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Wong PY, Mal J, Sandak A, Luo L, Jian J, Pradhan N. Advances in microbial self-healing concrete: A critical review of mechanisms, developments, and future directions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 947:174553. [PMID: 38972424 PMCID: PMC11299504 DOI: 10.1016/j.scitotenv.2024.174553] [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: 05/07/2024] [Revised: 06/26/2024] [Accepted: 07/04/2024] [Indexed: 07/09/2024]
Abstract
The self-healing bioconcrete, or bioconcrete as concrete containing microorganisms with self-healing capacities, presents a transformative strategy to extend the service life of concrete structures. This technology harnesses the biological capabilities of specific microorganisms, such as bacteria and fungi, which are integral to the material's capacity to autonomously mend cracks, thereby maintaining structural integrity. This review highlights the complex biochemical pathways these organisms utilize to produce healing compounds like calcium carbonate, and how environmental parameters, such as pH, temperature, oxygen, and moisture critically affect the repair efficacy. A comprehensive analysis of recently published peer-reviewed literature, and contemporary experimental research forms the backbone of this review with a focus on microbiological aspects of the self-healing process. The review assesses the challenges facing self-healing bioconcrete, including the longevity of microbial spores and the cost implications for large-scale implementation. Further, attention is given to potential research directions, such as investigating alternative biological agents and optimizing the concrete environment to support microbial activity. The culmination of this investigation is a call to action for integrating self-healing bioconcrete in construction on a broader scale, thereby realizing its potential to fortify infrastructure resilience and sustainability.
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Affiliation(s)
- Pui Yan Wong
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong Special Administrative Region
| | - Joyabrata Mal
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj 211004, Uttar Pradesh, India
| | - Anna Sandak
- InnoRenew CoE, Livade 6a, 6310 Izola, Slovenia; Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia; Andrej Marušič Institute, University of Primorska, Titov trg 4, 6000 Koper, Slovenia
| | - Lijun Luo
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong Special Administrative Region
| | - Jianxiong Jian
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong Special Administrative Region
| | - Nirakar Pradhan
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong Special Administrative Region.
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Nag M, Pallavi J, Chakraborty S, Roychoudhury T, Mondal S, Ghosh A, Saha C, Banerjee M, Seal A. Bacterial endosymbionts of a nitrogen-fixing yeast Rhodotorula mucilaginosa JGTA-S1 - insights into a yet unknown micro-ecosystem. Mol Omics 2024. [PMID: 39263696 DOI: 10.1039/d3mo00273j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Rhodotorula mucilaginosa JGTA-S1 is a yeast strain capable of fixing nitrogen and improving nitrogen nutrition in rice plants because of its nitrogen-fixing endobacteria, namely Stutzerimonas (Pseudomonas) stutzeri and Bradyrhizobium sp. To gain a deeper understanding of yeast endosymbionts, we conducted a whole-genome shotgun metagenomic analysis of JGTA-S1 cells grown under conditions of nitrogen sufficiency and deficiency. Our results showed that the endosymbiont population varied depending on the nitrogen regime. Upon mechanical disruption of yeast cells, we obtained endosymbionts in culturable form viz. Bacillus velezensis and Staphylococcus sp. under nitrogen-replete conditions and Lysinibacillus telephonicus., Brevibacillus sp., and Niallia circulans under nitrogen-depleted conditions. S. stutzeri and Bradyrhizobium sp. the previously reported endosymbionts remained unculturable. The culturable endosymbionts Staphylococcus sp. and Bacillus velezensis appear to possess genes for dissimilatory nitrate reduction (DNRA), an alternative pathway for ammonia synthesis. However, our findings suggest that these endosymbionts are facultative as they survive outside the host. The fitness of the yeast was not affected by curing of these microbes. Curing the yeast diazotrophic endosymbionts took a toll on its fitness. Our results also showed that the populations of S. stutzeri and B. velezensis increased significantly under nitrogen-depleted conditions compared to nitrogen-sufficient conditions. The importance of DNRA and nitrogen fixation is also reflected in the metagenomic reads of JGTA-S1.
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Affiliation(s)
- Mayurakshi Nag
- Department of Biotechnology and Dr B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata - 700019, India.
| | - Janardhan Pallavi
- Center for Innovation in Molecular and Pharmaceutical Sciences (CIMPS), Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India
| | - Sandipan Chakraborty
- Center for Innovation in Molecular and Pharmaceutical Sciences (CIMPS), Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India
| | - Trina Roychoudhury
- Department of Biotechnology and Dr B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata - 700019, India.
| | - Sangita Mondal
- Department of Biological Sciences Bose Institute, Unified Academic Campus, EN 80. Sector V, Bidhan Nagar, Kolkata - 700091, India
| | - Abhrajyoti Ghosh
- Department of Biological Sciences Bose Institute, Unified Academic Campus, EN 80. Sector V, Bidhan Nagar, Kolkata - 700091, India
| | - Chinmay Saha
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Manidipa Banerjee
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Anindita Seal
- Department of Biotechnology and Dr B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata - 700019, India.
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Kaviraj M, Kumar U, Snigdha A, Chatterjee S. Nitrate reduction to ammonium: a phylogenetic, physiological, and genetic aspects in Prokaryotes and eukaryotes. Arch Microbiol 2024; 206:297. [PMID: 38861039 DOI: 10.1007/s00203-024-04009-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 06/12/2024]
Abstract
The microbe-mediated conversion of nitrate (NO3-) to ammonium (NH4+) in the nitrogen cycle has strong implications for soil health and crop productivity. The role of prokaryotes, eukaryotes and their phylogeny, physiology, and genetic regulations are essential for understanding the ecological significance of this empirical process. Several prokaryotes (bacteria and archaea), and a few eukaryotes (fungi and algae) are reported as NO3- reducers under certain conditions. This process involves enzymatic reactions which has been catalysed by nitrate reductases, nitrite reductases, and NH4+-assimilating enzymes. Earlier reports emphasised that single-cell prokaryotic or eukaryotic organisms are responsible for this process, which portrayed a prominent gap. Therefore, this study revisits the similarities and uniqueness of mechanism behind NO3- -reduction to NH4+ in both prokaryotes and eukaryotes. Moreover, phylogenetic, physiological, and genetic regulation also shed light on the evolutionary connections between two systems which could help us to better explain the NO3--reduction mechanisms over time. Reports also revealed that certain transcription factors like NtrC/NtrB and Nit2 have shown a major role in coordinating the expression of NO3- assimilation genes in response to NO3- availability. Overall, this review provides a comprehensive information about the complex fermentative and respiratory dissimilatory nitrate reduction to ammonium (DNRA) processes. Uncovering the complexity of this process across various organisms may further give insight into sustainable nitrogen management practices and might contribute to addressing global environmental challenges.
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Affiliation(s)
- Megha Kaviraj
- ICAR- National Rice Research Institute, Cuttack, 753006, Odisha, India.
- The University of Burdwan, Burdwan, 713104, West Bengal, India.
| | - Upendra Kumar
- ICAR- National Rice Research Institute, Cuttack, 753006, Odisha, India.
| | - Alisha Snigdha
- Siksha 'O' Anusandhan University, Bhubaneswar, 751003, Odisha, India
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Saghaï A, Hallin S. Diversity and ecology of NrfA-dependent ammonifying microorganisms. Trends Microbiol 2024; 32:602-613. [PMID: 38462391 DOI: 10.1016/j.tim.2024.02.007] [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: 11/22/2023] [Revised: 02/11/2024] [Accepted: 02/13/2024] [Indexed: 03/12/2024]
Abstract
Nitrate ammonifiers are a taxonomically diverse group of microorganisms that reduce nitrate to ammonium, which is released, and thereby contribute to the retention of nitrogen in ecosystems. Despite their importance for understanding the fate of nitrate, they remain a largely overlooked group in the nitrogen cycle. Here, we present the latest advances on free-living microorganisms using NrfA to reduce nitrite during ammonification. We describe their diversity and ecology in terrestrial and aquatic environments, as well as the environmental factors influencing the competition for nitrate with denitrifiers that reduce nitrate to gaseous nitrogen species, including the greenhouse gas nitrous oxide (N2O). We further review the capacity of ammonifiers for other redox reactions, showing that they likely play multiple roles in the cycling of elements.
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Affiliation(s)
- Aurélien Saghaï
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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She Z, Wang J, Pan X, Ma D, Gao Y, Wang S, Chuai X, Mu Y, Yue Z. Multi-omics insights into biogeochemical responses to organic matter addition in an acidic pit lake: Implications for bioremediation. WATER RESEARCH 2024; 254:121404. [PMID: 38442608 DOI: 10.1016/j.watres.2024.121404] [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: 08/07/2023] [Revised: 01/30/2024] [Accepted: 02/29/2024] [Indexed: 03/07/2024]
Abstract
Acidic pit lakes (APLs) emerge as reservoirs of acid mine drainage in flooded open-pit mines, representing extreme ecosystems and environmental challenges worldwide. The bioremediation of these oligotrophic waters necessitates the addition of organic matter, but the biogeochemical response of APLs to exogenous organic matter remains inadequately comprehended. This study delves into the biogeochemical impacts and remediation effects of digestate-derived organic matter within an APL, employing a multi-omics approach encompassing geochemical analyses, amplicon and metagenome sequencing, and ultra-high resolution mass spectrometry. The results indicated that digestate addition first stimulated fungal proliferation, particularly Ascomycetes and Basidiomycetes, which generated organic acids through lignocellulosic hydrolysis and fermentation. These simple compounds further supported heterotrophic growth, including Acidiphilium, Acidithrix, and Clostridium, thereby facilitating nitrate, iron, and sulfate reduction linked with acidity consumption. Nutrients derived from digestate also promoted the macroscopic development of acidophilic algae. Notably, the increased sulfate reduction-related genes primarily originated from assimilatory metabolism, thus connecting sulfate decrease to organosulfur increase. Assimilatory and dissimilatory sulfate reduction collectively contributed to sulfate removal and metal fixation. These findings yield multi-omics insights into APL biogeochemical responses to organic matter addition, enhancing the understanding of carbon-centered biogeochemical cycling in extreme ecosystems and guiding organic amendment-based bioremediation in oligotrophic polluted environments.
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Affiliation(s)
- Zhixiang She
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei, Anhui 230009, China; Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Jin Wang
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei, Anhui 230009, China; Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui 230009, China.
| | - Xin Pan
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei, Anhui 230009, China; Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Ding Ma
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei, Anhui 230009, China; Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Yijun Gao
- Luohe Mining Company Ltd, Anhui Maanshan Iron and Steel Mining Resources Group, Hefei, Anhui 230009, China
| | - Shaoping Wang
- Nanshan Mining Company Ltd, Anhui Maanshan Iron and Steel Mining Resources Group, Ma'anshan, Anhui 243000, China
| | - Xin Chuai
- Nanshan Mining Company Ltd, Anhui Maanshan Iron and Steel Mining Resources Group, Ma'anshan, Anhui 243000, China
| | - Yang Mu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Zhengbo Yue
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei, Anhui 230009, China; Anhui Engineering Research Center of Industrial Wastewater Treatment and Resource Recovery, Hefei University of Technology, Hefei, Anhui 230009, China; Key Laboratory of Nanominerals and Pollution Control of Anhui Higher Education Institutes, Hefei University of Technology, Hefei, Anhui 230009, China.
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Diver P, Ward BA, Cunliffe M. Physiological and morphological plasticity in response to nitrogen availability of a yeast widely distributed in the open ocean. FEMS Microbiol Ecol 2024; 100:fiae053. [PMID: 38599628 PMCID: PMC11062419 DOI: 10.1093/femsec/fiae053] [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: 08/09/2023] [Revised: 04/02/2024] [Accepted: 04/09/2024] [Indexed: 04/12/2024] Open
Abstract
Yeasts are prevalent in the open ocean, yet we have limited understanding of their ecophysiological adaptations, including their response to nitrogen availability, which can have a major role in determining the ecological potential of other planktonic microbes. In this study, we characterized the nitrogen uptake capabilities and growth responses of marine-occurring yeasts. Yeast isolates from the North Atlantic Ocean were screened for growth on diverse nitrogen substrates, and across a concentration gradient of three environmentally relevant nitrogen substrates: nitrate, ammonium, and urea. Three strains grew with enriched nitrate while two did not, demonstrating that nitrate utilization is present but not universal in marine yeasts, consistent with existing knowledge of nonmarine yeast strains. Naganishia diffluens MBA_F0213 modified the key functional trait of cell size in response to nitrogen concentration, suggesting yeast cell morphology changes along chemical gradients in the marine environment. Meta-analysis of the reference DNA barcode in public databases revealed that the genus Naganishia has a global ocean distribution, strengthening the environmental applicability of the culture-based observations. This study provides novel quantitative understanding of the ecophysiological and morphological responses of marine-derived yeasts to variable nitrogen availability in vitro, providing insight into the functional ecology of yeasts within pelagic open ocean environments.
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Affiliation(s)
- Poppy Diver
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, United Kingdom
- School of Ocean and Earth Science, University of Southampton, Waterfront Campus, European Way, Southampton, SO14 3ZH, United Kingdom
| | - Ben A Ward
- School of Ocean and Earth Science, University of Southampton, Waterfront Campus, European Way, Southampton, SO14 3ZH, United Kingdom
| | - Michael Cunliffe
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, United Kingdom
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth, PL4 8AA, United Kingdom
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Narsing Rao MP, Singh RN, Sani RK, Banerjee A. Genome-based approach to evaluate the metabolic potentials and exopolysaccharides production of Bacillus paralicheniformis CamBx3 isolated from a Chilean hot spring. Front Microbiol 2024; 15:1377965. [PMID: 38628868 PMCID: PMC11018918 DOI: 10.3389/fmicb.2024.1377965] [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: 01/28/2024] [Accepted: 03/13/2024] [Indexed: 04/19/2024] Open
Abstract
In the present study, a thermophilic strain designated CamBx3 was isolated from the Campanario hot spring, Chile. Based on 16S rRNA gene sequence, phylogenomic, and average nucleotide identity analysis the strain CamBx3 was identified as Bacillus paralicheniformis. Genome analysis of B. paralicheniformis CamBx3 revealed the presence of genes related to heat tolerance, exopolysaccharides (EPS), dissimilatory nitrate reduction, and assimilatory sulfate reduction. The pangenome analysis of strain CamBx3 with eight Bacillus spp. resulted in 26,562 gene clusters, 7,002 shell genes, and 19,484 cloud genes. The EPS produced by B. paralicheniformis CamBx3 was extracted, partially purified, and evaluated for its functional activities. B. paralicheniformis CamBx3 EPS with concentration 5 mg mL-1 showed an optimum 92 mM ferrous equivalent FRAP activity, while the same concentration showed a maximum 91% of Fe2+ chelating activity. B. paralicheniformis CamBx3 EPS (0.2 mg mL-1) demonstrated β-glucosidase inhibition. The EPS formed a viscoelastic gel at 45°C with a maximum instantaneous viscosity of 315 Pa.s at acidic pH 5. The present study suggests that B. paralicheniformis CamBx3 could be a valuable resource for biopolymers and bioactive molecules for industrial applications.
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Affiliation(s)
- Manik Prabhu Narsing Rao
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Sede Talca, Talca, Chile
| | - Ram Nageena Singh
- Department of Chemical and Biological Engineering, South Dakota Mines, Rapid City, SD, United States
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota Mines, Rapid City, SD, United States
| | - Rajesh K. Sani
- Department of Chemical and Biological Engineering, South Dakota Mines, Rapid City, SD, United States
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota Mines, Rapid City, SD, United States
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota Mines, Rapid City, SD, United States
- BioWRAP (Bioplastics With Regenerative Agricultural Properties), Rapid City, SD, United States
| | - Aparna Banerjee
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Sede Talca, Talca, Chile
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Chen C, Ai J, Chen L, Li Y, Tang X, Li J. Nitrogen metabolism pathways and functional microorganisms in typical karst wetlands. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:22494-22506. [PMID: 38407711 DOI: 10.1007/s11356-024-32587-5] [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: 08/19/2023] [Accepted: 02/18/2024] [Indexed: 02/27/2024]
Abstract
Aha Lake artificial reservoir wetland, Niangniang Mountain karst mountain wetland, and Caohai plateau lake wetland are typical karst wetlands in Guizhou Province with unique topography and geomorphic features. They were selected as research objects in this study to explore microorganisms and functional genes in nitrogen metabolism adopting macro-genome sequencing technology. It was found that Proteobacteria, Actinobacteria, and Acidobacteria were the dominant phyla in nitrogen metabolism in these three wetlands, similar to previous studies. However, at the genus level, there was a significant difference, with the dominant bacteria being Bradyrhizobium, Methylocystis, and Anaeromyxobacter. Six nitrogen metabolism pathways, including nitrogen fixation, nitrification, denitrification, dissimilatory nitrate reduction, assimilatory nitrate reduction, and complete nitrification, comammox, were revealed, but anaerobic ammonia oxidation genes were not detected. Nitrogen metabolism microorganisms and pathways were more affected by SOM, pH, NO3-, and EC in karst wetlands. This study further discussed microorganisms and functions of nitrogen metabolism in karst wetlands, which was of great significance to nitrogen cycles of karst wetland ecosystems.
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Affiliation(s)
- Chen Chen
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 550025, China
| | - Jia Ai
- Ecological and Environmental Monitoring Center, Guizhou, 558013, Qiannan, China
| | - Li Chen
- College of Civil Engineering, Chongqing Vocational Institute of Engineering, Chongqing, 402260, China
| | - Yancheng Li
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 550025, China.
- Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang, 550025, Guizhou, China.
| | - Xin Tang
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 550025, China
| | - Jiang Li
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, 550025, China
- Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang, 550025, Guizhou, China
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Maruyama R, Yasumoto K, Mizusawa N, Iijima M, Yasumoto-Hirose M, Iguchi A, Hermawan OR, Hosono T, Takada R, Song KH, Shinjo R, Watabe S, Yasumoto J. Metagenomic analysis of the microbial communities and associated network of nitrogen metabolism genes in the Ryukyu limestone aquifer. Sci Rep 2024; 14:4356. [PMID: 38388732 PMCID: PMC10883930 DOI: 10.1038/s41598-024-54614-8] [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: 02/17/2023] [Accepted: 02/14/2024] [Indexed: 02/24/2024] Open
Abstract
While microbial biogeochemical activities such as those involving denitrification and sulfate reduction have been considered to play important roles in material cycling in various aquatic ecosystems, our current understanding of the microbial community in groundwater ecosystems is remarkably insufficient. To assess the groundwater in the Ryukyu limestone aquifer of Okinawa Island, which is located in the southernmost region of Japan, we performed metagenomic analysis on the microbial communities at the three sites and screened for functional genes associated with nitrogen metabolism. 16S rRNA amplicon analysis showed that bacteria accounted for 94-98% of the microbial communities, which included archaea at all three sites. The bacterial communities associated with nitrogen metabolism shifted by month at each site, indicating that this metabolism was accomplished by the bacterial community as a whole. Interestingly, site 3 contained much higher levels of the denitrification genes such as narG and napA than the other two sites. This site was thought to have undergone denitrification that was driven by high quantities of dissolved organic carbon (DOC). In contrast, site 2 was characterized by a high nitrate-nitrogen (NO3-N) content and a low amount of DOC, and this site yielded a moderate amount of denitrification genes. Site 1 showed markedly low amounts of all nitrogen metabolism genes. Overall, nitrogen metabolism in the Ryukyu limestone aquifer was found to change based on environmental factors.
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Affiliation(s)
- Rio Maruyama
- Kitasato University School of Marine Biosciences, 1-15-1 Kitasato, Minami, Sagamihara, Kanagawa, 252-0373, Japan
| | - Ko Yasumoto
- Kitasato University School of Marine Biosciences, 1-15-1 Kitasato, Minami, Sagamihara, Kanagawa, 252-0373, Japan
| | - Nanami Mizusawa
- Kitasato University School of Marine Biosciences, 1-15-1 Kitasato, Minami, Sagamihara, Kanagawa, 252-0373, Japan
| | - Mariko Iijima
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan
| | | | - Akira Iguchi
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan
| | - Oktanius Richard Hermawan
- Department of Earth and Environmental Science, Graduate School of Science and Technology, Kumamoto University, 2-39-1, Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
| | - Takahiro Hosono
- Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
- International Research Organization for Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
| | - Ryogo Takada
- Center for Strategic Research Project, University of the Ryukyus, Nishihara, Senbaru, Okinawa, 903-0213, Japan
| | - Ke-Han Song
- Department of Physics and Earth Sciences, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
| | - Ryuichi Shinjo
- Department of Physics and Earth Sciences, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
- Research Institute for Humanity and Nature, 457-4 Motoyama, Kamigamo, Kita-ku, Kyoto, 603-8047, Japan
| | - Shugo Watabe
- Kitasato University School of Marine Biosciences, 1-15-1 Kitasato, Minami, Sagamihara, Kanagawa, 252-0373, Japan
| | - Jun Yasumoto
- Faculty of Agriculture, University of the Ryukyus, 1 Senbaru, Nishihara, Nakagami, Okinawa, 903-0213, Japan.
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Kyei-Baffour ES, Owusu-Boateng K, Isawumi A, Mosi L. Pseudogenomic insights into the evolution of Mycobacterium ulcerans. BMC Genomics 2024; 25:87. [PMID: 38253991 PMCID: PMC10802024 DOI: 10.1186/s12864-024-10001-1] [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: 08/14/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Buruli ulcer (BU) disease, caused by Mycobacterium ulcerans (MU), and characterized by necrotic ulcers is still a health problem in Africa and Australia. The genome of the bacterium has several pseudogenes due to recent evolutionary events and environmental pressures. Pseudogenes are genetic elements regarded as nonessential in bacteria, however, they are less studied due to limited available tools to provide understanding of their evolution and roles in MU pathogenicity. RESULTS This study developed a bioinformatic pipeline to profile the pseudogenomes of sequenced MU clinical isolates from different countries. One hundred and seventy-two MU genomes analyzed revealed that pseudogenomes of African strains corresponded to the two African lineages 1 and 2. Pseudogenomes were lineage and location specific and African lineage 1 was further divided into A and B. Lineage 2 had less relaxation in positive selection than lineage 1 which may signify different evolutionary points. Based on the Gil-Latorre model, African MU strains may be in the latter stages of evolutionary adaption and are adapting to an environment rich in metabolic resources with a lower temperature and decreased UV radiation. The environment fosters oxidative metabolism and MU may be less reliant on some secondary metabolites. In-house pseudogenomes from Ghana and Cote d'Ivoire were different from other African strains, however, they were identified as African strains. CONCLUSION Our bioinformatic pipeline provides pseudogenomic insights to complement other whole genome analyses, providing a better view of the evolution of the genome of MU and suggest an adaptation model which is important in understanding transmission. MU pseudogene profiles vary based on lineage and country, and an apparent reduction in insertion sequences used for the detection of MU which may adversely affect the sensitivity of diagnosis.
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Affiliation(s)
- Edwin Sakyi Kyei-Baffour
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Kwabena Owusu-Boateng
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
- Department of Microbial Sciences, University of Surrey, Surrey, UK
| | - Abiola Isawumi
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Lydia Mosi
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana.
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11
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Jiang JP, Leng S, Liao YF, Liu X, Li DX, Chu C, Yu XY, Liu CH. The potential role of subseafloor fungi in driving the biogeochemical cycle of nitrogen under anaerobic conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 897:165374. [PMID: 37422230 DOI: 10.1016/j.scitotenv.2023.165374] [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: 04/29/2023] [Revised: 07/01/2023] [Accepted: 07/05/2023] [Indexed: 07/10/2023]
Abstract
Fungi represent the dominant eukaryotic group of organisms in anoxic marine sedimentary ecosystems, ranging from a few centimeters to ~ 2.5 km below seafloor. However, little is known about how fungi can colonize anaerobic subseafloor environments for tens of millions of years and whether they play a role in elemental biogeochemical cycles. Based on metabolite detection, isotope tracer and gene analysis, we examined the anaerobic nitrogen conversion pathways of 19 fungal species (40 strains) isolated from1.3 to 2.5 km coal-bearing sediments below seafloor. Our results show for the first time that almost all fungi possess anaerobic denitrification, dissimilatory nitrate reduction to ammonium (DNRA), and nitrification pathways, but not anaerobic ammonium oxidation (anammox). Moreover, the distribution of fungi with different nitrogen-conversion abilities in subseafloor sediments was mainly determined by in situ temperature, CaCO3, and inorganic carbon contents. These findings suggest that fungi have multiple nitrogen transformation processes to cope with their requirements for a variety of nitrogen sources in nutrient deficient anaerobic subseafloor sedimentary environments.
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Affiliation(s)
- Jun-Peng Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Shuang Leng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yi-Fan Liao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xuan Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Dong-Xu Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Chen Chu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xiang-Yang Yu
- Jiangsu Key Laboratory for Food Quality, Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
| | - Chang-Hong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.
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12
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Gain G, Berne N, Feller T, Godaux D, Cenci U, Cardol P. Induction of photosynthesis under anoxic condition in Thalassiosira pseudonana and Euglena gracilis: interactions between fermentation and photosynthesis. FRONTIERS IN PLANT SCIENCE 2023; 14:1186926. [PMID: 37560033 PMCID: PMC10407231 DOI: 10.3389/fpls.2023.1186926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 06/28/2023] [Indexed: 08/11/2023]
Abstract
INTRODUCTION In their natural environment, microalgae can be transiently exposed to hypoxic or anoxic environments. Whereas fermentative pathways and their interactions with photosynthesis are relatively well characterized in the green alga model Chlamydomonas reinhardtii, little information is available in other groups of photosynthetic micro-eukaryotes. In C. reinhardtii cyclic electron flow (CEF) around photosystem (PS) I, and light-dependent oxygen-sensitive hydrogenase activity both contribute to restoring photosynthetic linear electron flow (LEF) in anoxic conditions. METHODS Here we analyzed photosynthetic electron transfer after incubation in dark anoxic conditions (up to 24 h) in two secondary microalgae: the marine diatom Thalassiosira pseudonana and the excavate Euglena gracilis. RESULTS Both species showed sustained abilities to prevent over-reduction of photosynthetic electron carriers and to restore LEF. A high and transient CEF around PSI was also observed specifically in anoxic conditions at light onset in both species. In contrast, at variance with C. reinhardtii, no sustained hydrogenase activity was detected in anoxic conditions in both species. DISCUSSION Altogether our results suggest that another fermentative pathway might contribute, along with CEF around PSI, to restore photosynthetic activity in anoxic conditions in E. gracilis and T. pseudonana. We discuss the possible implication of the dissimilatory nitrate reduction to ammonium (DNRA) in T. pseudonana and the wax ester fermentation in E. gracilis.
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Affiliation(s)
- Gwenaëlle Gain
- InBioS – PhytoSYSTEMS, Laboratoire de Génétique et Physiologie des Microalgues, ULiège, Liège, Belgium
| | - Nicolas Berne
- InBioS – PhytoSYSTEMS, Laboratoire de Génétique et Physiologie des Microalgues, ULiège, Liège, Belgium
| | - Tom Feller
- InBioS – PhytoSYSTEMS, Laboratoire de Génétique et Physiologie des Microalgues, ULiège, Liège, Belgium
| | - Damien Godaux
- InBioS – PhytoSYSTEMS, Laboratoire de Génétique et Physiologie des Microalgues, ULiège, Liège, Belgium
| | - Ugo Cenci
- Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, CNRS, UMR8576 – UGSF, Lille, France
| | - Pierre Cardol
- InBioS – PhytoSYSTEMS, Laboratoire de Génétique et Physiologie des Microalgues, ULiège, Liège, Belgium
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13
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Tribelhorn K, Twarużek M, Kosicki R, Straubinger RK, Ebel F, Ulrich S. A Chemically Defined Medium That Supports Mycotoxin Production by Stachybotrys chartarum Enabled Analysis of the Impact of Nitrogen and Carbon Sources on the Biosynthesis of Macrocyclic Trichothecenes and Stachybotrylactam. Appl Environ Microbiol 2023:e0016323. [PMID: 37338364 PMCID: PMC10370337 DOI: 10.1128/aem.00163-23] [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: 02/15/2023] [Accepted: 05/21/2023] [Indexed: 06/21/2023] Open
Abstract
Stachybotrys chartarum (Hypocreales, Ascomycota) is a toxigenic fungus that is frequently isolated from water-damaged buildings or improperly stored feed. The secondary metabolites formed by this mold have been associated with health problems in humans and animals. Several authors have studied the influence of environmental conditions on the production of mycotoxins, but these studies focused on undefined or complex substrates, such as building materials and media that impeded investigations of the influence of specific nutrients. In this study, a chemically defined cultivation medium was used to investigate the impact of several nitrogen and carbon sources on growth of S. chartarum and its production of macrocyclic trichothecenes (MTs) and stachybotrylactam (STLAC). Increasing concentrations of sodium nitrate were found to positively affect mycelial growth, the level of sporulation, and MT production, while ammonium nitrate and ammonium chloride had an inhibitory effect. Potato starch was the superior and most reliable carbon source tested. Additionally, we observed that the level of sporulation was correlated with the production of MTs but not with that of STLAC. In this study, we provide a chemically well-defined cultivation medium suitable for standardized in vitro testing of the capacity of S. chartarum isolates to produce macrocyclic trichothecenes. IMPORTANCE Macrocyclic trichothecenes (MTs) are highly toxic secondary metabolites that are produced by certain Stachybotrys chartarum strains, which consequently pose a risk for animals and humans. To identify hazardous, toxin-producing strains by analytical means, it is important to grow them under conditions that support MT production. Nutrients determine growth and development and thus the synthesis of secondary metabolites. Complex rich media are commonly used for diagnostics, but batch differences of supplements pose a risk for inconsistent data. We have established a chemically defined medium for S. chartarum and used it to analyze the impact of nitrogen and carbon sources. A key finding is that nitrate stimulates MT production, whereas ammonium suppresses it. Defining nutrients that support MT production will enable a more reliable identification of hazardous S. chartarum isolates. The new medium will also be instrumental in analyzing the biosynthetic pathways and regulatory mechanisms that control mycotoxin production in S. chartarum.
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Affiliation(s)
- Katharina Tribelhorn
- Chair of Bacteriology and Mycology, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Institute for Infectious Diseases and Zoonosis, LMU Munich, Munich, Germany
| | - Magdalena Twarużek
- Department of Physiology and Toxicology, Faculty of Biological Sciences, Kazimierz Wielki University, Bydgoszcz, Poland
| | - Robert Kosicki
- Department of Physiology and Toxicology, Faculty of Biological Sciences, Kazimierz Wielki University, Bydgoszcz, Poland
| | - Reinhard K Straubinger
- Chair of Bacteriology and Mycology, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Institute for Infectious Diseases and Zoonosis, LMU Munich, Munich, Germany
| | - Frank Ebel
- Chair of Bacteriology and Mycology, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Institute for Infectious Diseases and Zoonosis, LMU Munich, Munich, Germany
| | - Sebastian Ulrich
- Chair of Bacteriology and Mycology, Department of Veterinary Sciences, Faculty of Veterinary Medicine, Institute for Infectious Diseases and Zoonosis, LMU Munich, Munich, Germany
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14
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Li Y, Liao Z, Hui C, Zheng J, Yuan S, Zhang W. Hydraulic characteristics in channel confluence affect the nitrogen dynamics through altering interactions among multi-trophic microbiota. WATER RESEARCH 2023; 235:119882. [PMID: 36947927 DOI: 10.1016/j.watres.2023.119882] [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: 11/22/2022] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
Identifying the distribution of multi-trophic microbiota under the complicated hydrodynamic characteristics of channel confluences and evaluating the microbial contributions to biogeochemical processes are vital for river regulation and ecological function protection. However, relevant studies mainly focus on bacterial community distribution in confluence, neglecting the essential role of multi-trophic microbiota in the aquatic ecosystems and biogeochemical processes. To address this knowledge gap, this study investigated the distribution of multi-trophic microbiota and the underlying assembly process under the hydraulic characteristics in the confluence and described the direct and indirect effects of multi-trophic microbiota on the nitrogen dynamics. Results revealed that, in a river confluence, eukaryotic communities were governed by deterministic processes (52.4%) and bacterial communities were determined by stochastic processes (74.3%). The response of higher trophic levels to environmental factors was intensively higher than that of lower trophic microbiota, resulting in higher trophic microbiota were significantly different between regions with varied environmental conditions (P < 0.05). Flow velocity was the driving force controlling the assembly and composition of multi-trophic microbiota and interactions among multi-trophic levels, and further made a significant difference to nitrogen dynamics. In regions with lower flow velocity, interactions among multi-trophic levels were more complex. There were intense nitrate and nitrite reduction and anammox reactions via direct impacts of protozoan and metazoan and the top-down control (protozoan and metazoan prey on heterotrophic bacteria) among multi-trophic microbiota. Results and findings reveal the ecological effect on river nitrogen removal in a river confluence under complex hydraulic conditions and provide useful information for river management.
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Affiliation(s)
- Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China.
| | - Ziying Liao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Cizhang Hui
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China.
| | - Jinhai Zheng
- Key Laboratory of Ministry of Education for Coastal Disaster and Protection, Hohai University, Nanjing 210024, China
| | - Saiyu Yuan
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, China
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
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15
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Kurtz BE, Landmeyer JE, Culter JK. Precipitation, submarine groundwater discharge of nitrogen, and red tides along the southwest Florida Gulf coast. Heliyon 2023; 9:e16046. [PMID: 37215903 PMCID: PMC10196494 DOI: 10.1016/j.heliyon.2023.e16046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 04/05/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023] Open
Abstract
Blooms of the dinoflagellate Karenia brevis occur almost every year along the southwest Florida Gulf coast. Long-duration blooms with especially high concentrations of K. brevis, known as red tides, destroy marine life through production of neurotoxins. Current hypotheses are that red tides originate in oligotrophic waters far offshore using nitrogen (N) from upwelling bottom water or, alternatively, from blooms of Trichodesmium, followed by advection to nearshore waters. But the amount of N available from terrestrial sources does not appear to be adequate to maintain a nearshore red tide. To explain this discrepancy, we hypothesize that contemporary red tides are associated with release of N from offshore submarine groundwater discharge (SGD) that has accumulated in benthic sediment biomass by dissimilatory nitrate reduction to ammonium (DNRA). The release occurs when sediment labile organic carbon (LOC), used as the electron donor in DNRA, is exhausted. Detritus from the resulting destruction of marine life restores the sediment LOC to continue the cycle of red tides. The severity of individual red tides increases with increased bloom-year precipitation in the geographic region where the SGD originates, while the severity of ordinary blooms is relatively unaffected.
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Affiliation(s)
- Bruce E. Kurtz
- New College of Florida, 5800 Bay Shore Rd., Sarasota, FL 34243, USA
| | | | - James K. Culter
- Mote Marine Laboratory, 1600 Ken Thompson Pkwy, Sarasota, FL 34236, USA
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16
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Saini JS, Manni M, Hassler C, Cable RN, Duhaime MB, Zdobnov EM. Genomic insights into the coupling of a Chlorella-like microeukaryote and sulfur bacteria in the chemocline of permanently stratified Lake Cadagno. THE ISME JOURNAL 2023; 17:903-915. [PMID: 37031343 DOI: 10.1038/s41396-023-01396-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 04/10/2023]
Abstract
Meromictic Lake Cadagno is a permanently stratified system with a persistent microbial bloom within the oxic-anoxic boundary called the chemocline. The association between oxygenic and anoxygenic photosynthesis within the chemocline has been known for at least two decades. Although anoxygenic purple and green sulfur bacteria have been well studied, reports on oxygenic phytoplankton have remained sparse since their discovery in the 1920s. Nearly a century later, this study presents the first near-complete genome of a photosynthetic microbial eukaryote from the chemocline of Lake Cadagno, provisionally named Chlorella-like MAG. The 18.9 Mbp nuclear genome displays a high GC content (71.5%), and the phylogenetic placement suggests that it is a novel species of the genus Chlorella of Chlorophytes. Functional annotation of the Chlorella-like metagenome-assembled genome predicted 10,732 protein-coding genes, with an approximate 0.6% proportion potentially involved in carbon, sulfur, and nitrogen (C, N, and S) metabolism. In addition to C4 photosynthesis, this study detected genes for heat shock proteins (HSPs) in the Chlorella-like algae, consistent with the other Chlorella species. Altogether, the genomic insights in this study suggest the cooperation of photosynthetic algae with phototrophic sulfur bacteria via C, N, and S metabolism, which may aid their collective persistence in the Lake Cadagno chemocline. Furthermore, this work additionally presents the chloroplast genome of Cryptomonas-like species, which was likely to be presumed as cyanobacteria in previous studies because of the presence of phycobilisomes.
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Affiliation(s)
- Jaspreet S Saini
- Department F.-A Forel for Environmental and Aquatic Sciences, Earth and Environmental Sciences, University of Geneva, Geneva, Switzerland.
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
| | - Mosè Manni
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christel Hassler
- Department F.-A Forel for Environmental and Aquatic Sciences, Earth and Environmental Sciences, University of Geneva, Geneva, Switzerland
- Institute of Earth Sciences, University of Lausanne, Lausanne, Switzerland
| | - Rachel N Cable
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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17
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Huang J, Mellage A, Garcia JP, Glöckler D, Mahler S, Elsner M, Jakus N, Mansor M, Jiang H, Kappler A. Metabolic Performance and Fate of Electrons during Nitrate-Reducing Fe(II) Oxidation by the Autotrophic Enrichment Culture KS Grown at Different Initial Fe/N Ratios. Appl Environ Microbiol 2023; 89:e0019623. [PMID: 36877057 PMCID: PMC10057050 DOI: 10.1128/aem.00196-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 02/11/2023] [Indexed: 03/07/2023] Open
Abstract
Autotrophic nitrate-reducing Fe(II)-oxidizing (NRFeOx) microorganisms fix CO2 and oxidize Fe(II) coupled to denitrification, influencing carbon, iron, and nitrogen cycles in pH-neutral, anoxic environments. However, the distribution of electrons from Fe(II) oxidation to either biomass production (CO2 fixation) or energy generation (nitrate reduction) in autotrophic NRFeOx microorganisms has not been quantified. We therefore cultivated the autotrophic NRFeOx culture KS at different initial Fe/N ratios, followed geochemical parameters, identified minerals, analyzed N isotopes, and applied numerical modeling. We found that at all initial Fe/N ratios, the ratios of Fe(II)oxidized to nitratereduced were slightly higher (5.11 to 5.94 at Fe/N ratios of 10:1 and 10:0.5) or lower (4.27 to 4.59 at Fe/N ratios of 10:4, 10:2, 5:2, and 5:1) than the theoretical ratio for 100% Fe(II) oxidation being coupled to nitrate reduction (5:1). The main N denitrification product was N2O (71.88 to 96.29% at Fe/15N ratios of 10:4 and 5:1; 43.13 to 66.26% at an Fe/15N ratio of 10:1), implying that denitrification during NRFeOx was incomplete in culture KS. Based on the reaction model, on average 12% of electrons from Fe(II) oxidation were used for CO2 fixation while 88% of electrons were used for reduction of NO3- to N2O at Fe/N ratios of 10:4, 10:2, 5:2, and 5:1. With 10 mM Fe(II) (and 4, 2, 1, or 0.5 mM nitrate), most cells were closely associated with and partially encrusted by the Fe(III) (oxyhydr)oxide minerals, whereas at 5 mM Fe(II), most cells were free of cell surface mineral precipitates. The genus Gallionella (>80%) dominated culture KS regardless of the initial Fe/N ratios. Our results showed that Fe/N ratios play a key role in regulating N2O emissions, for distributing electrons between nitrate reduction and CO2 fixation, and for the degree of cell-mineral interactions in the autotrophic NRFeOx culture KS. IMPORTANCE Autotrophic NRFeOx microorganisms that oxidize Fe(II), reduce nitrate, and produce biomass play a key role in carbon, iron, and nitrogen cycles in pH-neutral, anoxic environments. Electrons from Fe(II) oxidation are used for the reduction of both carbon dioxide and nitrate. However, the question is how many electrons go into biomass production versus energy generation during autotrophic growth. Here, we demonstrated that in the autotrophic NRFeOx culture KS cultivated at Fe/N ratios of 10:4, 10:2, 5:2, and 5:1, ca. 12% of electrons went into biomass formation, while 88% of electrons were used for reduction of NO3- to N2O. Isotope analysis also showed that denitrification during NRFeOx was incomplete in culture KS and the main N denitrification product was N2O. Therefore, most electrons stemming from Fe(II) oxidation seemed to be used for N2O formation in culture KS. This is environmentally important for the greenhouse gas budget.
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Affiliation(s)
- Jianrong Huang
- Geomicrobiology, Department of Geoscience, University of Tuebingen, Tuebingen, Germany
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Adrian Mellage
- Hydrogeology, Civil and Environmental Engineering, University of Kassel, Kassel, Germany
- Hydrogeology, Department of Geosciences, University of Tuebingen, Tuebingen, Germany
| | - Julian Pavon Garcia
- Hydrogeology, Department of Geosciences, University of Tuebingen, Tuebingen, Germany
| | - David Glöckler
- Analytical Chemistry and Water Chemistry, Technical University of Munich, Munich, Germany
| | - Susanne Mahler
- Analytical Chemistry and Water Chemistry, Technical University of Munich, Munich, Germany
| | - Martin Elsner
- Analytical Chemistry and Water Chemistry, Technical University of Munich, Munich, Germany
| | - Natalia Jakus
- Geomicrobiology, Department of Geoscience, University of Tuebingen, Tuebingen, Germany
- School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Muammar Mansor
- Geomicrobiology, Department of Geoscience, University of Tuebingen, Tuebingen, Germany
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Andreas Kappler
- Geomicrobiology, Department of Geoscience, University of Tuebingen, Tuebingen, Germany
- Cluster of Excellence, EXC 2124, Controlling Microbes to Fight Infection, Tuebingen, Germany
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18
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Muñoz-Gómez SA. Energetics and evolution of anaerobic microbial eukaryotes. Nat Microbiol 2023; 8:197-203. [PMID: 36646908 DOI: 10.1038/s41564-022-01299-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/30/2022] [Indexed: 01/18/2023]
Abstract
Mitochondria and aerobic respiration have been suggested to be required for the evolution of eukaryotic cell complexity. Aerobic respiration is several times more energetically efficient than fermentation. Moreover, aerobic respiration occurs at internalized mitochondrial membranes that are not constrained by a sublinear scaling with cell volume. However, diverse and complex anaerobic eukaryotes (for example, free-living and parasitic unicellular, and even small multicellular, eukaryotes) that exclusively rely on fermentation for energy generation have evolved repeatedly from aerobic ancestors. How do fermenting eukaryotes maintain their cell volumes and complexity while relying on such a low energy-yielding process? Here I propose that reduced rates of ATP generation in fermenting versus respiring eukaryotes are compensated for by longer cell cycles that satisfy lifetime energy demands. A literature survey and growth efficiency calculations show that fermenting eukaryotes divide approximately four to six times slower than aerobically respiring counterparts with similar cell volumes. Although ecological advantages such as competition avoidance offset lower growth rates and yields in the short term, fermenting eukaryotes inevitably have fewer physiological and ecological possibilities, which ultimately constrain their long-term evolutionary trajectories.
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19
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Xu L, Chen Y, Wang Z, Zhang Y, He Y, Zhang A, Chen H, Xue G. Discovering dominant ammonia assimilation: Implication for high-strength nitrogen removal in full scale biological treatment of landfill leachate. CHEMOSPHERE 2023; 312:137256. [PMID: 36395888 DOI: 10.1016/j.chemosphere.2022.137256] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/14/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
Landfill leachate containing high-strength nitrogen is generated in domestic waste landfilling. The integration of anoxic and aerobic process (AO) based on nitrification and denitrification, has been a mainstream process of biological nitrogen removal (BNR). But the high-strength organics as well as aerobic effluent reflux might change the biochemical environment designed and operated as AO. In view of the nitrogen balance in a full scale landfill leachate treatment plant with two-stage AO, we found that approximately 90% removal of total nitrogen (TN) and ammonia (NH4+-N) focused on primary anoxic and aerobic stage. Meanwhile, the less nitrate and nitrite in the aerobic effluent were incapable of sustaining denitrification or anaerobic ammonia oxidation (anammox). The high reflux flow from aerobic to anoxic process enabled the similar microbial community and functional genes in anoxic and aerobic process units. However, the functional genes involving ammonia assimilation in all process units showcased the highest abundance compared to those correlated with other BNR pathways, including nitrification and denitrification, assimilatory and dissimilatory nitrate reduction, nitrogen fixation and anammox. The ammonia assimilation dominated the removals of TN and NH4+-N, rather than other BNR mechanism. The insight of dominant ammonia assimilation is favorable for illustrating the authentic BNR mechanism of landfill leachate in AO, thereby guiding the optimization of engineering design and operation.
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Affiliation(s)
- Lei Xu
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Yuting Chen
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Zheng Wang
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Yu Zhang
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Yueling He
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Ai Zhang
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Hong Chen
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Gang Xue
- College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200000, China.
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20
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Lv K, Guo X, Wang C, Su Q, Liu D, Xiao S, Yang Z. Sediment nitrogen contents controlled by microbial community in a eutrophic tributary in Three Gorges Reservoir, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 314:120312. [PMID: 36183874 DOI: 10.1016/j.envpol.2022.120312] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 06/16/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Nitrogen pollution caused serious environmental problems in reservoir ecosystems. Reducing nitrogen pollution by enhancing nitrogen removal in river sediments deserved intensive research. Distributions of nitrogen contents in sediment-water interface were characterized along the Xiangxi bay (XXB), a eutrophic tributary in Three Gorges Reservoir, China. More than 47% of total Kjeldahl nitrogen (TKN) and 67% of total organic nitrogen (TON) were degraded during burial. Higher TN, TON and NH4+ consuming at downstream sites indicated stronger nitrogen mineralization and release due to higher turbulence of the overlying density currents. Nitrifying bacteria, denitrifying bacteria, anaerobic ammonium oxidizing (anammox) bacteria and nitrite/nitrate-dependent anaerobic methane oxidation (N-DAMO) bacteria were detected in nitrate-ammonium transition zone. Nitrogen contents transitions were responded to microbial stakeholders indicated microbially mediated nitrogen cycling in sediments. The dissolved oxygen and nitrate availabilities were the key limits of denitrification and associated reactions. These results suggested microbial mediated nitrogen cycling processes in sediments were critical for nitrogen removal in aquatic ecosystems, and replenishing dissolved oxygen and nitrate was expected to enhance sediment denitrification and strengthen potential environmental self-purification.
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Affiliation(s)
- Kun Lv
- Engineering Research Center of Eco-Environment in the Three Gorges Reservoir Region, Ministry of Education, Yichang, China
| | - Xiaojuan Guo
- Hubei Field Observation and Scientific Research Stations for Water Ecosystem in Three Gorges Reservoir, China Three Gorges University, Yichang, China
| | - Congfeng Wang
- Engineering Research Center of Eco-Environment in the Three Gorges Reservoir Region, Ministry of Education, Yichang, China; Hubei Field Observation and Scientific Research Stations for Water Ecosystem in Three Gorges Reservoir, China Three Gorges University, Yichang, China
| | - Qingqing Su
- Engineering Research Center of Eco-Environment in the Three Gorges Reservoir Region, Ministry of Education, Yichang, China; Hubei Field Observation and Scientific Research Stations for Water Ecosystem in Three Gorges Reservoir, China Three Gorges University, Yichang, China
| | - Defu Liu
- Hubei Field Observation and Scientific Research Stations for Water Ecosystem in Three Gorges Reservoir, China Three Gorges University, Yichang, China
| | - Shangbin Xiao
- Engineering Research Center of Eco-Environment in the Three Gorges Reservoir Region, Ministry of Education, Yichang, China
| | - Zhengjian Yang
- Engineering Research Center of Eco-Environment in the Three Gorges Reservoir Region, Ministry of Education, Yichang, China.
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21
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Zheng Y, Deng W, Liu D, Li Y, Peng K, Lorimer GH, Wang J. Redox and spectroscopic properties of mammalian nitrite reductase-like hemoproteins. J Inorg Biochem 2022; 237:111982. [PMID: 36116154 DOI: 10.1016/j.jinorgbio.2022.111982] [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: 04/02/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 01/18/2023]
Abstract
Besides the canonical pathway of L-arginine oxidation to produce nitric oxide (NO) in vivo, the nitrate-nitrite-NO pathway has been widely accepted as another source for circulating NO in mammals, especially under hypoxia. To date, there have been at least ten heme-containing nitrite reductase-like proteins discovered in mammals with activities mainly identified in vitro, including four globins (hemoglobin, myoglobin, neuroglobin (Ngb), cytoglobin (Cygb)), three mitochondrial respiratory chain enzymes (cytochrome c oxidase, cytochrome bc1, cytochrome c), and three other heme proteins (endothelial nitric oxide synthase, cytochrome P450 and indoleamine 2,3-dioxygenase 1 (IDO1)). The pathophysiological functions of these proteins are closely related to their redox and spectroscopic properties, as well as their protein structure, although the physiological roles of Ngb, Cygb and IDO1 remain unclear. So far, comprehensive summaries of the redox and spectroscopic properties of these nitrite reductase-like hemoproteins are still lacking. In this review, we have mainly summarized the published data on the application of ultraviolet-visible, electron paramagnetic resonance, circular dichroism and resonance Raman spectroscopies, and X-ray crystallography in studying nitrite reductase-like activity of these 10 proteins, in order to sort out the relationships among enzymatic function, structure and spectroscopic characterization, which might help in understanding their roles in redox biology and medicine.
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Affiliation(s)
- Yunlong Zheng
- Hubei University of Technology Autism & Depression Diagnosis and Intervention Institute, Hubei University of Technology, Wuhan, Hubei, China; International Joint Research Center for General Health, Precision Medicine & Nutrition, Hubei University of Technology, Wuhan, Hubei, China; Department of Biomedicine and Biopharmacology, Hubei University of Technology, Wuhan, Hubei, China
| | - Wenwen Deng
- Hubei University of Technology Autism & Depression Diagnosis and Intervention Institute, Hubei University of Technology, Wuhan, Hubei, China; International Joint Research Center for General Health, Precision Medicine & Nutrition, Hubei University of Technology, Wuhan, Hubei, China; Department of Biomedicine and Biopharmacology, Hubei University of Technology, Wuhan, Hubei, China
| | - Di Liu
- Hubei University of Technology Autism & Depression Diagnosis and Intervention Institute, Hubei University of Technology, Wuhan, Hubei, China; International Joint Research Center for General Health, Precision Medicine & Nutrition, Hubei University of Technology, Wuhan, Hubei, China; Department of Biomedicine and Biopharmacology, Hubei University of Technology, Wuhan, Hubei, China
| | - Youheng Li
- Hubei University of Technology Autism & Depression Diagnosis and Intervention Institute, Hubei University of Technology, Wuhan, Hubei, China; International Joint Research Center for General Health, Precision Medicine & Nutrition, Hubei University of Technology, Wuhan, Hubei, China; Department of Biomedicine and Biopharmacology, Hubei University of Technology, Wuhan, Hubei, China
| | - Kang Peng
- Hubei University of Technology Autism & Depression Diagnosis and Intervention Institute, Hubei University of Technology, Wuhan, Hubei, China; International Joint Research Center for General Health, Precision Medicine & Nutrition, Hubei University of Technology, Wuhan, Hubei, China; Department of Biomedicine and Biopharmacology, Hubei University of Technology, Wuhan, Hubei, China
| | | | - Jun Wang
- Hubei University of Technology Autism & Depression Diagnosis and Intervention Institute, Hubei University of Technology, Wuhan, Hubei, China; International Joint Research Center for General Health, Precision Medicine & Nutrition, Hubei University of Technology, Wuhan, Hubei, China; Department of Biomedicine and Biopharmacology, Hubei University of Technology, Wuhan, Hubei, China.
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22
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Zou G, Niu L, Li Y, Zhang W, Wang L, Li Y, Zhang H, Wang L, Gao Y. Depth induced assembly discrepancy of multitrophic microbial communities affect microbial nitrogen transformation processes in river cross-sections. ENVIRONMENTAL RESEARCH 2022; 214:113913. [PMID: 35843280 DOI: 10.1016/j.envres.2022.113913] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/06/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Understanding how the structures and functions of bacterial and microeukaryotic communities vary within cross-sections will improve managements aimed at restoring river ecological functions. However, no comprehensive investigation has examined how microbial community characteristics vary within cross-sections, which makes the accurate calculation and prediction of microbial metabolic processing of substances in rivers difficult. Here, the distributions, co-occurrence networks, and assemblies of bacterial and microeukaryotic communities and their feedback to nitrogen transformation in cross-sections of the Yangtze River were studied by coupling ecological theory, biogeochemistry, and DNA meta-barcoding methods. The study found that depth in cross-sections was the primary driving factor regulating the composition of sediment bacterial and microeukaryotic communities. Co-occurrence network analysis indicated that the effect of bacteria on the co-occurrence network decreased and the network become more simplified and instability with depth in river cross-sections. Quantified using the β-nearest taxon index, the H2 layer sediment (depth 10-20 m) displayed the largest variation in selection processes for microbial assemblies, while homogeneous selection and homogenizing dispersal contributed most to the bacterial and microeukaryotic assemblies in the H3 layer (depth >20 m). Cross-sectional depth and denitrification genes had a significant quadratic correlation, with the highest microbial nitrogen-removal potential occurring in the H2 layer sediment. Structural equation models showed that the sediment nitrogen distributions were regulated by distinct environmental pathways at different depths, and that the H2 layer sediment was primary driven by bacterial community. In this layer, river cross-sectional depth influenced nitrogen transformation by regulating the distribution of sediment particle sizes, which then influenced the assembly of the multitrophic microbial communities. This study will improve river management by clarifying the importance of cross-sectional depth to the ecological function of rivers.
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Affiliation(s)
- Guanhua Zou
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210024, PR China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210024, PR China.
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210024, PR China.
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210024, PR China
| | - Linqiong Wang
- College of Oceanography, Hohai University, Xikang Road #1, Nanjing, 210024, PR China
| | - Yuanyuan Li
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210024, PR China
| | - Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210024, PR China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210024, PR China
| | - Yu Gao
- Key Laboratory of Integrated Regulation and Resource Development of Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing, 210024, PR China
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23
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Torres-Franco AF, Silva G, Freitas MP, Passos F, Mota Filho CR, Figueredo CC. Effect of digestate loading rates on microalgae-based treatment under low LED light intensity. ENVIRONMENTAL TECHNOLOGY 2022; 43:3023-3036. [PMID: 33830869 DOI: 10.1080/09593330.2021.1914178] [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: 09/12/2020] [Accepted: 03/30/2021] [Indexed: 06/12/2023]
Abstract
Low red-LED irradiances are an attractive alternative for enhancing microalgae photobioreactors treating digestate due to their potential contribution in decreasing area footprints with low energy consumptions. However, more information is required regarding the influence of digestate load on treatment performance and biomass valorisation when low-intensity red-LEDs are applied. Thus, this study assessed microalgae-based photobioreactors treating food waste digestate under different concentrations (5%, 25%, 50%, and 75%, v/v) at low red-LED irradiance (15 µmol·m-2·s-1). The removal efficiencies of soluble chemical oxygen demand (sCOD) at the end of the experiment ranged from 45% to 75% when treating influent loads between 5.3 and 79.1 g sCOD·m-3·d-1 (5% and 75%-digestate), respectively. Total ammonia nitrogen (TAN) was applied in loading rates between 3.2 and 48.5 g TAN·m-3·d-1 (5% and 75%, respectively) and removed with maximum efficiencies of 90%-100% in all trials. Nitrification-denitrification was proportionally more relevant when treating 5%-digestate, whereas volatilisation was the primary process in 25%, 50% and 75% concentrations. Microalgae presented adequate yields in all treatments, except in 75%-digestate, likely due to the blocking of light by the high solids concentrations. The assessment of the microalgae community and chlorophyll-a and carotenoids suggested that chlorophytes, mainly Dictyosphaerium pulchellum and Scenedesmus sp. grew autotrophically, whereas cyanobacteria Pseudanabaena sp. grew mixotrophically. Moreover, the sustainability of red LED lighting applications can be increased by anaerobic digestion or agricultural valorisation of the biomass, enabled by its high N and P contents. Low-intensity red-LEDs may have promissory applications in the treatment of high-strength wastewaters.
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Affiliation(s)
- Andrés Felipe Torres-Franco
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Gabriela Silva
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Matheus Pascoal Freitas
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Fabiana Passos
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - César Rossas Mota Filho
- Department of Sanitary and Environmental Engineering, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Cleber Cunha Figueredo
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
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24
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Moncelon R, Metzger E, Pineau P, Emery C, Bénéteau E, de Lignières C, Philippine O, Robin FX, Dupuy C. Drivers for primary producers' dynamics: New insights on annual benthos pelagos monitoring in anthropised freshwater marshes (Charente-Maritime, France). WATER RESEARCH 2022; 221:118718. [PMID: 35749922 DOI: 10.1016/j.watres.2022.118718] [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: 03/01/2022] [Revised: 06/03/2022] [Accepted: 06/04/2022] [Indexed: 06/15/2023]
Abstract
Wetlands, especially marshes, support many services such as carbon catchment control or water purification led by primary producers such as phytoplankton and microphytobenthos (PB). The impact of the sedimentary compartment, as source and sink of essential nutrients for the water column, is often neglected in the study of their dynamics and water purification capacity of the systems. This work compared monthly (between February 2020 and April 2021) the benthic and pelagic primary producers' dynamics in two anthropised freshwater marshes (Marans and Genouillé), with the simultaneous follow-up of physico-chemical parameters of the water column and nutrient fluxes at the sediment-water (SWI) interface. It was suggested a strong contribution of phytoplankton (pumping) and the benthic compartment (denitrification) to the water purification of these two nitrates (NO3-)-rich marshes. Total phytoplankton production fluctuated between ∼5 (winter) and 1500 mg C m-3 d-1 (fall) at Marans and between 40 (winter) and ∼750 mg C m-3 d-1 (spring) at Genouillé. At Marans, soluble reactive phosphorus (SRP) benthic effluxes (-2.101 to -6.102 µmol m-2 d-1 in fall and summer, respectively) coincided with phytoplankton bloom periods. These effluxes were inhibited by NO3- penetration in the sediment (0 to 5.104 µmol m-2 d-1), by inhibiting iron respiration. At Genouillé, inhibition of SRP effluxes depended on denitrification rate and on P stocks in the sediment, where slight SRP effluxes (-101 µmol m-2 d-1) could have co-occurred with slight NO3- influxes (5.102 µmol m-2 d-1) in spring. The presence of PB (between 10-60 and 40-120 mg gsed-1 at Marans and Genouillé, respectively), suggested a strong contribution of the benthic compartment to the total primary production (benthic and pelagic through resuspension processes) in these environments. This work encourages to consider the benthos and the pelagos as a unicum to provide better sustainable management of such systems and limit eutrophication risks in coastal areas.
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Affiliation(s)
- Raphaël Moncelon
- Laboratoire LIENSs, UMR 7266, La Rochelle Université, Bâtiment ILE, 2 Rue Olympe de Gouges, La Rochelle, France.
| | - Edouard Metzger
- Laboratoire de Planétologie et Géosciences, CNRS, Université d'Angers, Nantes Université, Le Mans Université, Angers, France
| | - Philippe Pineau
- Laboratoire LIENSs, UMR 7266, La Rochelle Université, Bâtiment ILE, 2 Rue Olympe de Gouges, La Rochelle, France
| | - Claire Emery
- Laboratoire LIENSs, UMR 7266, La Rochelle Université, Bâtiment ILE, 2 Rue Olympe de Gouges, La Rochelle, France
| | - Eric Bénéteau
- Laboratoire de Planétologie et Géosciences, CNRS, Université d'Angers, Nantes Université, Le Mans Université, Angers, France
| | - Charlotte de Lignières
- Laboratoire LIENSs, UMR 7266, La Rochelle Université, Bâtiment ILE, 2 Rue Olympe de Gouges, La Rochelle, France
| | | | | | - Christine Dupuy
- Laboratoire LIENSs, UMR 7266, La Rochelle Université, Bâtiment ILE, 2 Rue Olympe de Gouges, La Rochelle, France
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25
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Upreti K, Rivera-Monroy VH, Maiti K, Giblin AE, Castañeda-Moya E. Dissimilatory nitrate reduction to ammonium (DNRA) is marginal relative to denitrification in emerging-eroding wetlands in a subtropical oligohaline and eutrophic coastal delta. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 819:152942. [PMID: 35007602 DOI: 10.1016/j.scitotenv.2022.152942] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/18/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Nitrate (NO3-) and ammonium (NH4+) are reactive nitrogen (Nr) forms that can exacerbate eutrophication in coastal regions. NO3- can be lost to the atmosphere as N2 gas driven by direct denitrification, coupled nitrification-denitrification and annamox or retained within the ecosystems through conversion of NO3- to NH4+ via dissimilatory nitrate reduction to ammonium (DNRA). Denitrification and DNRA are competitive pathways and hence it is critical to evaluate their functional biogeochemical role. However, there is limited information about the environmental factors driving DNRA in oligohaline habitats, especially within deltaic regions where steep salinity gradients define wetland spatiotemporal distribution. Here we use the Isotope Pairing Technique to evaluate the effect of temperature (10, 20, 30 °C) and in situ soil/sediment organic matter (OM%) on total denitrification (Dtotal = direct + coupled nitrification) and DNRA rates in oligohaline forested/marsh wetlands soils and benthic sediment habitats at two sites representing prograding (Wax Lake Delta, WLD) and eroding (Barataria- Lake Cataouatche, BLC) deltaic stages in the Mississippi River Delta Plain (MRDP). Both sites receive MR water with high NO3- (>40 μM) concentrations during the year via river diversions. Denitrification rates were significantly higher (range: 18.0 ± 0.4-113.0 ± 10.6 μmol m-2 h-1) than DNRA rates (range: 0.7 ± 0.2-9.2 ± 0.3 μmol m-2 h-1). Therefore, DNRA represented on average < 10% of the total NO3- reduction (DNRA + Dtotal). Unlike denitrification, DNRA showed no consistent response to temperature. These results indicate that DNRA in wetland soils and benthic sediment is not a major nitrogen transformation in oligohaline regions across the MRDP regardless of wide range of OM% content in these eroding and prograding delta lobes.
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Affiliation(s)
- Kiran Upreti
- Department of Oceanography and Coastal Sciences, College of the Coast and Enviroment, Louisiana State University, Baton Rouge, LA 70808, USA
| | - Victor H Rivera-Monroy
- Department of Oceanography and Coastal Sciences, College of the Coast and Enviroment, Louisiana State University, Baton Rouge, LA 70808, USA.
| | - Kanchan Maiti
- Department of Oceanography and Coastal Sciences, College of the Coast and Enviroment, Louisiana State University, Baton Rouge, LA 70808, USA
| | - Anne E Giblin
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
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26
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Nitrate Water Contamination from Industrial Activities and Complete Denitrification as a Remediation Option. WATER 2022. [DOI: 10.3390/w14050799] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Freshwater is a scarce resource that continues to be at high risk of pollution from anthropogenic activities, requiring remediation in such cases for its continuous use. The agricultural and mining industries extensively use water and nitrogen (N)-dependent products, mainly in fertilizers and explosives, respectively, with their excess accumulating in different water bodies. Although removal of NO3 from water and soil through the application of chemical, physical, and biological methods has been studied globally, these methods seldom yield N2 gas as a desired byproduct for nitrogen cycling. These methods predominantly cause secondary contamination with deposits of chemical waste such as slurry brine, nitrite (NO2), ammonia (NH3), and nitrous oxide (N2O), which are also harmful and fastidious to remove. This review focuses on complete denitrification facilitated by bacteria as a remedial option aimed at producing nitrogen gas as a terminal byproduct. Synergistic interaction of different nitrogen metabolisms from different bacteria is highlighted, with detailed attention to the optimization of their enzymatic activities. A biotechnological approach to mitigating industrial NO3 contamination using indigenous bacteria from wastewater is proposed, holding the prospect of optimizing to the point of complete denitrification. The approach was reviewed and found to be durable, sustainable, cost effective, and environmentally friendly, as opposed to current chemical and physical water remediation technologies.
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27
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Frey B, Varliero G, Qi W, Stierli B, Walthert L, Brunner I. Shotgun Metagenomics of Deep Forest Soil Layers Show Evidence of Altered Microbial Genetic Potential for Biogeochemical Cycling. Front Microbiol 2022; 13:828977. [PMID: 35300488 PMCID: PMC8921678 DOI: 10.3389/fmicb.2022.828977] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 02/11/2022] [Indexed: 11/29/2022] Open
Abstract
Soil microorganisms such as Bacteria and Archaea play important roles in the biogeochemical cycling of soil nutrients, because they act as decomposers or are mutualistic or antagonistic symbionts, thereby influencing plant growth and health. In the present study, we investigated the vertical distribution of soil metagenomes to a depth of 1.5 m in Swiss forests of European beech and oak species on calcareous bedrock. We explored the functional genetic potential of soil microorganisms with the aim to disentangle the effects of tree genus and soil depth on the genetic repertoire, and to gain insight into the microbial C and N cycling. The relative abundance of reads assigned to taxa at the domain level indicated a 5-10 times greater abundance of Archaea in the deep soil, while Bacteria showed no change with soil depth. In the deep soil there was an overrepresentation of genes for carbohydrate-active enzymes, which are involved in the catalyzation of the transfer of oligosaccharides, as well as in the binding of carbohydrates such as chitin or cellulose. In addition, N-cycling genes (NCyc) involved in the degradation and synthesis of N compounds, in nitrification and denitrification, and in nitrate reduction were overrepresented in the deep soil. Consequently, our results indicate that N-transformation in the deep soil is affected by soil depth and that N is used not only for assimilation but also for energy conservation, thus indicating conditions of low oxygen in the deep soil. Using shotgun metagenomics, our study provides initial findings on soil microorganisms and their functional genetic potential, and how this may change depending on soil properties, which shift with increasing soil depth. Thus, our data provide novel, deeper insight into the "dark matter" of the soil.
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Affiliation(s)
- Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Gilda Varliero
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
- Centre for Microbial Ecology and Genomics, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Weihong Qi
- Functional Genomics Center Zurich (FGCZ), ETH Zürich/University of Zurich, Zurich, Switzerland
| | - Beat Stierli
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Lorenz Walthert
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Ivano Brunner
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
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28
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Zhang W, Yang G, Wang H, Li Y, Niu L, Zhang H, Wang L. Predicting bend-induced heterogeneity in sediment microbial communities by integrating bacteria-based index of biotic integrity and supervised learning algorithms. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 304:114267. [PMID: 34896801 DOI: 10.1016/j.jenvman.2021.114267] [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: 05/23/2021] [Revised: 11/30/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Prioritizing the relationship between heterogeneity of sediment habitats and river bends is critical when planning and reconstructing urban rivers. However, the exact relationship between ecological heterogeneity and river bends remains ambiguous. Therefore, this research proposed a new approach to quantify and predict bend-induced ecological heterogeneity, incorporating the bacteria-based index of biotic integrity (Ba-IBI), path model, and random forest regression model. The developed Ba-IBI quantified heterogeneity in sediment microbial communities, ranging from low (1.40) to high (3.97). A path model was developed and validated in order to further investigate the relative contributions of environmental factors to the Ba-IBI. The established path model, which was considered acceptable with a CMIN/df = 1.949 < 4, suggested that primary environmental factors affecting the sediment bacterial communities were flow velocity and ammonium concentration in sediment. To further characterize the relationship between environmental factors and the Ba-IBI, a function was constructed using the random forest regression model that predicts the responses of sediment bacterial communities to environmental factors with R2 = 0.6126. The proposed approach and prediction tools will provide knowledge to improve natural channel design and post-project evaluations in river restoration projects.
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Affiliation(s)
- Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Gang Yang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Haolan Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China.
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
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29
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Elementary vectors and autocatalytic sets for resource allocation in next-generation models of cellular growth. PLoS Comput Biol 2022; 18:e1009843. [PMID: 35104290 PMCID: PMC8853647 DOI: 10.1371/journal.pcbi.1009843] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 02/17/2022] [Accepted: 01/18/2022] [Indexed: 11/19/2022] Open
Abstract
Traditional (genome-scale) metabolic models of cellular growth involve an approximate biomass “reaction”, which specifies biomass composition in terms of precursor metabolites (such as amino acids and nucleotides). On the one hand, biomass composition is often not known exactly and may vary drastically between conditions and strains. On the other hand, the predictions of computational models crucially depend on biomass. Also elementary flux modes (EFMs), which generate the flux cone, depend on the biomass reaction. To better understand cellular phenotypes across growth conditions, we introduce and analyze new classes of elementary vectors for comprehensive (next-generation) metabolic models, involving explicit synthesis reactions for all macromolecules. Elementary growth modes (EGMs) are given by stoichiometry and generate the growth cone. Unlike EFMs, they are not support-minimal, in general, but cannot be decomposed “without cancellations”. In models with additional (capacity) constraints, elementary growth vectors (EGVs) generate a growth polyhedron and depend also on growth rate. However, EGMs/EGVs do not depend on the biomass composition. In fact, they cover all possible biomass compositions and can be seen as unbiased versions of elementary flux modes/vectors (EFMs/EFVs) used in traditional models. To relate the new concepts to other branches of theory, we consider autocatalytic sets of reactions. Further, we illustrate our results in a small model of a self-fabricating cell, involving glucose and ammonium uptake, amino acid and lipid synthesis, and the expression of all enzymes and the ribosome itself. In particular, we study the variation of biomass composition as a function of growth rate. In agreement with experimental data, low nitrogen uptake correlates with high carbon (lipid) storage. Next-generation, genome-scale metabolic models allow to study the reallocation of cellular resources upon changing environmental conditions, by not only modeling flux distributions, but also expression profiles of the catalyzing proteome. In particular, they do no longer assume a fixed biomass composition. Methods to identify optimal solutions in such comprehensive models exist, however, an unbiased understanding of all feasible allocations is missing so far. Here we develop new concepts, called elementary growth modes and vectors, that provide a generalized definition of minimal pathways, thereby extending classical elementary flux modes (used in traditional models with a fixed biomass composition). The new concepts provide an understanding of all possible flux distributions and of all possible biomass compositions. In other words, elementary growth modes and vectors are the unique functional units in any comprehensive model of cellular growth. As an example, we show that lipid accumulation upon nitrogen starvation is a consequence of resource allocation and does not require active regulation. Our work puts current approaches on a theoretical basis and allows to seamlessly transfer existing workflows (e.g. for the design of cell factories) to next-generation metabolic models.
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Fuchsman CA, Cherubini L, Hays MD. An analysis of protists in Pacific oxygen deficient zones: implications for Prochlorococcus and N 2 -producing bacteria. Environ Microbiol 2022; 24:1790-1804. [PMID: 34995411 DOI: 10.1111/1462-2920.15893] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 11/26/2022]
Abstract
Ocean oxygen deficient zones (ODZs) host 30%-50% of marine N2 production. Cyanobacteria photosynthesizing in the ODZ create a secondary chlorophyll maximum and provide organic matter to N2 -producing bacteria. This chlorophyll maximum is thought to occur due to reduced grazing in anoxic waters. We first examine ODZ protists with long amplicon reads. We then use non-primer-based methods to examine the composition and relative abundance of protists in metagenomes from the Eastern Tropical North and South Pacific ODZs and compare these data to the oxic Hawaii Ocean Time-series (HOT) in the North Pacific. We identify and quantify protists in proportion to the total microbial community. From metagenomic data, we see a large drop in abundance of fungi and protists such as choanoflagellates, radiolarians, cercozoa and ciliates in the ODZs but not in the oxic mesopelagic at HOT. Diplonemid euglenozoa were the only protists that increased in the ODZ. Dinoflagellates and foraminifera reads were also present in the ODZ though less abundant compared to oxic waters. Denitrification has been found in foraminifera but not yet in dinoflagellates. DNA techniques cannot separate dinoflagellate cells and cysts. Metagenomic analysis found taxonomic groups missed by amplicon sequencing and identified trends in abundance.
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Affiliation(s)
- Clara A Fuchsman
- University of Maryland Center for Environmental Science Horn Point Laboratory, Cambridge, MD, 21613, USA
| | - Luca Cherubini
- Maryland Sea Grant College, College Park, MD, 20740, USA
| | - Matthew D Hays
- University of Maryland Center for Environmental Science Horn Point Laboratory, Cambridge, MD, 21613, USA
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Aquatic Hyphomycete Taxonomic Relatedness Translates into Lower Genetic Divergence of the Nitrate Reductase Gene. J Fungi (Basel) 2021; 7:jof7121066. [PMID: 34947048 PMCID: PMC8708292 DOI: 10.3390/jof7121066] [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: 11/03/2021] [Revised: 11/27/2021] [Accepted: 12/06/2021] [Indexed: 12/04/2022] Open
Abstract
Aquatic hyphomycetes are key microbial decomposers in freshwater that are capable of producing extracellular enzymes targeting complex molecules of leaf litter, thus, being crucial to nutrient cycling in these ecosystems. These fungi are also able to assimilate nutrients (e.g., nitrogen) from stream water, immobilizing these nutrients in the decomposing leaf litter and increasing its nutritional value for higher trophic levels. Evaluating the aquatic hyphomycete functional genetic diversity is, thus, pivotal to understanding the potential impacts of biodiversity loss on nutrient cycling in freshwater. In this work, the inter- and intraspecific taxonomic (ITS1-5.8S-ITS2 region) and functional (nitrate reductase gene) diversity of 40 aquatic hyphomycete strains, belonging to 23 species, was evaluated. A positive correlation was found between the taxonomic and nitrate reductase gene divergences. Interestingly, some cases challenged this trend: Dactylella cylindrospora (Orbiliomycetes) and Thelonectria rubi (Sordariomycetes), which were phylogenetically identical but highly divergent regarding the nitrate reductase gene; and Collembolispora barbata (incertae sedis) and Tetracladium apiense (Leotiomycetes), which exhibited moderate taxonomic divergence but no divergence in the nitrate reductase gene. Additionally, Tricladium chaetocladium (Leotiomycetes) strains were phylogenetically identical but displayed a degree of nitrate reductase gene divergence above the average for the interspecific level. Overall, both inter- and intraspecific functional diversity were observed among aquatic hyphomycetes.
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Khan MJ, Das S, Vinayak V, Pant D, Ghangrekar MM. Live diatoms as potential biocatalyst in a microbial fuel cell for harvesting continuous diafuel, carotenoids and bioelectricity. CHEMOSPHERE 2021; 291:132841. [PMID: 34767852 DOI: 10.1016/j.chemosphere.2021.132841] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/18/2021] [Accepted: 11/07/2021] [Indexed: 02/05/2023]
Abstract
Microbial fuel cell (MFC) with live diatoms (Nitzschia palea) displacing bacteria in the anodic chamber generated electrical potential. Unlike other microalgae, diatoms fix 25% of atmospheric CO2, thus releasing O2. They perform photolysis of water by photosynthesis in the plastid during light photoperiod and cellular respiration in the mitochondria during dark, producing electrons and protons, respectively. The electrogenic property of diatom was explored and evaluated by comparing the potential changes with reference fuel cell without diatoms and that operated with diatoms in the anodic chamber. Such photosynthetic diatom microbial fuel cell (PDMFC) employed f/2 media rich in nitrates, phosphates, metasilicates, trace metals and vitamins as the anolyte and potassium permanganate as catholyte enhanced the output voltage by 3rd day. The maximum power density for PDMFC was 12.62 mWm-2 and coulombic efficiency of 22.95%. Besides this, the fixed diatom cells at anode showed about 64.28% increase in lipid production on 15th day compared to that on 1st day along with the increment in formation of complex fatty acid methyl esters and carotenoids during its operation. Hence, diatoms can be envisaged to substitute bacteria in the anodic chamber of MFC to simultaneously produce bioelectricity and other valuable compounds. Further their silica nanoporous architecture serve as good absorbents for heavy metal removal found in many wastewaters.
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Affiliation(s)
- Mohd Jahir Khan
- Diatom Nanoengineering and Metabolism Laboratory (DNM), School of Applied Sciences, Dr Harisingh Gour Central University, Sagar, Madhya Pradesh, 470003, India
| | - Sovik Das
- Department of Civil Engineering, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Vandana Vinayak
- Diatom Nanoengineering and Metabolism Laboratory (DNM), School of Applied Sciences, Dr Harisingh Gour Central University, Sagar, Madhya Pradesh, 470003, India.
| | - Deepak Pant
- Separation & Conversion Technology, Flemish Institute for Technological Research (VITO), Boeretang 200, Mol, Belgium
| | - M M Ghangrekar
- Department of Civil Engineering, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
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Yang N, Zhang C, Wang L, Li Y, Zhang W, Niu L, Zhang H, Wang L. Nitrogen cycling processes and the role of multi-trophic microbiota in dam-induced river-reservoir systems. WATER RESEARCH 2021; 206:117730. [PMID: 34619413 DOI: 10.1016/j.watres.2021.117730] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/25/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
The nitrogen (N) cycle is one of the most important nutrient cycles in river systems, and it plays an important role in maintaining biogeochemical balance and global climate stability. One of the main ways that humans have altered riverine ecosystems is through the construction of hydropower dams, which have major effects on biogeochemical cycles. Most previous studies examining the effects of damming on N cycling have focused on the whole budget or flux along rivers, and the role of river as N sources or sinks at the global or catchment scale. However, so far there is still lack of comprehensive and systematic summarize on N cycling and the controlling mechanisms in reservoirs affected by dam impoundment. In this review, we firstly summarize N cycling processes along the longitudinal riverine-transition-lacustrine gradient and the vertically stratified epilimnion-thermocline-hypolimnion gradient. Specifically, we highlight the direct and indirect roles of multi-trophic microbiota and their interactions in N cycling and discuss the main factors controlling these biotic processes. In addition, future research directions and challenges in incorporating multi-trophic levels in bioassessment, environmental flow design, as well as reservoir regulation and restoration are summarized. This review will aid future studies of N fluxes along dammed rivers and provide an essential reference for reservoir management to meet ecological needs.
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Affiliation(s)
- Nan Yang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, P R China
| | - Chi Zhang
- College of Mechanics and Materials, Hohai University, Xikang Road #1, Nanjing 210098, P R China
| | - Linqiong Wang
- College of Oceanography, Hohai University, Xikang Road #1, Nanjing 210098, P R China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, P R China.
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, P R China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, P R China
| | - Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, P R China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Xikang Road #1, Nanjing 210098, P R China
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Biochar and Zeolite as Alternative Biofilter Media for Denitrification of Aquaculture Effluents. WATER 2021. [DOI: 10.3390/w13192703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Denitrification processes are crucial in aquaculture as they convert the undesirable nitrate to safer forms of nitrogen. Conventionally, plastic media are used for the biofiltration of wastewater. However, alternative media may be as effective/better than plastic and enhance the sustainability of the system. This study evaluated biochar and zeolite as alternatives for the denitrification of aquaculture effluents. Triplicates of laboratory-scale bioreactors were fabricated to compare the denitrification efficiencies of biochar and zeolite to that of plastic. The bioreactors were fed synthetic aquaculture wastewater having nitrate loading rates of 50, 125, and 150 mg/L. Zeolite exhibited highest values of surface roughness in terms of arithmetic mean height (0.89 µm), maximum height (6.52 µm), and root-mean-square height (1.17 µm), as corroborated by surface profilometry and scanning electron microscopy. The results revealed that under pseudo-steady-state conditions, zeolite displayed the highest nitrate removal efficiency (maximum 95.02 ± 0.01%), which was followed by biochar and plastic (maximum 92.91 ± 0.01% and 92.57 ± 0.02%, respectively) due to its extraordinary surface roughness that provided better adhesion to the bacteria. However, by the end of the study, all the media exhibited comparable rates. Thus, both zeolite and biochar are sustainable alternatives of biomedia for nitrate removal. However, time and labor constraints must be accounted for to scale-up such bioreactors.
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Schutte CA, Huanca-Valenzuela P, Lavik G, Marchant HK, de Beer D. Advection Drives Nitrate Past the Microphytobenthos in Intertidal Sands, Fueling Deeper Denitrification. Front Microbiol 2021; 12:556268. [PMID: 34220727 PMCID: PMC8250833 DOI: 10.3389/fmicb.2021.556268] [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] [Received: 04/27/2020] [Accepted: 05/10/2021] [Indexed: 11/18/2022] Open
Abstract
Nitrification rates are low in permeable intertidal sand flats such that the water column is the primary source of nitrate to the sediment. During tidal inundation, nitrate is supplied to the pore space by advection rather than diffusion, relieving the microorganisms that reside in the sand from nitrate limitation and supporting higher denitrification rates than those observed under diffusive transport. Sand flats are also home to an abundant community of benthic photosynthetic microorganisms, the microphytobenthos (MPB). Diatoms are an important component of the MPB that can take up and store high concentrations of nitrate within their cells, giving them the potential to alter nitrate availability in the surrounding porewater. We tested whether nitrate uptake by the MPB near the sediment surface decreases its availability to denitrifiers along deeper porewater flow paths. In laboratory experiments, we used NOx (nitrate + nitrite) microbiosensors to confirm that, in the spring, net NOx consumption in the zone of MPB photosynthetic activity was stimulated by light. The maximum potential denitrification rate, measured at high spatial resolution using microsensors with acetylene and nitrate added, occurred below 1.4 cm, much deeper than light-induced NOx uptake (0.13 cm). Therefore, the shallower MPB had the potential to decrease NOx supply to the deeper sediments and limit denitrification. However, when applying a realistic downward advective flow to sediment from our study site, NOx always reached the depths of maximum denitrification potential, regardless of light availability or season. We conclude that during tidal inundation porewater advection overwhelms any influence of shallow NOx uptake by the MPB and drives water column NOx to the depths of maximum denitrification potential.
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Affiliation(s)
- Charles A Schutte
- Microsensors Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Gaute Lavik
- Biogeochemistry Department, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Hannah K Marchant
- Biogeochemistry Department, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Dirk de Beer
- Microsensors Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
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Gomaa F, Utter DR, Powers C, Beaudoin DJ, Edgcomb VP, Filipsson HL, Hansel CM, Wankel SD, Zhang Y, Bernhard JM. Multiple integrated metabolic strategies allow foraminiferan protists to thrive in anoxic marine sediments. SCIENCE ADVANCES 2021; 7:7/22/eabf1586. [PMID: 34039603 PMCID: PMC8153729 DOI: 10.1126/sciadv.abf1586] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 04/05/2021] [Indexed: 05/14/2023]
Abstract
Oceanic deoxygenation is increasingly affecting marine ecosystems; many taxa will be severely challenged, yet certain nominally aerobic foraminifera (rhizarian protists) thrive in oxygen-depleted to anoxic, sometimes sulfidic, sediments uninhabitable to most eukaryotes. Gene expression analyses of foraminifera common to severely hypoxic or anoxic sediments identified metabolic strategies used by this abundant taxon. In field-collected and laboratory-incubated samples, foraminifera expressed denitrification genes regardless of oxygen regime with a putative nitric oxide dismutase, a characteristic enzyme of oxygenic denitrification. A pyruvate:ferredoxin oxidoreductase was highly expressed, indicating the capability for anaerobic energy generation during exposure to hypoxia and anoxia. Near-complete expression of a diatom's plastid genome in one foraminiferal species suggests kleptoplasty or sequestration of functional plastids, conferring a metabolic advantage despite the host living far below the euphotic zone. Through a unique integration of functions largely unrecognized among "typical" eukaryotes, benthic foraminifera represent winning microeukaryotes in the face of ongoing oceanic deoxygenation.
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Affiliation(s)
- Fatma Gomaa
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Daniel R Utter
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Christopher Powers
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - David J Beaudoin
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Virginia P Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | | | - Colleen M Hansel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Scott D Wankel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - Joan M Bernhard
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA.
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37
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Toussaint E, De Borger E, Braeckman U, De Backer A, Soetaert K, Vanaverbeke J. Faunal and environmental drivers of carbon and nitrogen cycling along a permeability gradient in shallow North Sea sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 767:144994. [PMID: 33550059 DOI: 10.1016/j.scitotenv.2021.144994] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/14/2020] [Accepted: 12/30/2020] [Indexed: 06/12/2023]
Abstract
Ecosystem functions are driven by abiotic and biotic factors, but due to high collinearity of both, it is often difficult to disentangle the drivers of these ecosystem functions. We studied sedimentological and faunal controls of benthic organic matter mineralization, a crucial ecosystem process provided for by sediments of shelf seas. Subtidal benthic habitats representative of the wide permeability gradient found in the Belgian Part of the North Sea (Northeast Atlantic Shelf) were characterized in terms of sediment descriptors, macrofauna, and sediment biogeochemistry was estimated. Our results confirmed a strong correlation between sediment characteristics and macrofauna, and estimated sediment biogeochemical process rates were clearly linked to both. Results of variance partitioning and statistical modelling showed that oxic mineralization and nitrification were mainly regulated by faunal activities whereas anoxic mineralization was regulated by sediment properties, with permeability as a decisive factor. Both biotic and abiotic factors were needed to explain variability in oxygen consumption and total mineralization estimates, suggesting that macrofaunal activities have different effects across habitats. The statistical models were a useful tool to interpret the impact of anthropogenic activities in the study area and represent a step towards predicting the effects of human activities on crucial ecosystem functions.
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Affiliation(s)
- Elise Toussaint
- Ghent University, Department of Biology, Marine Biology Research Group, Krijgslaan 281/S8, 9000 Ghent, Belgium; Royal Belgian Institute of Natural Sciences, Operational Directorate Natural Environment, Marine Ecology and Management, Rue Vautier 29, 1000 Brussels, Belgium.
| | - Emil De Borger
- Ghent University, Department of Biology, Marine Biology Research Group, Krijgslaan 281/S8, 9000 Ghent, Belgium; Royal Netherlands Institute of Sea Research (NIOZ), Department of Estuarine and Delta Systems,Korringaweg 7, P.O. Box 140, 4401, NT, Yerseke, the Netherlands; Utrecht University, Heidelberglaan 8, 3584, CS, Utrecht, the Netherlands
| | - Ulrike Braeckman
- Ghent University, Department of Biology, Marine Biology Research Group, Krijgslaan 281/S8, 9000 Ghent, Belgium
| | - Annelies De Backer
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Aquatic Environment and Quality, Ankerstraat 1, 8400 Oostende, Belgium
| | - Karline Soetaert
- Ghent University, Department of Biology, Marine Biology Research Group, Krijgslaan 281/S8, 9000 Ghent, Belgium; Royal Netherlands Institute of Sea Research (NIOZ), Department of Estuarine and Delta Systems,Korringaweg 7, P.O. Box 140, 4401, NT, Yerseke, the Netherlands; Utrecht University, Heidelberglaan 8, 3584, CS, Utrecht, the Netherlands
| | - Jan Vanaverbeke
- Ghent University, Department of Biology, Marine Biology Research Group, Krijgslaan 281/S8, 9000 Ghent, Belgium; Royal Belgian Institute of Natural Sciences, Operational Directorate Natural Environment, Marine Ecology and Management, Rue Vautier 29, 1000 Brussels, Belgium
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Merz E, Dick GJ, de Beer D, Grim S, Hübener T, Littmann S, Olsen K, Stuart D, Lavik G, Marchant HK, Klatt JM. Nitrate respiration and diel migration patterns of diatoms are linked in sediments underneath a microbial mat. Environ Microbiol 2020; 23:1422-1435. [PMID: 33264477 DOI: 10.1111/1462-2920.15345] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/23/2020] [Accepted: 11/30/2020] [Indexed: 12/12/2022]
Abstract
Diatoms are among the few eukaryotes known to store nitrate (NO3 - ) and to use it as an electron acceptor for respiration in the absence of light and O2 . Using microscopy and 15 N stable isotope incubations, we studied the relationship between dissimilatory nitrate/nitrite reduction to ammonium (DNRA) and diel vertical migration of diatoms in phototrophic microbial mats and the underlying sediment of a sinkhole in Lake Huron (USA). We found that the diatoms rapidly accumulated NO3 - at the mat-water interface in the afternoon and 40% of the population migrated deep into the sediment, where they were exposed to dark and anoxic conditions for ~75% of the day. The vertical distribution of DNRA rates and diatom abundance maxima coincided, suggesting that DNRA was the main energy generating metabolism of the diatom population. We conclude that the illuminated redox-dynamic ecosystem selects for migratory diatoms that can store nitrate for respiration in the absence of light. A major implication of this study is that the dominance of DNRA over denitrification is not explained by kinetics or thermodynamics. Rather, the dynamic conditions select for migratory diatoms that perform DNRA and can outcompete sessile denitrifiers.
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Affiliation(s)
- Elisa Merz
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, Germany
| | - Gregory J Dick
- Geomicrobiology Lab, Department of Earth & Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Dirk de Beer
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, Germany
| | - Sharon Grim
- Geomicrobiology Lab, Department of Earth & Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Thomas Hübener
- Department of Botany and Botanical Garden, University of Rostock, Institute of Biosciences, Germany
| | - Sten Littmann
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, Germany
| | - Kirk Olsen
- Geomicrobiology Lab, Department of Earth & Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Dack Stuart
- University of Michigan, Cooperative Institute for Great Lakes Research, Ann Arbor, Michigan, USA
| | - Gaute Lavik
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, Germany
| | - Hannah K Marchant
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, Germany
| | - Judith M Klatt
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, Bremen, Germany.,Geomicrobiology Lab, Department of Earth & Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
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Lateral Gene Transfer Mechanisms and Pan-genomes in Eukaryotes. Trends Parasitol 2020; 36:927-941. [DOI: 10.1016/j.pt.2020.07.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 07/20/2020] [Accepted: 07/20/2020] [Indexed: 02/06/2023]
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40
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Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibrio vulgaris. ISME JOURNAL 2020; 14:2862-2876. [PMID: 32934357 DOI: 10.1038/s41396-020-00753-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 08/09/2020] [Accepted: 08/17/2020] [Indexed: 11/08/2022]
Abstract
Elevated nitrate in the environment inhibits sulfate reduction by important microorganisms of sulfate-reducing bacteria (SRB). Several SRB may respire nitrate to survive under elevated nitrate, but how SRB that lack nitrate reductase survive to elevated nitrate remains elusive. To understand nitrate adaptation mechanisms, we evolved 12 populations of a model SRB (i.e., Desulfovibrio vulgaris Hildenborough, DvH) under elevated NaNO3 for 1000 generations, analyzed growth and acquired mutations, and linked their genotypes with phenotypes. Nitrate-evolved (EN) populations significantly (p < 0.05) increased nitrate tolerance, and whole-genome resequencing identified 119 new mutations in 44 genes of 12 EN populations, among which six functional gene groups were discovered with high mutation frequencies at the population level. We observed a high frequency of nonsense or frameshift mutations in nitrosative stress response genes (NSR: DVU2543, DVU2547, and DVU2548), nitrogen regulatory protein C family genes (NRC: DVU2394-2396, DVU2402, and DVU2405), and nitrate cluster (DVU0246-0249 and DVU0251). Mutagenesis analysis confirmed that loss-of-functions of NRC and NSR increased nitrate tolerance. Also, functional gene groups involved in fatty acid synthesis, iron regulation, and two-component system (LytR/LytS) known to be responsive to multiple stresses, had a high frequency of missense mutations. Mutations in those gene groups could increase nitrate tolerance through regulating energy metabolism, barring entry of nitrate into cells, altering cell membrane characteristics, or conferring growth advantages at the stationary phase. This study advances our understanding of nitrate tolerance mechanisms and has important implications for linking genotypes with phenotypes in DvH.
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Yang Y, Chen Y, Zhang G, Sun J, Guo L, Jiang M, Ou B, Zhang W, Si H. Transcriptomic Analysis of Staphylococcus aureus Under the Stress Condition Caused by Litsea cubeba L. Essential Oil via RNA Sequencing. Front Microbiol 2020; 11:1693. [PMID: 33013718 PMCID: PMC7509438 DOI: 10.3389/fmicb.2020.01693] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/29/2020] [Indexed: 01/31/2023] Open
Abstract
Litsea cubeba L. essential oil (LCEO) is a natural essential oil with considerable antimicrobial activity, and it can gradually replace some chemical additives in the food industry. However, the genetic evidences of stress response of bacteria under sub-lethal treatment with LCEO is limited. To this end, transcriptomic analysis of Staphylococcus aureus 29213 under a low concentration of LCEO was performed. Bacterial RNA samples were extracted from 1/4 MIC (0.07 μL/mL) of LCEO-treated and non-treated S. aureus 29213. The transcriptional results were obtained by RNA sequencing (RNA-Seq). After treated with LCEO of S. aureus 29213, 300, and 242 genes were significantly up and down-regulated. Up-regulated genes were mainly related to cell membrane (wall) stress stimulon including genes related to two-component regulatory system (VraS), histidine metabolism (hisABCD etc.) and L-lysine biosynthesis (thrA, lysC, asd etc.). Significant differences were also founded between LCEO-treated and non-treated groups in peptidoglycan biosynthesis related pathways. Down-regulated genes were related to nitrogen metabolism (NarGHIJ etc.), carotenoid biosynthesis (all) and pyruvate metabolism (phdA, pflB, pdhC etc.) of S. aureus 29213 in an LCEO-existing environment compared to the control. At the same time, we confirmed that LCEO can significantly affect the staphyloxanthin level of S. aureus 29213 for the first time, which is closely related to the redox state of S. aureus 29213. These evidences expanded the knowledge of stress response of S. aureus 29213 strain under sub-lethal concentration of LCEO.
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Affiliation(s)
- Yunqiao Yang
- College of Animal Sciences and Technology, Guangxi University, Nanning, China
| | - Yunru Chen
- College of Animal Sciences and Technology, Guangxi University, Nanning, China
| | - Geyin Zhang
- College of Animal Sciences and Technology, Guangxi University, Nanning, China
| | - Junying Sun
- College of Animal Sciences and Technology, Guangxi University, Nanning, China
| | - Lei Guo
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, China
| | - Mingsheng Jiang
- College of Animal Sciences and Technology, Guangxi University, Nanning, China
| | - Bingming Ou
- College of Life Science, Zhaoqing University, Zhaoqing, China
| | - Weiyu Zhang
- College of Animal Sciences and Technology, Guangxi University, Nanning, China
| | - Hongbin Si
- College of Animal Sciences and Technology, Guangxi University, Nanning, China
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Chlamydomonas reinhardtii, an Algal Model in the Nitrogen Cycle. PLANTS 2020; 9:plants9070903. [PMID: 32708782 PMCID: PMC7412212 DOI: 10.3390/plants9070903] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 02/06/2023]
Abstract
Nitrogen (N) is an essential constituent of all living organisms and the main limiting macronutrient. Even when dinitrogen gas is the most abundant form of N, it can only be used by fixing bacteria but is inaccessible to most organisms, algae among them. Algae preferentially use ammonium (NH4+) and nitrate (NO3−) for growth, and the reactions for their conversion into amino acids (N assimilation) constitute an important part of the nitrogen cycle by primary producers. Recently, it was claimed that algae are also involved in denitrification, because of the production of nitric oxide (NO), a signal molecule, which is also a substrate of NO reductases to produce nitrous oxide (N2O), a potent greenhouse gas. This review is focused on the microalga Chlamydomonas reinhardtii as an algal model and its participation in different reactions of the N cycle. Emphasis will be paid to new actors, such as putative genes involved in NO and N2O production and their occurrence in other algae genomes. Furthermore, algae/bacteria mutualism will be considered in terms of expanding the N cycle to ammonification and N fixation, which are based on the exchange of carbon and nitrogen between the two organisms.
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Anaerobic metabolism of Foraminifera thriving below the seafloor. ISME JOURNAL 2020; 14:2580-2594. [PMID: 32641728 PMCID: PMC7490399 DOI: 10.1038/s41396-020-0708-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/09/2020] [Accepted: 06/23/2020] [Indexed: 02/06/2023]
Abstract
Foraminifera are single-celled eukaryotes (protists) of large ecological importance, as well as environmental and paleoenvironmental indicators and biostratigraphic tools. In addition, they are capable of surviving in anoxic marine environments where they represent a major component of the benthic community. However, the cellular adaptations of Foraminifera to the anoxic environment remain poorly constrained. We sampled an oxic-anoxic transition zone in marine sediments from the Namibian shelf, where the genera Bolivina and Stainforthia dominated the Foraminifera community, and use metatranscriptomics to characterize Foraminifera metabolism across the different geochemical conditions. Relative Foraminifera gene expression in anoxic sediment increased an order of magnitude, which was confirmed in a 10-day incubation experiment where the development of anoxia coincided with a 20–40-fold increase in the relative abundance of Foraminifera protein encoding transcripts, attributed primarily to those involved in protein synthesis, intracellular protein trafficking, and modification of the cytoskeleton. This indicated that many Foraminifera were not only surviving but thriving, under the anoxic conditions. The anaerobic energy metabolism of these active Foraminifera was characterized by fermentation of sugars and amino acids, fumarate reduction, and potentially dissimilatory nitrate reduction. Moreover, the gene expression data indicate that under anoxia Foraminifera use the phosphogen creatine phosphate as an ATP store, allowing reserves of high-energy phosphate pool to be maintained for sudden demands of increased energy during anaerobic metabolism. This was co-expressed alongside genes involved in phagocytosis and clathrin-mediated endocytosis (CME). Foraminifera may use CME to utilize dissolved organic matter as a carbon and energy source, in addition to ingestion of prey cells via phagocytosis. These anaerobic metabolic mechanisms help to explain the ecological success of Foraminifera documented in the fossil record since the Cambrian period more than 500 million years ago.
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Li Q, Lei Y, Morard R, Li T, Wang B. Diversity hotspot and unique community structure of foraminifera in the world's deepest marine blue hole - Sansha Yongle Blue Hole. Sci Rep 2020; 10:10257. [PMID: 32581270 PMCID: PMC7314809 DOI: 10.1038/s41598-020-67221-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/01/2020] [Indexed: 11/09/2022] Open
Abstract
Marine blue holes are precious geological heritages with high scientific research values. Their physical and chemical characteristics are unique because of the steep-walled structure and isolated water column which create isolated ecosystems in geographically restricted areas. The Sansha Yongle Blue Hole (SYBH) is the world's deepest marine blue hole. Here, we generated the first DNA metabarcoding dataset from SYBH sediment focusing on foraminifera, a group of protists that have colonized various marine environments. We collected sediment samples from SYBH along a depth gradient to characterize the foraminiferal diversity and compared them with the foraminiferal diversity of the costal Jiaozhou Bay (JZB) and the abyssal Northwest Pacific Ocean (NWP). We amplified the SSU rDNA of foraminifera and sequenced them with high-throughput sequencing. The results showed that the foraminiferal assemblages in SYBH were vertically structured in response to the abiotic gradients and diversity was higher than in JZB and NWP. This study illustrates the capacity of foraminifera to colonize hostile environments and shows that blue holes are natural laboratories to explore physiological innovation associated with anoxia.
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Affiliation(s)
- Qingxia Li
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanli Lei
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Raphaёl Morard
- MARUM Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse, 28359, Bremen, Germany
| | - Tiegang Li
- Key Laboratory of Marine Sedimentology and Environmental Geology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China.
- Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Baodong Wang
- Key Laboratory of Marine Sedimentology and Environmental Geology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
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Zhang X, Ward BB, Sigman DM. Global Nitrogen Cycle: Critical Enzymes, Organisms, and Processes for Nitrogen Budgets and Dynamics. Chem Rev 2020; 120:5308-5351. [DOI: 10.1021/acs.chemrev.9b00613] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xinning Zhang
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
- Princeton Environmental Institute, Princeton University, Princeton, New Jersey 08544, United States
| | - Bess B. Ward
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
- Princeton Environmental Institute, Princeton University, Princeton, New Jersey 08544, United States
| | - Daniel M. Sigman
- Department of Geosciences, Princeton University, Princeton, New Jersey 08544, United States
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Murphy AE, Bulseco AN, Ackerman R, Vineis JH, Bowen JL. Sulphide addition favours respiratory ammonification (DNRA) over complete denitrification and alters the active microbial community in salt marsh sediments. Environ Microbiol 2020; 22:2124-2139. [DOI: 10.1111/1462-2920.14969] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 02/14/2020] [Accepted: 02/28/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Anna E. Murphy
- Department of Marine and Environmental Sciences Marine Science Center, Northeastern University Nahant Massachusetts 01908 USA
- INSPIRE Environmental, Inc 513 Broadway Suite 314, Newport Rhode Island 02840 USA
| | - Ashley N. Bulseco
- Department of Marine and Environmental Sciences Marine Science Center, Northeastern University Nahant Massachusetts 01908 USA
- The Ecosystems Center Marine Biological Laboratory Woods Hole Massachusetts 02543 USA
| | - Ross Ackerman
- Biology Department, Bates College Lewiston Maine 04240 USA
| | - Joseph H. Vineis
- Department of Marine and Environmental Sciences Marine Science Center, Northeastern University Nahant Massachusetts 01908 USA
| | - Jennifer L. Bowen
- Department of Marine and Environmental Sciences Marine Science Center, Northeastern University Nahant Massachusetts 01908 USA
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Yang N, Li Y, Zhang W, Lin L, Qian B, Wang L, Niu L, Zhang H. Cascade dam impoundments restrain the trophic transfer efficiencies in benthic microbial food web. WATER RESEARCH 2020; 170:115351. [PMID: 31810033 DOI: 10.1016/j.watres.2019.115351] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 05/25/2023]
Abstract
Determination of the effects of cascade dams on benthic microbial ecosystem is essential for dam regulation and ecological function protection. However, no comprehensive investigation has yet shown the ecosystem-level responses of microbiota to dam impoundments. This study conducted DNA metabarcoding and microbial food web analysis for multiple species and their interrelationships along a cascade dam-affected river. The composition, distribution and diversity of bacteria, protozoans and metazoans were obviously different between river and reservoirs, mainly controlled by hydrological (P < 0.01) and nutrient parameters (P < 0.05). Those three groups make up a co-occurrence network, with most edges direct from higher to lower trophic levels or vice versa and more than 50% keystones participate in the food web, indicating the significant role of predator-prey relationships. Based on the microbial food web analysis, the predator biomass, especially at higher trophic levels, decreased by about 10% from the riverine to the lacustrine system. The structural equation model illustrates that both bottom-up forces (environmental factors particularly velocity and nutrient concentrations) and top-down forces (higher trophic levels) critically control microbial food web patterns (P < 0.05). As a result of dam impoundments, the lower velocity in the reservoirs has direct negative effects on trophic transfer efficiencies that may be further magnified by nutrient accumulation, probably leading to an increase of eutrophication and posing a risk to water quality. The results suggest the potential ecological risk in the reservoirs and highlight the need to consider from the perspective of ecosystem during the operation of cascade dams.
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Affiliation(s)
- Nan Yang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China.
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Li Lin
- Department of Basin Water Environment, Changjiang River Scientific Research Institute, Wuhan, 430010, China; Hubei Provincial Key Laboratory of Basin Water Resources and Ecological Environment Sciences, Changjiang River Scientific Research Institute, Wuhan, 430010, China
| | - Bao Qian
- Hydrology Bureau of Changjiang Water Resources Commission, Wuhan, Hubei, 430010, China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
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Strategies among phytoplankton in response to alleviation of nutrient stress in a subtropical gyre. ISME JOURNAL 2019; 13:2984-2997. [PMID: 31439897 DOI: 10.1038/s41396-019-0489-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 07/07/2019] [Accepted: 08/02/2019] [Indexed: 11/08/2022]
Abstract
Despite generally low primary productivity and diatom abundances in oligotrophic subtropical gyres, the North Atlantic Subtropical Gyre (NASG) exhibits significant diatom-driven carbon export on an annual basis. Subsurface pulses of nutrients likely fuel brief episodes of diatom growth, but the exact mechanisms utilized by diatoms in response to these nutrient injections remain understudied within near-natural settings. Here we simulated delivery of subsurface nutrients and compare the response among eukaryotic phytoplankton using a combination of physiological techniques and metatranscriptomics. We show that eukaryotic phytoplankton groups exhibit differing levels of transcriptional responsiveness and expression of orthologous genes in response to release from nutrient limitation. In particular, strategies for use of newly delivered nutrients are distinct among phytoplankton groups. Diatoms channel new nitrate to growth-related strategies while physiological measurements and gene expression patterns of other groups suggest alternative strategies. The gene expression patterns displayed here provide insights into the cellular mechanisms that underlie diatom subsistence during chronic nitrogen-depleted conditions and growth upon nutrient delivery that can enhance carbon export from the surface ocean.
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Kennedy F, Martin A, Bowman JP, Wilson R, McMinn A. Dark metabolism: a molecular insight into how the Antarctic sea-ice diatom Fragilariopsis cylindrus survives long-term darkness. THE NEW PHYTOLOGIST 2019; 223:675-691. [PMID: 30985935 PMCID: PMC6617727 DOI: 10.1111/nph.15843] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/02/2019] [Indexed: 05/27/2023]
Abstract
Light underneath Antarctic sea-ice is below detectable limits for up to 4 months of the year. The ability of Antarctic sea-ice diatoms to survive this prolonged darkness relies on their metabolic capability. This study is the first to examine the proteome of a prominent sea-ice diatom in response to extended darkness, focusing on the protein-level mechanisms of dark survival. The Antarctic diatom Fragilariopsis cylindrus was grown under continuous light or darkness for 120 d. The whole cell proteome was quantitatively analysed by nano-LC-MS/MS to investigate metabolic changes that occur during sustained darkness and during recovery under illumination. Enzymes of metabolic pathways, particularly those involved in respiratory processes, tricarboxylic acid cycle, glycolysis, the Entner-Doudoroff pathway, the urea cycle and the mitochondrial electron transport chain became more abundant in the dark. Within the plastid, carbon fixation halted while the upper sections of the glycolysis, gluconeogenesis and pentose phosphate pathways became less active. We have discovered how F. cylindrus utilises an ancient alternative metabolic mechanism that enables its capacity for long-term dark survival. By sustaining essential metabolic processes in the dark, F. cylindrus retains the functionality of the photosynthetic apparatus, ensuring rapid recovery upon re-illumination.
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Affiliation(s)
- Fraser Kennedy
- Institute for Marine and Antarctic StudiesUniversity of TasmaniaHobart7000TasmaniaAustralia
| | - Andrew Martin
- Institute for Marine and Antarctic StudiesUniversity of TasmaniaHobart7000TasmaniaAustralia
| | - John P. Bowman
- Centre for Food Safety and InnovationTasmanian Institute of AgricultureHobart7000TasmaniaAustralia
| | - Richard Wilson
- Central Science LaboratoryUniversity of TasmaniaHobart7000TasmaniaAustralia
| | - Andrew McMinn
- Institute for Marine and Antarctic StudiesUniversity of TasmaniaHobart7000TasmaniaAustralia
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50
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Metabolic preference of nitrate over oxygen as an electron acceptor in foraminifera from the Peruvian oxygen minimum zone. Proc Natl Acad Sci U S A 2019; 116:2860-2865. [PMID: 30728294 DOI: 10.1073/pnas.1813887116] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Benthic foraminifera populate a diverse range of marine habitats. Their ability to use alternative electron acceptors-nitrate (NO3 -) or oxygen (O2)-makes them important mediators of benthic nitrogen cycling. Nevertheless, the metabolic scaling of the two alternative respiration pathways and the environmental determinants of foraminiferal denitrification rates are yet unknown. We measured denitrification and O2 respiration rates for 10 benthic foraminifer species sampled in the Peruvian oxygen minimum zone (OMZ). Denitrification and O2 respiration rates significantly scale sublinearly with the cell volume. The scaling is lower for O2 respiration than for denitrification, indicating that NO3 - metabolism during denitrification is more efficient than O2 metabolism during aerobic respiration in foraminifera from the Peruvian OMZ. The negative correlation of the O2 respiration rate with the surface/volume ratio is steeper than for the denitrification rate. This is likely explained by the presence of an intracellular NO3 - storage in denitrifying foraminifera. Furthermore, we observe an increasing mean cell volume of the Peruvian foraminifera, under higher NO3 - availability. This suggests that the cell size of denitrifying foraminifera is not limited by O2 but rather by NO3 - availability. Based on our findings, we develop a mathematical formulation of foraminiferal cell volume as a predictor of respiration and denitrification rates, which can further constrain foraminiferal biogeochemical cycling in biogeochemical models. Our findings show that NO3 - is the preferred electron acceptor in foraminifera from the OMZ, where the foraminiferal contribution to denitrification is governed by the ratio between NO3 - and O2.
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