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Chung CW, Ng IS. Tailoring nitrogen and phosphorus levels for tunable glycogen and protein production in halophilic Cyanobacterium aponinum PCC10605. BIORESOURCE TECHNOLOGY 2024; 406:131052. [PMID: 38944314 DOI: 10.1016/j.biortech.2024.131052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Cyanobacteria hold promise for simultaneous carbon capture and chemicals production, but the regulation and effect of nitrogen (N) and phosphorus (P) remains unclear. This study investigates major productions of glycogen, protein, and C-phycocyanin (C-PC) in Cyanobacterium aponinum PCC10605 under different N/P levels, alongside changes in light and CO2. Increasing nitrate (NO3-) from 2 to 6 mM resulted in a 9.7-fold increase in C-PC and reduced glycogen to 8.9 %. On the other hand, elevating phosphorus from 0.1 to 2 mM under limited nitrogen enhanced biomass and glycogen through the upregulation of carbonic anhydrase, ADP-glucose pyrophosphorylase, and glycogen phosphorylase. Changes in phosphorus levels and CO2 inlet concentrations affected metabolites accumulation and carbon capture efficiency, leading to the best condition of 76 % uptake capacity in direct air capture (DAC). All findings underscore the trade-off between glycogen and protein, representing the importance of N/P levels in nutrient modulation of PCC10605.
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Affiliation(s)
- Cheng-Wei Chung
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan.
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2
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Yusefi-Tanha E, Fallah S, Pokhrel LR, Rostamnejadi A. Role of particle size-dependent copper bioaccumulation-mediated oxidative stress on Glycine max (L.) yield parameters with soil-applied copper oxide nanoparticles. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:28905-28921. [PMID: 38564134 PMCID: PMC11058571 DOI: 10.1007/s11356-024-33070-x] [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: 10/11/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024]
Abstract
Increased impetus on the application of nano-fertilizers to improve sustainable food production warrants understanding of nanophytotoxicity and its underlying mechanisms before its application could be fully realized. In this study, we evaluated the potential particle size-dependent effects of soil-applied copper oxide nanoparticles (nCuO) on crop yield and quality attributes (photosynthetic pigments, seed yield and nutrient quality, seed protein, and seed oil), including root and seed Cu bioaccumulation and a suite of oxidative stress biomarkers, in soybean (Glycine max L.) grown in field environment. We synthesized three distinct sized (25 nm = S [small], 50 nm = M [medium], and 250 nm = L [large]) nCuO with same surface charge and compared with soluble Cu2+ ions (CuCl2) and water-only controls. Results showed particle size-dependent effects of nCuO on the photosynthetic pigments (Chla and Chlb), seed yield, potassium and phosphorus accumulation in seed, and protein and oil yields, with nCuO-S showing higher inhibitory effects. Further, increased root and seed Cu bioaccumulation led to concomitant increase in oxidative stress (H2O2, MDA), and as a response, several antioxidants (SOD, CAT, POX, and APX) increased proportionally, with nCuO treatments including Cu2+ ion treatment. These results are corroborated with TEM ultrastructure analysis showing altered seed oil bodies and protein storage vacuoles with nCuO-S treatment compared to control. Taken together, we propose particle size-dependent Cu bioaccumulation-mediated oxidative stress as a mechanism of nCuO toxicity. Future research investigating the potential fate of varied size nCuO, with a focus on speciation at the soil-root interface, within the root, and edible parts such as seed, will guide health risk assessment of nCuO.
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Affiliation(s)
- Elham Yusefi-Tanha
- Department of Agronomy, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
| | - Sina Fallah
- Department of Agronomy, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
| | - Lok Raj Pokhrel
- Department of Public Health, The Brody School of Medicine, East Carolina University, Greenville, NC, USA.
| | - Ali Rostamnejadi
- Faculty of Electromagnetics, Malek Ashtar University of Technology, Tehran, Iran
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3
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Yuan J, Deng X, Xie X, Chen L, Wei C, Feng C, Qiu G. Blind spots of universal primers and specific FISH probes for functional microbe and community characterization in EBPR systems. ISME COMMUNICATIONS 2024; 4:ycae011. [PMID: 38524765 PMCID: PMC10958769 DOI: 10.1093/ismeco/ycae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 03/26/2024]
Abstract
Fluorescence in situ hybridization (FISH) and 16S rRNA gene amplicon sequencing are commonly used for microbial ecological analyses in biological enhanced phosphorus removal (EBPR) systems, the successful application of which was governed by the oligonucleotides used. We performed a systemic evaluation of commonly used probes/primers for known polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs). Most FISH probes showed blind spots and covered nontarget bacterial groups. Ca. Competibacter probes showed promising coverage and specificity. Those for Ca. Accumulibacter are desirable in coverage but targeted out-group bacteria, including Ca. Competibacter, Thauera, Dechlorosoma, and some polyphosphate-accumulating Cyanobacteria. Defluviicoccus probes are good in specificity but poor in coverage. Probes targeting Tetrasphaera or Dechloromonas showed low coverage and specificity. Specifically, DEMEF455, Bet135, and Dech453 for Dechloromonas covered Ca. Accumulibacter. Special attentions are needed when using these probes to resolve the PAO/GAO phenotype of Dechloromonas. Most species-specific probes for Ca. Accumulibacter, Ca. Lutibacillus, Ca. Phosphoribacter, and Tetrasphaera are highly specific. Overall, 1.4% Ca. Accumulibacter, 9.6% Ca. Competibacter, 43.3% Defluviicoccus, and 54.0% Dechloromonas in the MiDAS database were not covered by existing FISH probes. Different 16S rRNA amplicon primer sets showed distinct coverage of known PAOs and GAOs. None of them covered all members. Overall, 520F-802R and 515F-926R showed the most balanced coverage. All primers showed extremely low coverage of Microlunatus (<36.0%), implying their probably overlooked roles in EBPR systems. A clear understanding of the strength and weaknesses of each probe and primer set is a premise for rational evaluation and interpretation of obtained community results.
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Affiliation(s)
- Jing Yuan
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
| | - Xuhan Deng
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
| | - Xiaojing Xie
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
| | - Liping Chen
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
| | - Chaohai Wei
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
- Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
- Key Laboratory of Pollution Control and Ecological Restoration in Industrial Clusters, Ministry of Education, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
| | - Chunhua Feng
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
- Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
- Key Laboratory of Pollution Control and Ecological Restoration in Industrial Clusters, Ministry of Education, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
| | - Guanglei Qiu
- School of Environment and Energy, South China University of Technology, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
- Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
- Key Laboratory of Pollution Control and Ecological Restoration in Industrial Clusters, Ministry of Education, 382 Waihuandong Road, University Town, Guangzhou, Guangdong 510006, China
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4
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Zhan Y, Xu S, Hou Z, Gao X, Su J, Peng B, Zhao J, Wang Z, Cheng M, Zhang A, Guo Y, Ding G, Li J, Wei Y. Co-inoculation of phosphate-solubilizing bacteria and phosphate accumulating bacteria in phosphorus-enriched composting regulates phosphorus transformation by facilitating polyphosphate formation. BIORESOURCE TECHNOLOGY 2023; 390:129870. [PMID: 37839642 DOI: 10.1016/j.biortech.2023.129870] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 10/17/2023]
Abstract
This study aimed to explore the impact of co-inoculating phosphate-solubilizing bacteria (PSB) and phosphate accumulating bacteria (PAB) on phosphorus forms transformation, microbial biomass phosphorus (MBP) and polyphosphate (Poly-P) accumulation, bacterial community composition in composting, using high throughput sequencing, PICRUSt 2, network analysis, structural equation model (SEM) and random forest (RF) analysis. The results demonstrated PSB-PAB co-inoculation (T1) reduced Olsen-P content (1.4 g) but had higher levels of MBP (74.2 mg/kg) and Poly-P (419 A.U.) compared to PSB-only (T0). The mantel test revealed a significantly positive correlation between bacterial diversity and both bioavailable P and MBP. Halocella was identified as a key genus related to Poly-P synthesis by network analysis. SEM and RF analysis showed that pH and bacterial community had the most influence on Poly-P synthesis, and PICRUSt 2 analysis revealed inoculation of PAB increased ppk gene abundance in T1. Thus, PSB-PAB co-inoculation provides a new idea for phosphorus management.
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Affiliation(s)
- Yabin Zhan
- Key Laboratory of Fertilization from Agricultural Wastes, Ministry of Agriculture and Rural Affairs, Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, Hubei 430064, China; College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China
| | - Shaoqi Xu
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China
| | - Zhuonan Hou
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China
| | - Xin Gao
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China
| | - Jing Su
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Bihui Peng
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China
| | - Jinyue Zhao
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China
| | - Zhigang Wang
- DBN Agriculture Science and Technology Group CO., Ltd., DBN Pig Academy, Beijing 102629, China
| | - Meidi Cheng
- College of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, China
| | - Ake Zhang
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Fuyang Academy of Agricultural Sciences, Fuyang 236065, China
| | - Yanbin Guo
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China
| | - Guochun Ding
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China
| | - Ji Li
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China
| | - Yuquan Wei
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, 100193 Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China.
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5
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Salama DM, Osman SA, Shaaban EA, Abd Elwahed MS, Abd El-Aziz ME. Effect of foliar application of phosphorus nanoparticles on the performance and sustainable agriculture of sweet corn. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108058. [PMID: 37778115 DOI: 10.1016/j.plaphy.2023.108058] [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: 07/25/2023] [Revised: 09/09/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
Traditional phosphorus fertilizers are necessary for plant growth but about 80-90% are lost into the surrounding environment via irrigation, therefore nano-fertilizers have been developed as slow-release fertilizers to achieve sustainable agriculture. This trial investigated the impact of the foliar application of hydroxyapatite nanoparticles (HA-NPs) as a source of nano-phosphorus (P-NPs) on two cultivars of sweet corn (yellow and white) throughout two seasons. The morphology and structure of the prepared HA-NPs were characterized via transmission electron microscopy (TEM) and X-ray diffractometry (XRD). In addition, agro-morphological criteria, chemical contents (i.e., photosynthetic pigments, phenols, indoles, minerals, etc.), and genomic template stability percentage (GTS%) were evaluated in the produced sweet corn. The application of 50 mg/l HA-NPs improved the growth characteristics, yield per hectare, leaf pigments, and chemical content of yellow sweet corn, whereas the application of 100 mg/l of HA-NPs to white sweet corn enhanced the vegetative characteristics, production, photosynthetic pigments, phenols, and indoles. The difference in results may be due to the presence of a +ve unique band with SCoT-4 and SCot-2 primers at 1250 and 470 bp in yellow and white corn treated with 50 and 100 mg/l, respectively. The minimum GTS% was recorded at a concentration of 75 mg/l for both white and yellow corn. The HA-NPs can be applied as a foliar source of P-NPs to achieve agricultural sustainability.
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Affiliation(s)
- Dina M Salama
- Vegetable Research Department, National Research Centre, 33 El Bohouth St., Dokki, Giza, P.O. 12622, Egypt.
| | - Samira A Osman
- Genetics and Cytology Department, National Research Centre, 33 El Bohouth St., Dokki, Giza, P.O. 12622, Egypt
| | - Essam A Shaaban
- Pomology Department, National Research Centre, 33 El Bohouth St., Dokki, Giza, P.O. 12622, Egypt
| | - M S Abd Elwahed
- Botany Department, National Research Centre, 33 El Bohouth St., Dokki, Giza, P.O. 12622, Egypt
| | - Mahmoud E Abd El-Aziz
- Polymers & Pigments Department, National Research Centre, 33 El Bohouth St., Dokki, Giza, P.O. 12622, Egypt.
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6
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Pearce NJT, Parsons CT, Pomfret SM, Yates AG. Periphyton Phosphorus Uptake in Response to Dynamic Concentrations in Streams: Assimilation and Changes to Intracellular Speciation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:4643-4655. [PMID: 36897624 PMCID: PMC10035032 DOI: 10.1021/acs.est.2c06285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 02/15/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Effective modeling and management of phosphorus (P) losses from landscapes to receiving waterbodies requires an adequate understanding of P retention and remobilization along the terrestrial-aquatic continuum. Within aquatic ecosystems, the stream periphyton can transiently store bioavailable P through uptake and incorporation into biomass during subscouring and baseflow conditions. However, the capacity of stream periphyton to respond to dynamic P concentrations, which are ubiquitous in streams, is largely unknown. Our study used artificial streams to impose short periods (48 h) of high SRP concentration on stream periphyton acclimated to P scarcity. We examined periphyton P content and speciation through nuclear magnetic resonance spectroscopy to elucidate the intracellular storage and transformation of P taken up across a gradient of transiently elevated SRP availabilities. Our study demonstrates that the stream periphyton not only takes up significant quantities of P following a 48-h high P pulse but also sustains supplemental growth over extended periods of time (10 days), following the reestablishment of P scarcity by efficiently assimilating P stored as polyphosphates into functional biomass (i.e., phospho-monoesters and phospho-diesters). Although P uptake and intracellular storage approached an upper limit across the experimentally imposed SRP pulse gradient, our findings demonstrate the previously underappreciated extent to which the periphyton can modulate the timing and magnitude of P delivery from streams. Further elucidating these intricacies in the transient storage potential of periphyton highlights opportunities to enhance the predictive capacity of watershed nutrient models and potentially improve watershed P management.
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Affiliation(s)
- Nolan J. T. Pearce
- University
of Western Ontario & Canadian Rivers Institute, 1156 Richmond Street, London, Ontario N6A 3K8, Canada
| | - Chris T. Parsons
- Ecohydrology
Research Group and The Water Institute, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
- Watershed
Hydrology and Ecology Research Division, Environment and Climate Change Canada, 867 Lakeshore Road, Burlington, Ontario L7S 1A1, Canada
| | - Sarah M. Pomfret
- University
of Western Ontario & Canadian Rivers Institute, 1156 Richmond Street, London, Ontario N6A 3K8, Canada
| | - Adam G. Yates
- University
of Western Ontario & Canadian Rivers Institute, 1156 Richmond Street, London, Ontario N6A 3K8, Canada
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Solhtalab M, Moller SR, Gu AZ, Jaisi D, Aristilde L. Selectivity in Enzymatic Phosphorus Recycling from Biopolymers: Isotope Effect, Reactivity Kinetics, and Molecular Docking with Fungal and Plant Phosphatases. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:16441-16452. [PMID: 36283689 PMCID: PMC9670850 DOI: 10.1021/acs.est.2c04948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/05/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Among ubiquitous phosphorus (P) reserves in environmental matrices are ribonucleic acid (RNA) and polyphosphate (polyP), which are, respectively, organic and inorganic P-containing biopolymers. Relevant to P recycling from these biopolymers, much remains unknown about the kinetics and mechanisms of different acid phosphatases (APs) secreted by plants and soil microorganisms. Here we investigated RNA and polyP dephosphorylation by two common APs, a plant purple AP (PAP) from sweet potato and a fungal phytase from Aspergillus niger. Trends of δ18O values in released orthophosphate during each enzyme-catalyzed reaction in 18O-water implied a different extent of reactivity. Subsequent enzyme kinetics experiments revealed that A. niger phytase had 10-fold higher maximum rate for polyP dephosphorylation than the sweet potato PAP, whereas the sweet potato PAP dephosphorylated RNA at a 6-fold faster rate than A. niger phytase. Both enzymes had up to 3 orders of magnitude lower reactivity for RNA than for polyP. We determined a combined phosphodiesterase-monoesterase mechanism for RNA and terminal phosphatase mechanism for polyP using high-resolution mass spectrometry and 31P nuclear magnetic resonance, respectively. Molecular modeling with eight plant and fungal AP structures predicted substrate binding interactions consistent with the relative reactivity kinetics. Our findings implied a hierarchy in enzymatic P recycling from P-polymers by phosphatases from different biological origins, thereby influencing the relatively longer residence time of RNA versus polyP in environmental matrices. This research further sheds light on engineering strategies to enhance enzymatic recycling of biopolymer-derived P, in addition to advancing environmental predictions of this P recycling by plants and microorganisms.
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Affiliation(s)
- Mina Solhtalab
- Department
of Biological and Environmental Engineering, College of Agriculture
and Life Sciences, Cornell University, Ithaca, New York 14853, United States
- Department
of Civil and Environmental Engineering, McCormick School of Engineering
and Applied Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Spencer R. Moller
- Department
of Plant and Soil Sciences, University of
Delaware, Newark, Delaware 19716, United States
| | - April Z. Gu
- School
of Civil and Environmental Engineering, College of Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Deb Jaisi
- Department
of Plant and Soil Sciences, University of
Delaware, Newark, Delaware 19716, United States
| | - Ludmilla Aristilde
- Department
of Biological and Environmental Engineering, College of Agriculture
and Life Sciences, Cornell University, Ithaca, New York 14853, United States
- Department
of Civil and Environmental Engineering, McCormick School of Engineering
and Applied Science, Northwestern University, Evanston, Illinois 60208, United States
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8
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Reciprocal Inclusion of Microbiomes and Environmental Justice Contributes Solutions to Global Environmental Health Challenges. mSystems 2022; 7:e0146221. [PMID: 35642845 PMCID: PMC9239259 DOI: 10.1128/msystems.01462-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Generations of colonialism, industrialization, intensive agriculture, and anthropogenic climate change have radically altered global ecosystems and by extension, their environmental microbiomes. The environmental consequences of global change disproportionately burden racialized communities, those with lower socioeconomic status, and other systematically underserved populations. Environmental justice seeks to balance the relationships between environmental burden, beneficial ecosystem functions, and local communities. Given their direct links to human and ecosystem health, microbes are embedded within social and environmental justice. Considering scientific and technological advances is becoming an important step in developing actionable solutions to global equity challenges. Here we identify areas where inclusion of microbial knowledge and research can support planetary health goals. We offer guidelines for strengthening a reciprocal integration of environmental justice into environmental microbiology research. Microbes form intimate relationships with the environment and society, thus microbiologists have numerous and unique opportunities to incorporate equity into their research, teaching, and community engagement.
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Geerlings NMJ, Kienhuis MVM, Hidalgo-Martinez S, Hageman R, Vasquez-Cardenas D, Middelburg JJ, Meysman FJR, Polerecky L. Polyphosphate Dynamics in Cable Bacteria. Front Microbiol 2022; 13:883807. [PMID: 35663875 PMCID: PMC9159916 DOI: 10.3389/fmicb.2022.883807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/18/2022] [Indexed: 11/14/2022] Open
Abstract
Cable bacteria are multicellular sulfide oxidizing bacteria that display a unique metabolism based on long-distance electron transport. Cells in deeper sediment layers perform the sulfide oxidizing half-reaction whereas cells in the surface layers of the sediment perform the oxygen-reducing half-reaction. These half-reactions are coupled via electron transport through a conductive fiber network that runs along the shared cell envelope. Remarkably, only the sulfide oxidizing half-reaction is coupled to biosynthesis and growth whereas the oxygen reducing half-reaction serves to rapidly remove electrons from the conductive fiber network and is not coupled to energy generation and growth. Cells residing in the oxic zone are believed to (temporarily) rely on storage compounds of which polyphosphate (poly-P) is prominently present in cable bacteria. Here we investigate the role of poly-P in the metabolism of cable bacteria within the different redox environments. To this end, we combined nanoscale secondary ion mass spectrometry with dual-stable isotope probing (13C-DIC and 18O-H2O) to visualize the relationship between growth in the cytoplasm (13C-enrichment) and poly-P activity (18O-enrichment). We found that poly-P was synthesized in almost all cells, as indicated by 18O enrichment of poly-P granules. Hence, poly-P must have an important function in the metabolism of cable bacteria. Within the oxic zone of the sediment, where little growth is observed, 18O enrichment in poly-P granules was significantly lower than in the suboxic zone. Thus, both growth and poly-P metabolism appear to be correlated to the redox environment. However, the poly-P metabolism is not coupled to growth in cable bacteria, as many filaments from the suboxic zone showed poly-P activity but did not grow. We hypothesize that within the oxic zone, poly-P is used to protect the cells against oxidative stress and/or as a resource to support motility, while within the suboxic zone, poly-P is involved in the metabolic regulation before cells enter a non-growing stage.
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Affiliation(s)
- Nicole M. J. Geerlings
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
- *Correspondence: Nicole M. J. Geerlings,
| | | | - Silvia Hidalgo-Martinez
- Excellence centre for Microbial Systems Technology, University of Antwerp, Wilrijk, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Renee Hageman
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
| | - Diana Vasquez-Cardenas
- Excellence centre for Microbial Systems Technology, University of Antwerp, Wilrijk, Belgium
| | | | - Filip J. R. Meysman
- Excellence centre for Microbial Systems Technology, University of Antwerp, Wilrijk, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Lubos Polerecky
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
- Lubos Polerecky,
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10
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Liu R, Wei X, Song W, Wang L, Cao J, Wu J, Thomas T, Jin T, Wang Z, Wei W, Wei Y, Zhai H, Yao C, Shen Z, Du J, Fang J. Novel Chloroflexi genomes from the deepest ocean reveal metabolic strategies for the adaptation to deep-sea habitats. MICROBIOME 2022; 10:75. [PMID: 35538590 PMCID: PMC9088039 DOI: 10.1186/s40168-022-01263-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 03/24/2022] [Indexed: 05/04/2023]
Abstract
BACKGROUND The deep sea harbors the majority of the microbial biomass in the ocean and is a key site for organic matter (OM) remineralization and storage in the biosphere. Microbial metabolism in the deep ocean is greatly controlled by the generally depleted but periodically fluctuating supply of OM. Currently, little is known about metabolic potentials of dominant deep-sea microbes to cope with the variable OM inputs, especially for those living in the hadal trenches-the deepest part of the ocean. RESULTS In this study, we report the first extensive examination of the metabolic potentials of hadal sediment Chloroflexi, a dominant phylum in hadal trenches and the global deep ocean. In total, 62 metagenome-assembled-genomes (MAGs) were reconstructed from nine metagenomic datasets derived from sediments of the Mariana Trench. These MAGs represent six novel species, four novel genera, one novel family, and one novel order within the classes Anaerolineae and Dehalococcoidia. Fragment recruitment showed that these MAGs are globally distributed in deep-sea waters and surface sediments, and transcriptomic analysis indicated their in situ activities. Metabolic reconstruction showed that hadal Chloroflexi mainly had a heterotrophic lifestyle, with the potential to degrade a wide range of organic carbon, sulfur, and halogenated compounds. Our results revealed for the first time that hadal Chloroflexi harbor pathways for the complete hydrolytic or oxidative degradation of various recalcitrant OM, including aromatic compounds (e.g., benzoate), polyaromatic hydrocarbons (e.g., fluorene), polychlorobiphenyl (e.g., 4-chlorobiphenyl), and organochlorine compounds (e.g., chloroalkanes, chlorocyclohexane). Moreover, these organisms showed the potential to synthesize energy storage compounds (e.g., trehalose) and had regulatory modules to respond to changes in nutrient conditions. These metabolic traits suggest that Chloroflexi may follow a "feast-or-famine" metabolic strategy, i.e., preferentially consume labile OM and store the energy intracellularly under OM-rich conditions, and utilize the stored energy or degrade recalcitrant OM for survival under OM-limited condition. CONCLUSION This study expands the current knowledge on metabolic strategies in deep-ocean Chlorolfexi and highlights their significance in deep-sea carbon, sulfur, and halogen cycles. The metabolic plasticity likely provides Chloroflexi with advantages for survival under variable and heterogenic OM inputs in the deep ocean. Video Abstract.
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Affiliation(s)
- Rulong Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China.
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China.
| | - Xing Wei
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Weizhi Song
- Centre for Marine Science & Innovation and School of Biological Earth and Environmental Science, University of New South Wales, Kensington, Australia
| | - Li Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Junwei Cao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Jiaxin Wu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Torsten Thomas
- Centre for Marine Science & Innovation and School of Biological Earth and Environmental Science, University of New South Wales, Kensington, Australia
| | - Tao Jin
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Zixuan Wang
- Tidal Flat Research Center of Jiangsu Province, Nanjing, Jiangsu, China
| | - Wenxia Wei
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Yuli Wei
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Haofeng Zhai
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Cheng Yao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Ziyi Shen
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Jiangtao Du
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
- National Engineering Research Center for Oceanic Fisheries, Shanghai Ocean University, Shanghai, China
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
- Department of Natural Sciences, Hawaii Pacific University, Honolulu, HI, USA.
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11
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Li Y, Xiong X, Zhang C, Liu A. Sustainable restoration of anoxic freshwater using environmentally-compatible oxygen-carrying biochar: Performance and mechanisms. WATER RESEARCH 2022; 214:118204. [PMID: 35219183 DOI: 10.1016/j.watres.2022.118204] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
The long-term decline in dissolved oxygen (DO) levels in freshwater systems including rivers and lakes has become a worldwide concern, which can threaten biodiversity, nutrient biogeochemistry, water quality and ultimately human health. Herein, we report a sustainable restoration strategy for anoxic freshwater using local sediment-based biochar as novel oxygen nanobubble carriers. Column incubation experiments were conducted with water and sediment samples from an urban tributary of the Yangtze River. The oxygen-carrying sediment-based biochar (O-SBC) showed long-lasting re-oxygenation performance for anoxic river waters during 28-day period, in which DO was rapidly elevated from ∼0.14 to ∼7.87 mg/L and gradually maintained at ∼4.78 mg/L until the end. O-SBC with multiple functions switched the sediments from a source to a sink of nutrients, and its release of oxygen nanobubbles contributed further decrements of 66.3% NH4+-N and 142.9% PO43--P except for physical blocking and physicochemical adsorption. Notably, a comprehensive focus on restoration mechanism was explored in view of microbial community response. The re-oxygenation was followed by a ∼5.05% increase of bacterial diversity (Shannon index) in water, but a ∼2.40% decrease in sediments. A proliferation of some specific aerobic populations was observed, of which the nitrifying Nitrospira abundances were ∼10-fold higher in the water from O-SBC than the control. Additionally, functional genes involved in nitrous oxide reduction, polyphosphate synthesis/degradation, and thiosulfate oxidation were also enriched. Taken together, our findings can not only expand the promising candidates for oxygen nanobubble carriers based on sediment recycling, but also highlight the microbial molecular mechanisms for anoxic freshwater restoration based on nutrient cycle regulation.
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Affiliation(s)
- Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China.
| | - Xinyan Xiong
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, PR China
| | - Chi Zhang
- College of Mechanics and Materials, Hohai University, Xikang Road #1, Nanjing 210098, PR China.
| | - An Liu
- College of Chemistry and Environmental Engineering, Shenzhen University, Xueyuan Avenue #1066, Shenzhen 518060, PR China
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12
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Park Y, Malliakas CD, Zhou Q, Gu AZ, Aristilde L. Molecular Coordination, Structure, and Stability of Metal-Polyphosphate Complexes Resolved by Molecular Modeling and X-ray Scattering: Structural Insights on the Biological Fate of Polyphosphate. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:14185-14193. [PMID: 34623819 DOI: 10.1021/acs.est.1c04782] [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: 06/13/2023]
Abstract
Polyphosphate-accumulating organisms (PAOs), which can store high levels of phosphate (Pi) in the form of polyphosphate (polyP), are employed to engineer enhanced biological P removal (EBPR) from wastewaters. Co-localization of Mg and K in polyP granules of PAOs has been reported, and higher abundance of Mg-polyP granules relative to other metal complexes was correlated positively with EBPR performance stability. However, the underlying mechanism remains unknown. Here, we obtained molecular structural information of hydrated polyP complexes with four physiologically relevant metal cations (Na+, K+, Ca2+, and Mg2+) using computational and experimental techniques. Molecular dynamics simulations revealed that Mg-polyP and K-polyP complexes were the most and least stable of the complexes, respectively, suggesting that the co-occurrence of these complexes facilitates variable polyP bioavailability. The relative thermodynamic stability reflected the strength of metal chelation whereby the coordination distance between the polyP ligand O and the metal was 1.71-2.01 Å for Mg2+ but this distance was 2.64-2.70 Å for K+. Pair distribution function analysis of X-ray scattering data obtained with a Mg-polyP solution corroborated the theoretical Mg-polyP coordination geometry. These findings implied a possible mechanistic role of metal complexation in the P cycling traits of PAOs in engineered and natural systems.
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Affiliation(s)
- Yeonsoo Park
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14853, United States
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Christos D Malliakas
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Qing Zhou
- Department of Civil and Environmental Engineering, College of Engineering, Cornell University, Ithaca, New York 14853, United States
- School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China
| | - April Z Gu
- Department of Civil and Environmental Engineering, College of Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Ludmilla Aristilde
- Department of Biological and Environmental Engineering, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14853, United States
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, Illinois 60208, United States
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