driving excess electrons to O2 (a Mehler-like reaction). Here, we performed a phenotypic and biophysical characterization of Anabaena mutants impaired in vegetative-specific Flv1A and Flv3A in order to address their physiological relevance in the bioenergetic processes occurring in diazotrophic Anabaena under variable CO2 conditions. We demonstrate that both Flv1A and Flv3A are required for proper induction of the Mehler-like reaction upon a sudden increase in light intensity, which is likely important for the activation of carbon-concentrating mechanisms and CO2 fixation. Under ambient CO2 diazotrophic conditions, Flv3A is responsible for moderate O2 photoreduction, independently of Flv1A, but only in the presence of Flv2 and Flv4. Strikingly, the lack of Flv3A resulted in strong downregulation of the heterocyst-specific uptake hydrogenase, which led to enhanced H2 photoproduction under both oxic and micro-oxic conditions. These results reveal a novel regulatory network between the Mehler-like reaction and the diazotrophic metabolism, which is of great interest for future biotechnological applications.
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Affiliation(s)
- Anita Santana‐Sánchez
- Molecular Plant Biology, Department of Life TechnologiesUniversity of TurkuTurkuFI‐20014Finland
| | - Lauri Nikkanen
- Molecular Plant Biology, Department of Life TechnologiesUniversity of TurkuTurkuFI‐20014Finland
| | - Elisa Werner
- Molecular Plant Biology, Department of Life TechnologiesUniversity of TurkuTurkuFI‐20014Finland
| | - Gábor Tóth
- Molecular Plant Biology, Department of Life TechnologiesUniversity of TurkuTurkuFI‐20014Finland
| | - Maria Ermakova
- Molecular Plant Biology, Department of Life TechnologiesUniversity of TurkuTurkuFI‐20014Finland
| | - Sergey Kosourov
- Molecular Plant Biology, Department of Life TechnologiesUniversity of TurkuTurkuFI‐20014Finland
| | - Julia Walter
- Molecular Plant Biology, Department of Life TechnologiesUniversity of TurkuTurkuFI‐20014Finland
| | - Meilin He
- Molecular Plant Biology, Department of Life TechnologiesUniversity of TurkuTurkuFI‐20014Finland
| | - Eva‐Mari Aro
- Molecular Plant Biology, Department of Life TechnologiesUniversity of TurkuTurkuFI‐20014Finland
| | - Yagut Allahverdiyeva
- Molecular Plant Biology, Department of Life TechnologiesUniversity of TurkuTurkuFI‐20014Finland
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Thanigaivel S, Rajendran S, Hoang TKA, Ahmad A, Luque R. Photobiological effects of converting biomass into hydrogen - Challenges and prospects. BIORESOURCE TECHNOLOGY 2023; 367:128278. [PMID: 36351535 DOI: 10.1016/j.biortech.2022.128278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
In comparison to other methods of producing hydrogen, the production of biohydrogen is significantly less harmful to the surrounding ecosystem when it was produced from the biological origin such as microalgae. It could take the place of conventional fossil fuels while avoiding the emission of greenhouse gases. The substrates such as food, agricultural waste, and industrial waste can be readily utilized after the necessary pretreatment, led to an increase in the yield of hydrogen. Improving the production of biofuels at each stage can have a significant impact on the final results, making this method a potentially useful instrument. As a consequence of this, numerous approaches to pretreat the algal biomass, numerous types of enzymes and catalyst that play a crucial role for hydrogen production, the variables that influence the production of hydrogen, and the potential applications of genetic engineering have all been comprehensively covered in this study.
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Affiliation(s)
- S Thanigaivel
- Department of Biotechnology, Faculty of Science & Humanities, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603203, India
| | - Saravanan Rajendran
- Departamento de Ingeniería Mecánica, Facultad de Ingeniería, Universidad de Tarapacá, Avda. General Velásquez 1775, Arica, Chile.
| | - Tuan K A Hoang
- Centre of Excellence in Transportation Electrification and Energy Storage, Hydro-Québec, 1806, boul. Lionel-Boulet, Varennes J3X 1S1, Canada
| | - Awais Ahmad
- Departamento de Quimica Organica, Universidad de Cordoba, Edificio Marie Curie (C-3), Ctra Nnal IV-A, Km 396, E14014 Cordoba, Spain
| | - Rafael Luque
- Departamento de Quimica Organica, Universidad de Cordoba, Edificio Marie Curie (C-3), Ctra Nnal IV-A, Km 396, E14014 Cordoba, Spain; Peoples Friendship University of Russia (RUDN University), 6 Miklukho Maklaya str., 117198 Moscow, Russian Federation
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27
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Liyun C. Influence of inoculation ratio on the performance and microbial community of bacterial-algal symbiotic system for rural wastewater treatment. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2023; 95:e10838. [PMID: 36744534 DOI: 10.1002/wer.10838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
In this study, co-culture of microalgae and activated sludge in photobioreactors (PBRs) was investigated at different inoculation ratios (0:1, 0.3:1, 0.7:1, and 1.3:1 sludge wt./algae wt.) for rural domestic wastewater treatment under direct solar radiation. Effluent qualities (such as pH, NO2 - , PO4 3- , and NH4 + -N concentrations) were assessed; bacterial and microalgal communities in co-culture system were compared. The microalgal and bacterial biomass fraction played a significant role in the performance and microbial community structure of the treatment system. In reactors with inoculation ratio of 0.3:1 and 0.7:1, the pH exceeded 9 or 10 under solar radiation, which led to some functional bacteria being missing. In the reactor with inoculation ratio of 1.3:1, activated sludge effectively prevented excessive increase in pH in the reactor. Similar observations were made for reactors with inoculation ratios below 1.3:1 by adding sludge halfway through the process. The results show that activated sludge can inhibit excessive increase in pH caused by algal photosynthesis, maintain the activity of nitrite-oxidizing bacteria in PBR, and reduce algae loss with the effluent. PRACTITIONER POINTS: Appropriate fraction of activated sludge can effectively inhibit the excessive increase in pH caused by algal photosynthesis in PBR. Adding activated sludge could maintain the activity of nitrite-oxidizing bacteria in PBR, and reduce microalgae loss with the effluent. Considering the stability of operation and biodiversity in PBR, a 1.3:1 inoculation ratio of activated sludge and microalgae is preferred.
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Affiliation(s)
- Cai Liyun
- Fujian Key University Laboratory of Estuarine Ecological Security and Environmental Health, School of Environmental Science and Engineering of Xiamen University TanKah Kee College, Zhangzhou, China
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Adam-Beyer N, Perner M. Activity-Based Screening of Metagenomic Fosmid Libraries for Hydrogen-Uptake Enzymes. Methods Mol Biol 2023; 2555:91-101. [PMID: 36306080 DOI: 10.1007/978-1-0716-2795-2_6] [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] [Indexed: 06/16/2023]
Abstract
Here, we outline how to identify hydrogenase enzymes from metagenomic fosmid libraries through an activity-based screening approach. A metagenomic fosmid library is constructed in E. coli and the fosmids are transferred into a hydrogenase deletion mutant of Shewanella oneidensis MR-1 (ΔhyaB) via triparental mating. If a fosmid clone exhibits hydrogen-uptake activity, S. oneidensis' phenotype is restored and hydrogenase activity is indicated by a color change of the medium from yellow to colorless. The screen enables screening of 48 metagenomic fosmid clones in parallel.
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Affiliation(s)
- Nicole Adam-Beyer
- Geomicrobiology, Department of Marine Biogeochemistry GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstraße, Kiel, Germany.
| | - Mirjam Perner
- Geomicrobiology, Department of Marine Biogeochemistry GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstraße, Kiel, Germany
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Eloffy MG, Elgarahy AM, Saber AN, Hammad A, El-Sherif DM, Shehata M, Mohsen A, Elwakeel KZ. Biomass-to-sustainable biohydrogen: insights into the production routes, and technical challenges. CHEMICAL ENGINEERING JOURNAL ADVANCES 2022. [DOI: 10.1016/j.ceja.2022.100410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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30
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Koch M, Noonan AJC, Qiu Y, Dofher K, Kieft B, Mottahedeh S, Shastri M, Hallam SJ. The survivor strain: isolation and characterization of Phormidium yuhuli AB48, a filamentous phototactic cyanobacterium with biotechnological potential. Front Bioeng Biotechnol 2022; 10:932695. [PMID: 36046667 PMCID: PMC9420970 DOI: 10.3389/fbioe.2022.932695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Despite their recognized potential, current applications of cyanobacteria as microbial cell factories remain in early stages of development. This is partly due to the fact that engineered strains are often difficult to grow at scale. This technical challenge contrasts with the dense and highly productive cyanobacteria populations thriving in many natural environments. It has been proposed that the selection of strains pre-adapted for growth in industrial photobioreactors could enable more productive cultivation outcomes. Here, we described the initial morphological, physiological, and genomic characterization of Phormidium yuhuli AB48 isolated from an industrial photobioreactor environment. P. yuhuli AB48 is a filamentous phototactic cyanobacterium with a growth rate comparable to Synechocystis sp. PCC 6803. The isolate forms dense biofilms under high salinity and alkaline conditions and manifests a similar nutrient profile to Arthrospira platensis (Spirulina). We sequenced, assembled, and analyzed the P. yuhuli AB48 genome, the first closed circular isolate reference genome for a member of the Phormidium genus. We then used cultivation experiments in combination with proteomics and metabolomics to investigate growth characteristics and phenotypes related to industrial scale cultivation, including nitrogen and carbon utilization, salinity, and pH acclimation, as well as antibiotic resistance. These analyses provide insight into the biological mechanisms behind the desirable growth properties manifested by P. yuhuli AB48 and position it as a promising microbial cell factory for industrial-scale bioproduction[221, 1631].
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Affiliation(s)
- Moritz Koch
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Avery J. C. Noonan
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, Canada
| | - Yilin Qiu
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
| | - Kalen Dofher
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
| | - Brandon Kieft
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | | | | | - Steven J. Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Steven J. Hallam,
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Stripp ST, Duffus BR, Fourmond V, Léger C, Leimkühler S, Hirota S, Hu Y, Jasniewski A, Ogata H, Ribbe MW. Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase. Chem Rev 2022; 122:11900-11973. [PMID: 35849738 PMCID: PMC9549741 DOI: 10.1021/acs.chemrev.1c00914] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Gases like H2, N2, CO2, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N2, CO2, and CO and the production of H2 require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N2 fixation by nitrogenase and H2 production by hydrogenase as well as CO2 and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.
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Affiliation(s)
- Sven T Stripp
- Freie Universität Berlin, Experimental Molecular Biophysics, Berlin 14195, Germany
| | | | - Vincent Fourmond
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Christophe Léger
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Institut Microbiologie, Bioénergies et Biotechnologie, CNRS, Aix Marseille Université, Marseille 13402, France
| | - Silke Leimkühler
- University of Potsdam, Molecular Enzymology, Potsdam 14476, Germany
| | - Shun Hirota
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan
| | - Yilin Hu
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Andrew Jasniewski
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Hideaki Ogata
- Nara Institute of Science and Technology, Division of Materials Science, Graduate School of Science and Technology, Nara 630-0192, Japan
- Hokkaido University, Institute of Low Temperature Science, Sapporo 060-0819, Japan
- Graduate School of Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Markus W Ribbe
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697-3900, United States
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
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Prasitwuttisak W, Hoshiko Y, Maeda T, Haraguchi A, Yanagawa K. Microbial Community Structures and Methanogenic Functions in Wetland Peat Soils. Microbes Environ 2022; 37. [PMID: 35851269 PMCID: PMC9530717 DOI: 10.1264/jsme2.me22004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methane metabolism in wetlands involves diverse groups of bacteria and archaea, which are responsible for the biological decomposition of organic matter under certain anoxic conditions. Recent advances in environmental omics revealed the phylogenetic diversity of novel microbial lineages, which have not been previously placed in the traditional tree of life. The present study aimed to verify the key players in methane production, either well-known archaeal members or recently identified lineages, in peat soils collected from wetland areas in Japan. Based on an analysis of microbial communities using 16S rRNA gene sequencing and the molecular cloning of the functional gene, mcrA, a marker gene for methanogenesis, methanogenic archaea belonging to Methanomicrobiales, Methanosarcinales, Methanobacteriales, and Methanomassiliicoccales were detected in anoxic peat soils, suggesting the potential of CH4 production in this natural wetland. “Candidatus Bathyarchaeia”, archaea with vast metabolic capabilities that is widespread in anoxic environments, was abundant in subsurface peat soils (up to 96% of the archaeal community) based on microbial gene quantification by qPCR. These results emphasize the importance of discovering archaea members outside of traditional methanogenic lineages that may have significant functions in the wetland biogeochemical cycle.
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Affiliation(s)
| | - Yuki Hoshiko
- Department of Biological Functions Engineering, Graduate School of Life Sciences and Systems Engineering, Kyushu Institute of Technology
| | - Toshinari Maeda
- Department of Biological Functions Engineering, Graduate School of Life Sciences and Systems Engineering, Kyushu Institute of Technology
| | - Akira Haraguchi
- Faculty of Environmental Engineering, The University of Kitakyushu
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Duan X, Zhang C, Struewing I, Li X, Allen J, Lu J. Cyanotoxin-encoding genes as powerful predictors of cyanotoxin production during harmful cyanobacterial blooms in an inland freshwater lake: Evaluating a novel early-warning system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 830:154568. [PMID: 35302035 PMCID: PMC9698223 DOI: 10.1016/j.scitotenv.2022.154568] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/26/2022] [Accepted: 03/10/2022] [Indexed: 05/06/2023]
Abstract
Freshwater harmful cyanobacterial blooms (HCBs) potentially produce excessive cyanotoxins, mainly microcystins (MCs), significantly threatening aquatic ecosystems and public health. Accurately predicting HCBs is thus essential to developing effective HCB mitigation and prevention strategies. We previously developed a novel early-warning system that uses cyanotoxin-encoding genes to predict cyanotoxin production in Harsha Lake, Ohio, USA, in 2015. In this study, we evaluated the efficacy of the early-warning system in forecasting the 2016 HCB in the same lake. We also examined potential HCB drivers and cyanobacterial community composition. Our results revealed that the cyanobacterial community was stable at the phylum level but changed dynamically at the genus level over time. Microcystis and Planktothrix were the major MC-producing genera that thrived in June and July and produced high concentrations of MCs (peak level 10.22 μg·L-1). The abundances of the MC-encoding gene cluster mcy and its transcript levels significantly correlated with total MC concentrations (before the MC concentrations peaked) and accurately predicted MC production as revealed by logistic equations. When the Microcystis-specific gene mcyG reached approximately 1.5 × 103 copies·mL-1 or when its transcript level reached approximately 2.4 copies·mL-1, total MC level exceeded 0.3 μg L-1 (a health advisory limit) approximately one week later (weekly sampling scheme). This study suggested that cyanotoxin-encoding genes are promising predictors of MC production in inland freshwater lakes, such as Harsha Lake. The evaluated early-warning system can be a useful tool to assist lake managers in predicting, mitigating, and/or preventing HCBs.
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Affiliation(s)
- Xiaodi Duan
- Pegasus Technical Services, Inc., Cincinnati, OH 45219, USA
| | - Chiqian Zhang
- Pegasus Technical Services, Inc., Cincinnati, OH 45219, USA
| | - Ian Struewing
- Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH 45268, USA
| | - Xiang Li
- Oak Ridge Institute for Science and Education at the United States Environmental Protection Agency, Cincinnati, OH 45268, USA
| | - Joel Allen
- Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH 45268, USA
| | - Jingrang Lu
- Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH 45268, USA.
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Hashem A, Shameem N, Parray JA, Abd‐Allah EF. Mycorrhizal Strategy for the Management of Hazardous Chromium Contaminants. CORE MICROBIOME 2022:298-314. [DOI: 10.1002/9781119830795.ch18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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35
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Giri DD, Dwivedi H, Khalaf D Alsukaibi A, Pal DB, Otaibi AA, Areeshi MY, Haque S, Gupta VK. Sustainable production of algae-bacteria granular consortia based biological hydrogen: New insights. BIORESOURCE TECHNOLOGY 2022; 352:127036. [PMID: 35331885 DOI: 10.1016/j.biortech.2022.127036] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Microbes recycling nutrient and detoxifying ecosystems are capable to fulfil the future energy need by producing biohydrogen by due to the coupling of autotrophic and heterotrophic microbes. In granules microbes mutualy exchanging nutrients and electrons for hydrogen production. The consortial biohydrogen production depend upon constituent microbes, their interdependence, competition for resources, and other operating parameters while remediating a waste material in nature or bioreactor. The present review deals with development of granular algae-bacteria consortia, hydrogen yield in coculture, important enzymes and possible engineering for improved hydrogen production.
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Affiliation(s)
- Deen Dayal Giri
- Department of Botany, Maharaj Singh College, Saharanpur-247001,Uttar Pradesh, India
| | - Himanshu Dwivedi
- Department of Botany, Maharaj Singh College, Saharanpur-247001,Uttar Pradesh, India
| | | | - Dan Bahadur Pal
- Department of Chemical Engineering, Birla Institute of Technology, Mesra, Ranchi-835215, Jharkhand, India
| | - Ahmed Al Otaibi
- Department of Chemistry, College of Sciences, University of Ha'il, Ha'il 2440, Saudi Arabia
| | - Mohammed Y Areeshi
- Research and Scientific Studies Unit, College of Nursing, Jazan University, Jazan 45142, Saudi Arabia; Medical Laboratory Technology Department, College of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing, Jazan University, Jazan 45142, Saudi Arabia; Bursa Uludağ University Faculty of Medicine,Görükle Campus, 16059, Nilüfer, Bursa, Turkey
| | - Vijai Kumar Gupta
- Center for Safe and Improved Food, SRUC, Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK; Biorefining and Advanced Materials Research Center, SRUC, Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK.
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Jiang C, Zhang S, Wang J, Xia X. The inhibitory effects of sunlight on nitrogen removal in riverine overlying water with suspended particles. CHEMOSPHERE 2022; 295:133941. [PMID: 35150703 DOI: 10.1016/j.chemosphere.2022.133941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/30/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Overlying water with suspended particles is a hot spot for nitrogen removal in river systems. Although light exposure affects nitrogen transformations and nitrogen removal in some environments, such effects have rarely been explored and quantified in riverine overlying water. Herein, we examined the difference between dark and light conditions in the community composition and abundance of nitrogen transformation microbes in simulated overlying water by high-throughput sequencing and qPCR. Moreover, 15N-labeling techniques were used to investigate variation in nitrogen removal rates (N2 and N2O) as well as nitrification rates between dark and light conditions. We found apparent differences in the bacterial community between light and dark microcosms. The abundance of Cyanobacteria was greatly elevated in light microcosms, with the diazotroph nifH gene abundance being 7.4-fold higher in the light microcosm (P < 0.01). However, due to the vulnerability of some specifies to UV damage, the diazotroph species richness was reduced. The abundances of ammonia-oxidizing archaeal amoA, ammonia-oxidizing bacterial amoA, and denitrifying nirS genes were 80.1%, 46.3%, and 50.7% lower in the light microcosm, respectively, owing to the differential inhibition of sunlight exposure on these microbes. Both 15N-N2 and 15N-N2O were significantly produced regardless of conditions with or without light. Due to the combined effects of reduced nitrification and denitrification, as well as potentially enhanced nitrogen fixation, the accumulated amounts of 15N-N2 and 15N-N2O were 6.2% and 44.8% lower, respectively, in the light microcosm. This study quantifies the inhibitory effect of sunlight exposure on nitrogen removal in riverine overlying water and reveals the underlying mechanisms, providing insights into our understanding of nitrogen transformations in river systems.
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Affiliation(s)
- Chenrun Jiang
- School of Environment, Beijing Normal University / State Key Joint Laboratory of Environmental Simulation and Pollution Control / Key Laboratory of Water and Sediment Sciences of Ministry of Education, Beijing, 100875, China
| | - Sibo Zhang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, 510006, China.
| | - Junfeng Wang
- School of Environment, Beijing Normal University / State Key Joint Laboratory of Environmental Simulation and Pollution Control / Key Laboratory of Water and Sediment Sciences of Ministry of Education, Beijing, 100875, China
| | - Xinghui Xia
- School of Environment, Beijing Normal University / State Key Joint Laboratory of Environmental Simulation and Pollution Control / Key Laboratory of Water and Sediment Sciences of Ministry of Education, Beijing, 100875, China.
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Using nanomaterials to increase the efficiency of chemical production in microbial cell factories: A comprehensive review. Biotechnol Adv 2022; 59:107982. [DOI: 10.1016/j.biotechadv.2022.107982] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/25/2022] [Accepted: 05/10/2022] [Indexed: 12/24/2022]
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Yin X, Wang W, Wang A, He M, Lin C, Ouyang W, Liu X. Microbial community structure and metabolic potential in the coastal sediments around the Yellow River Estuary. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 816:151582. [PMID: 34785215 DOI: 10.1016/j.scitotenv.2021.151582] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/05/2021] [Accepted: 11/06/2021] [Indexed: 06/13/2023]
Abstract
The Yellow River Estuary and Laizhou Bay are located on the northern Shandong Peninsula in the Bohai Sea in China and have been polluted by intensive anthropogenic activity. However, few studies have focused on the effect of these activities on the microbial communities and their ecological functions in this area. In this study, the combination of 16S rDNA gene sequencing and GeoChip technology was used to analyzed the microbial community component and their functional genes. Thaumarchaeot and Bacteroidetes are the most abundant phyla. The results of correlation analysis and redundancy analysis (RDA) showed water depth (r2 = 0.76, P = 0.005), total Na content (r2 = 0.63, P = 0.021) and total Ca content (r2 = 0.53, P = 0.05) in the sediments were the most significant environmental factors affecting the microbial community. The diversity of the microbial community and signal intensity of functional genes at nearshore sites (N sites) were higher than that at the offshore sites (O sites), but the component of microbial community and functional genes was similar in general. Functional genes for C, N, P and S cycle were detected at both nearshore and offshore sites, which illustrated that microbial communities were active in nutrient cycle. Proteobacteria contributes significantly to material cycle in microbial community. In addition, functional genes related to organic remediation and metal detoxification are also abundant. It indicated that the environmental pollution caused by anthropogenic activities has greatly affected the microbial community components and their biochemical functions in the Yellow River Estuary and surrounding areas. This study reveals the effect of anthropogenic activities on microbial communities and provides the basis for environmental management.
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Affiliation(s)
- Xiaobo Yin
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Wenting Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Aihua Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Mengchang He
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China.
| | - Chunye Lin
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Wei Ouyang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Xitao Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
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Influence of Mo and Fe on Photosynthetic and Nitrogenase Activities of Nitrogen-Fixing Cyanobacteria under Nitrogen Starvation. Cells 2022; 11:cells11050904. [PMID: 35269526 PMCID: PMC8909559 DOI: 10.3390/cells11050904] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 01/01/2023] Open
Abstract
The potential of cyanobacteria to perform a variety of distinct roles vital for the biosphere, including nutrient cycling and environmental detoxification, drives interest in studying their biodiversity. Increasing soil erosion and the overuse of chemical fertilizers are global problems in developed countries. The option might be to switch to organic farming, which entails largely the use of biofertilisers. Cyanobacteria are prokaryotic, photosynthetic organisms with considerable potential, within agrobiotechnology, to produce biofertilisers. They contribute significantly to plant drought resistance and nitrogen enrichment in the soil. This study sought, isolated, and investigated nitrogen-fixing cyanobacterial strains in rice fields, and evaluated the effect of Mo and Fe on photosynthetic and nitrogenase activities under nitrogen starvation. Cyanobacterial isolates, isolated from rice paddies in Kazakhstan, were identified as Trichormus variabilis K-31 (MZ079356), Cylindrospermum badium J-8 (MZ079357), Nostoc sp. J-14 (MZ079360), Oscillatoria brevis SH-12 (MZ090011), and Tolypothrix tenuis J-1 (MZ079361). The study of the influence of various concentrations of Mo and Fe on photosynthetic and nitrogenase activities under conditions of nitrogen starvation revealed the optimal concentrations of metals that have a stimulating effect on the studied parameters.
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Mapstone LJ, Leite MN, Purton S, Crawford IA, Dartnell L. Cyanobacteria and microalgae in supporting human habitation on Mars. Biotechnol Adv 2022; 59:107946. [DOI: 10.1016/j.biotechadv.2022.107946] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/21/2022] [Accepted: 03/15/2022] [Indexed: 12/16/2022]
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41
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Wise L, Marecos S, Randolph K, Hassan M, Nshimyumukiza E, Strouse J, Salimijazi F, Barstow B. Thermodynamic Constraints on Electromicrobial Protein Production. Front Bioeng Biotechnol 2022; 10:820384. [PMID: 35265598 PMCID: PMC8899463 DOI: 10.3389/fbioe.2022.820384] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/14/2022] [Indexed: 02/03/2023] Open
Abstract
Global consumption of protein is projected to double by the middle of the 21st century. However, protein production is one of the most energy intensive and environmentally damaging parts of the food supply system today. Electromicrobial production technologies that combine renewable electricity and CO2-fixing microbial metabolism could dramatically increase the energy efficiency of commodity chemical production. Here we present a molecular-scale model that sets an upper limit on the performance of any organism performing electromicrobial protein production. We show that engineered microbes that fix CO2 and N2 using reducing equivalents produced by H2-oxidation or extracellular electron uptake could produce amino acids with energy inputs as low as 64 MJ kg-1, approximately one order of magnitude higher than any previous estimate of the efficiency of electromicrobial protein production. This work provides a roadmap for development of engineered microbes that could significantly expand access to proteins produced with a low environmental footprint.
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Affiliation(s)
- Lucas Wise
- >
Department of Food Sciences, Cornell University, Ithaca, NY, United States
| | - Sabrina Marecos
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Katie Randolph
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Mohamed Hassan
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Eric Nshimyumukiza
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Jacob Strouse
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Farshid Salimijazi
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, United States
| | - Buz Barstow
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, United States
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Li H, Gu X, Chen H, Mao Z, Shen R, Zeng Q, Ge Y. Co-occurrence of multiple cyanotoxins and taste-and-odor compounds in the large eutrophic Lake Taihu, China: Dynamics, driving factors, and challenges for risk assessment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 294:118594. [PMID: 34848287 DOI: 10.1016/j.envpol.2021.118594] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 10/31/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
Cyanobacterial blooms producing toxic metabolites occur frequently in freshwater, yet the environmental behaviors of complex cyanobacterial metabolites remain largely unknown. In this study, the seasonal and spatial variations of several classes of cyanotoxins (microcystins, cylindrospermopsins, saxitoxins) and taste-and-odor (T&O) compounds (β-cyclocitral, β-ionone, geosmin, 2-methylisoborneol) in Lake Taihu were simultaneously investigated for the first time. The total cyanotoxins were dominated by microcystins with concentrations highest in November (mean 2209 ng/L) and lowest in February (mean 48.7 ng/L). Cylindrospermopsins were abundant in May with the highest content of 622.8 ng/L. Saxitoxins only occurred in May (mean 19.2 ng/L) and November (mean 198.5 ng/L). Extracellular T&O compounds were most concentrated in August, the highest being extracellular β-cyclocitral (mean 240.6 ng/L) followed by 2-methylisoborneol (mean 146.6 ng/L). Environment variables play conflicting roles in modulating the dynamics of different groups of cyanotoxins and T&O compounds. Total phosphorus (TP), total nitrogen (TN), chlorophyll-a and cyanobacteria density were important factors affecting the variation of total microcystins, β-cyclocitral and β-ionone concentrations. In contrast, total cylindrospermopsins, 2-methylisoborneol and geosmin concentrations were significantly influenced by water temperature and TP. There was a significant and linear relationship between microcystins and β-cyclocitral/β-ionone, while cylindrospermopsins were positively correlated with 2-methylisoborneol and geosmin. The perceptible odors may be good indicators for the existence of cyanotoxins. Hazard quotients revealed that potential human health risks from microcystins were high in August and November. Meanwhile, the risks from cylindrospermopsins were at moderate levels. Cylindrospermopsins and saxitoxins were first identified in this lake, suggesting that diverse cyanotoxins might co-occur more commonly than previously thought. Hence, the risks from other cyanotoxins beyond microcystins shouldn't be ignored. This study also highlights that the necessity for further assessing the combination effects of these complex metabolites.
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Affiliation(s)
- Hongmin Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography & Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaohong Gu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography & Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Huihui Chen
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography & Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Zhigang Mao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography & Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Ruijie Shen
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography & Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Qingfei Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography & Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - You Ge
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography & Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
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43
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Metabolic Model of the Nitrogen-Fixing Obligate Aerobe Azotobacter vinelandii Predicts Its Adaptation to Oxygen Concentration and Metal Availability. mBio 2021; 12:e0259321. [PMID: 34903060 PMCID: PMC8686835 DOI: 10.1128/mbio.02593-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
There is considerable interest in promoting biological nitrogen fixation (BNF) as a mechanism to reduce the inputs of nitrogenous fertilizers in agriculture, but considerable fundamental knowledge gaps still need to be addressed. BNF is catalyzed by nitrogenase, which requires a large input of energy in the form of ATP and low potential electrons. Diazotrophs that respire aerobically have an advantage in meeting the ATP demands of BNF but face challenges in protecting nitrogenase from inactivation by oxygen. Here, we constructed a genome-scale metabolic model of the nitrogen-fixing bacterium Azotobacter vinelandii, which uses a complex respiratory protection mechanism to consume oxygen at a high rate to keep intracellular conditions microaerobic. Our model accurately predicts growth rate under high oxygen and substrate concentrations, consistent with a large electron flux directed to the respiratory protection mechanism. While a partially decoupled electron transport chain compensates for some of the energy imbalance under high-oxygen conditions, it does not account for all substrate intake, leading to increased maintenance rates. Interestingly, the respiratory protection mechanism is required for accurate predictions even when ammonia is supplemented during growth, suggesting that the respiratory protection mechanism might be a core principle of metabolism and not just used for nitrogenase protection. We have also shown that rearrangement of flux through the electron transport system allows A. vinelandii to adapt to different oxygen concentrations, metal availability, and genetic disruption, which cause an ammonia excretion phenotype. Accurately determining the energy balance in an aerobic nitrogen-fixing metabolic model is required for future engineering approaches.
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Ataeian M, Vadlamani A, Haines M, Mosier D, Dong X, Kleiner M, Strous M, Hawley AK. Proteome and strain analysis of cyanobacterium Candidatus "Phormidium alkaliphilum" reveals traits for success in biotechnology. iScience 2021; 24:103405. [PMID: 34877483 PMCID: PMC8633866 DOI: 10.1016/j.isci.2021.103405] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/27/2021] [Accepted: 11/03/2021] [Indexed: 11/18/2022] Open
Abstract
Cyanobacteria encompass a diverse group of photoautotrophic bacteria with important roles in nature and biotechnology. Here we characterized Candidatus “Phormidium alkaliphilum,” an abundant member in alkaline soda lake microbial communities globally. The complete, circular whole-genome sequence of Ca. “P. alkaliphilum” was obtained using combined Nanopore and Illumina sequencing of a Ca. “P. alkaliphilum” consortium. Strain-level diversity of Ca. “P. alkaliphilum” was shown to contribute to photobioreactor robustness under different operational conditions. Comparative genomics of closely related species showed that adaptation to high pH was not attributed to specific genes. Proteomics at high and low pH showed only minimal changes in gene expression, but higher productivity in high pH. Diverse photosystem antennae proteins, and high-affinity terminal oxidase, compared with other soda lake cyanobacteria, appear to contribute to the success of Ca. “P. alkaliphilum” in photobioreactors and biotechnology applications. Closed genome of the cyanobacteria Ca. P. alkaliphilum from high-pH photobioreactor Genetic factors lead this Phormidium to outcompete other cyanobacteria in photobioreactor Adaptation to high pH and alkalinity is not linked to specific genes Strain-level diversity contributes Ca. P. alkaliphilum success in changing conditions
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Affiliation(s)
- Maryam Ataeian
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | | | - Marianne Haines
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Damon Mosier
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Xiaoli Dong
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Alyse K. Hawley
- Department of Geoscience, University of Calgary, Calgary, AB, Canada
- School of Engineering, University of British Columbia Okanagan, Kelowna, BC, Canada
- Corresponding author
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Phylosymbiosis in the Rhizosphere Microbiome Extends to Nitrogen Cycle Functional Potential. Microorganisms 2021; 9:microorganisms9122476. [PMID: 34946078 PMCID: PMC8709245 DOI: 10.3390/microorganisms9122476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 12/04/2022] Open
Abstract
Most plants rely on specialized root-associated microbes to obtain essential nitrogen (N), yet not much is known about the evolutionary history of the rhizosphere–plant interaction. We conducted a common garden experiment to investigate the plant root–rhizosphere microbiome association using chloridoid grasses sampled from around the world and grown from seed in a greenhouse. We sought to test whether plants that are more closely related phylogenetically have more similar root bacterial microbiomes than plants that are more distantly related. Using metagenome sequencing, we found that there is a conserved core and a variable rhizosphere bacterial microbiome across the chloridoid grasses. Additionally, phylogenetic distance among the host plant species was correlated with bacterial community composition, suggesting the plant hosts prefer specific bacterial lineages. The functional potential for N utilization across microbiomes fluctuated extensively and mirrored variation in the microbial community composition across host plants. Variation in the bacterial potential for N fixation was strongly affected by the host plants’ phylogeny, whereas variation in N recycling, nitrification, and denitrification was unaffected. This study highlights the evolutionary linkage between the N fixation traits of the microbial community and the plant host and suggests that not all functional traits are equally important for plant–microbe associations.
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46
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Biswal T, Shadangi KP, Sarangi PK. Application of Nanotechnology in the Production of Biohydrogen: A Review. Chem Eng Technol 2021. [DOI: 10.1002/ceat.202000565] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Trinath Biswal
- Veer Surendra Sai University of Technology Department of Chemistry 768018 Burla Odisha India
| | - Krushna Prasad Shadangi
- Veer Surendra Sai University of Technology Department of Chemical Engineering 768018 Burla Odisha India
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Yadav G, Mathimani T, Sekar M, Sindhu R, Pugazhendhi A. Strategic evaluation of limiting factors affecting algal growth - An approach to waste mitigation and carbon dioxide sequestration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 796:149049. [PMID: 34328896 DOI: 10.1016/j.scitotenv.2021.149049] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/10/2021] [Accepted: 07/11/2021] [Indexed: 06/13/2023]
Abstract
This work outlines major critical physico-chemical parameters that play a key role in increasing the fixation of CO2 from coal-fired flue gas CO2 into green microalgae biomass. Nitrogen concentration, gas flow rate, initial medium pH, and incident light intensity were determined to be the most important process variables with significant impact on CO2 fixation. Therefore, NaNO3 (500-3000 mg L-1), pH (6.8-8.0), light (50-200 mol m-2 s-1) and aeration (0.1-1.0 vvm) were varied to assess the biological assimilation potential of CO2 from the flue gas. The parameters that resulted in maximal CO2 fixation from raw flue gas, resulting in a maximum biomass density of 3.1 g L-1, were NaNO3 = 1500 mg L-1, pH =7.2-7.5, incident light intensity = 133.33 mol m-2 s-1, and 0.5-0.75 vvm aeration without any cost-incurring flue gas pre-treatment step. The inductively coupled plasma-mass spectrometer (ICP-MS) was used to investigate heavy metals uptake from raw flue gas, and it was discovered that no net intake of trace metals had a significant influence on biomass production. The research lays the path for efficient large-scale microalgal cultivations for industrial uses, as well as bolstering the circular economy concept.
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Affiliation(s)
- Geetanjali Yadav
- Department of Chemical Engineering, Polytechnique Montreal, Montreal H3S 1W9, QC, Canada; Department of Biotechnology, Indian Institute of Technology Kharagpur, 721302 West Bengal, India
| | - Thangavel Mathimani
- Department of Energy and Environment, National Institute of Technology, Tiruchirappalli 620 015, Tamil Nadu, India
| | - Manigandan Sekar
- Department of Aeronautical Engineering, Sathyabama Institute of Science and Technology, Chennai, India
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum 695 019, Kerala, India
| | - Arivalagan Pugazhendhi
- School of Renewable Energy, Maejo University, Chiang Mai 50290, Thailand; College of Medical and Health Science, Asia University, Taichung, Taiwan.
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48
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Discovery of nondiazotrophic Trichodesmium species abundant and widespread in the open ocean. Proc Natl Acad Sci U S A 2021; 118:2112355118. [PMID: 34750267 DOI: 10.1073/pnas.2112355118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2021] [Indexed: 11/18/2022] Open
Abstract
Filamentous and colony-forming cells within the cyanobacterial genus Trichodesmium might account for nearly half of nitrogen fixation in the sunlit ocean, a critical mechanism that sustains plankton's primary productivity. Trichodesmium has long been portrayed as a diazotrophic genus. By means of genome-resolved metagenomics, here we reveal that nondiazotrophic Trichodesmium species not only exist but also are abundant and widespread in the open ocean, benefiting from a previously overlooked functional lifestyle to expand the biogeography of this prominent marine genus. Near-complete environmental genomes for those closely related candidate species reproducibly shared functional features including a lack of genes related to nitrogen fixation, hydrogen recycling, and hopanoid lipid production concomitant with the enrichment of nitrogen assimilation genes. Our results elucidate fieldwork observations of Trichodesmium cells fixing carbon but not nitrogen. The Black Queen hypothesis and burden of low-oxygen concentration requirements provide a rationale to explain gene loss linked to nitrogen fixation among Trichodesmium species. Disconnecting taxonomic signal for this genus from a microbial community's ability to fix nitrogen will help refine our understanding of the marine nitrogen balance. Finally, we are reminded that established links between taxonomic lineages and functional traits do not always hold true.
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Cheng C, Sun T, Li H, He Q, Pavlostathis SG, Zhang J. New insights in correlating greenhouse gas emissions and microbial carbon and nitrogen transformations in wetland sediments based on genomic and functional analysis. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 297:113280. [PMID: 34273644 DOI: 10.1016/j.jenvman.2021.113280] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/15/2021] [Accepted: 07/11/2021] [Indexed: 06/13/2023]
Abstract
Greenhouse gas (GHG) emissions from constructed wetlands (CWs) lower the environmental and ecological benefits of CWs and thus have raised increasing environmental concern. To prevent GHGs emissions, it is important to assess and quantify the correlation of GHGs emission and microbial carbon and nitrogen transformations. In this study, two typical wetland substrate samples (mud sampled from Xiaomei River CW and sand sampled from Dongwen River CW) were used to build lab-scale vertical subsurface flow CW microcosms, labeled as XRCW and DRCW, respectively. The mean COD removal rate of the DRCW group (76.1%) was higher than that of XRCW group (60.6%). Both groups achieved a high extent of nitrogen nutrient removal, indicating a higher metabolic activity of nitrifying and denitrifying microorganisms in the system, especially in XRCW. The mean emission fluxes of N2O, CH4 and CO2 in the XRCW group were 52.7 μg/m2-h, 1.6 mg/m2-h and 100.4 mg/m2-h, which were higher than that in the DRCW group (30.0 μg/m2-h, 1.0 mg/m2-h and 28.0 mg/m2-h, respectively). The relation of GHG emissions to microbial carbon and nitrogen transformation was assessed by genomics and functional analysis. The release of GHGs by the XRCW group had a positive correlation with the relative abundance of Proteobacteria, while for the DRCW group a positive correlation was found with the relative abundance of Cyanobacteria. Nitrogen fixation by Cyanobacteria could be an approach to reduce GHG emissions. The release of CH4 and CO2 was positively correlated with glucose metabolism. N2O gas emission was affected by the species of denitrifiers. This study is of great importance to clarify the emissions of GHGs in vertical subsurface flow CWs, as it is relating to microbial carbon and nitrogen transformation. The connection is of great significance to control the emission of GHGs in wetlands.
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Affiliation(s)
- Cheng Cheng
- College of Environmental and Ecology, Chongqing University, Chongqing, 400045, PR China; Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, PR China
| | - Tianyi Sun
- College of Environmental and Ecology, Chongqing University, Chongqing, 400045, PR China
| | - Hanjie Li
- College of Environmental and Ecology, Chongqing University, Chongqing, 400045, PR China
| | - Qiang He
- College of Environmental and Ecology, Chongqing University, Chongqing, 400045, PR China
| | - Spyros G Pavlostathis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, United States
| | - Jian Zhang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, PR China.
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Priyadarshini P, Choudhury S, Tilgam J, Bharati A, Sreeshma N. Nitrogen fixing cereal: A rising hero towards meeting food security. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:912-920. [PMID: 34547550 DOI: 10.1016/j.plaphy.2021.09.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 09/05/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
Nitrogen serves as one of the primary components of major biomolecules and thus extends a significant contribution to crop growth and yield. But the inability of plants to utilize freely available atmospheric N2 makes the whole agricultural system dependent on chemical fertilizers, which incur significant input cost to supplement required quantities of nitrogen to crops. Only bacteria and archaea have been gifted with the power of drawing free N2 from air to convert them into NH3, which is one of the two utilizable forms of nitrogen taken up by plants. Legumes, the only family of crops, can engage themselves in symbiotic nitrogen fixation where they establish a mutualistic relationship with nitrogen-fixing bacteria and in turn, can waive off the necessity of adding nitrogen fertilizers. Sincere effort, therefore, has been undertaken to incorporate this capability of nitrogen-fixation into non-legume crops, especially cereals which make up a vital portion in the food basket. Biotechnological interventions have also played important role in providing nitrogen fixing trait to non-legumes. This review takes up an effort to look into and accumulate all the important updates to date regarding nitrogen-fixing non-legumes with a special focus on cereals, which is one of the most important future goals in the field of science in the present era.
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Affiliation(s)
- Parichita Priyadarshini
- ICAR-Crop Improvement Division, Indian Grassland and Fodder Research Institute, Jhansi, U.P., 284003, India
| | - Sharani Choudhury
- ICAR - National Institute for Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Jyotsana Tilgam
- ICAR- National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, U.P., 274103, India.
| | - Alka Bharati
- ICAR-Central Agroforestry Research Institute, Jhansi, U.P., 284003, India
| | - N Sreeshma
- ICAR - National Institute for Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India
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