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Wang Y, Hu Y, Liu Y, Chen Q, Xu J, Zhang F, Mao J, Shi Q, He C, Cai R, Lønborg C, Liu L, Guo A, Jiao N, Zheng Q. Heavy metal induced shifts in microbial community composition and interactions with dissolved organic matter in coastal sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172003. [PMID: 38569948 DOI: 10.1016/j.scitotenv.2024.172003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 04/05/2024]
Abstract
Heavy metals can impact the structure and function of coastal sediment. The dissolved organic matter (DOM) pool plays an important role in determining both the heavy metal toxicity and microbial community composition in coastal sediments. However, how heavy metals affect the interactions between microbial communities and DOM remains unclear. Here, we investigated the influence of heavy metals on the microbial community structure (including bacteria and archaea) and DOM composition in surface sediments of Beibu Gulf, China. Our results revealed firstly that chromium, zinc, cadmium, and lead were the heavy metals contributing to pollution in our studied area. Furthermore, the DOM chemical composition was distinctly different in the contaminated area from the uncontaminated area, characterized by a higher average O/C ratio and increased prevalence of carboxyl-rich alicyclic molecules (CRAM) and highly unsaturated compounds (HUC). This indicates that DOM in the contaminated area was more recalcitrant compared to the uncontaminated area. Except for differences in archaeal diversity between the two areas, there were no significant variations observed in the structure of archaea and bacteria, as well as the diversity of bacteria, across the two areas. Nevertheless, our co-occurrence network analysis revealed that the B2M28 and Euryarchaeota, dominating bacterial and archaeal groups in the contaminated area were strongly related to CRAM. The network analysis also unveiled correlations between active bacteria and elevated proportions of nitrogen-containing DOM molecules. In contrast, the archaea-DOM network exhibited strong associations with nitrogen- and sulfur-containing molecules. Collectively, these findings suggest that heavy metals indeed influence the interaction between microbial communities and DOM, potentially affecting the accumulation of recalcitrant compounds in coastal sediments.
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Affiliation(s)
- Yu Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China; College of Environmental and Ecology, Xiamen University, Xiamen, China
| | - Yuxing Hu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Yanting Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Qi Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Jinxin Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Fei Zhang
- Third Institute of Oceanography Ministry of Natural Resources, Xiamen, China
| | - Jinhua Mao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Quan Shi
- College of Chemical Engineering and Environment, China University of Petroleum (Beijing), Beijing, China
| | - Chen He
- College of Chemical Engineering and Environment, China University of Petroleum (Beijing), Beijing, China
| | - Ruanhong Cai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Christian Lønborg
- Department of Ecoscience, Section for Marine Diversity and Experimental Ecology, University of Aarhus, Roskilde, Denmark
| | - Lihua Liu
- Fujian Xiamen Environmental Monitoring Central Station, Xiamen, China
| | - Aixing Guo
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China.
| | - Qiang Zheng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China.
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Wang C, Lu B, Chen H, Chen H, Li T, Lu W, Chai X. Strengthen high-loading operation of wastewater treatment plants by composite micron powder carrier: Microscale control of carbon, nitrogen, and sulfur metabolic pathways. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166593. [PMID: 37634713 DOI: 10.1016/j.scitotenv.2023.166593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/10/2023] [Accepted: 08/24/2023] [Indexed: 08/29/2023]
Abstract
The concentration of activated sludge is a crucial factor influencing the capacity and efficiency of sewage wastewater treatment plants (WWTPs). However, high sludge concentrations can lead to sludge loss in the secondary sedimentation tank, resulting in reduced processing capacity, particularly during low-temperature stages and sludge bulking. This study investigated the impact of adding composite micron powder carriers (CMPC) in high-concentration powder carrier biofluidized bed (HPB) technology to the biochemical units of WWTPs on sludge concentration and settling performance. For the traditional activated sludge method (ASM), its hydraulic retention time (HRT) was 8 h, with an average effluent total nitrogen (TN) of 15.14 mg/L. Sludge bulking was prone to occur in low-temperature environments, resulting in a high average sludge volume index (SVI) of 560 mL/g. Conversely, with a CMPC dosage of 4 g/L, the HRT of HPB technology was 4.8 h, and the average effluent TN was 11.40 mg/L, with a removal efficiency of 67.43 %. During operation of HPB technology under high sludge concentration conditions (8 g/L), the average SVI remained at 85 mL/g, indicating excellent settling characteristics. Moreover, in the sequencing batch reactor (SBR), the SVI value of bulking sludge decreased from the original 695 to 111 mL/g by the 9th day of operation with the CMPC dosage of 2 g/L. At the same time, the filamentous bacteria almost disappeared, suggesting that CMPC inhibit the growth of filamentous bacteria. Metagenomic analysis demonstrated that CPMC enhance the utilization of small molecular fatty acids in activated sludge and promote electron transfer between nitrate and nitrite, thereby improving wastewater treatment capacity. Additionally, CMPC enhanced the relative abundance of Saprospiraceae in sludge, which accelerate the degradation of polysaccharides in extracellular polymeric substances, weaken sludge's hydrophilic properties, and improve sludge's settling performance. Overall, these findings suggested that CMPC effectively strengthen the high-loading operation of WWTPs by improving sludge concentration and sedimentation performance.
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Affiliation(s)
- ChengXian Wang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Bin Lu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Hao Chen
- Changsha Urban Research Institute of Construction Science, Changsha 410006, China
| | - Huizhen Chen
- Hunan Sanyou Environmental Protection Co. Ltd., Changsha 410205, China
| | - Tingting Li
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Wei Lu
- Shanghai Key Lab. of D&A for Metal-Functional Materials, School of Materials Science & Engineering, Tongji University, Shanghai 201804, China
| | - Xiaoli Chai
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China.
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Deng W, Zhao Z, Li Y, Cao R, Chen M, Tang K, Wang D, Fan W, Hu A, Chen G, Chen CTA, Zhang Y. Strategies of chemolithoautotrophs adapting to high temperature and extremely acidic conditions in a shallow hydrothermal ecosystem. MICROBIOME 2023; 11:270. [PMID: 38049915 PMCID: PMC10696704 DOI: 10.1186/s40168-023-01712-w] [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: 06/24/2023] [Accepted: 10/27/2023] [Indexed: 12/06/2023]
Abstract
BACKGROUND Active hydrothermal vents create extreme conditions characterized by high temperatures, low pH levels, and elevated concentrations of heavy metals and other trace elements. These conditions support unique ecosystems where chemolithoautotrophs serve as primary producers. The steep temperature and pH gradients from the vent mouth to its periphery provide a wide range of microhabitats for these specialized microorganisms. However, their metabolic functions, adaptations in response to these gradients, and coping mechanisms under extreme conditions remain areas of limited knowledge. In this study, we conducted temperature gradient incubations of hydrothermal fluids from moderate (pH = 5.6) and extremely (pH = 2.2) acidic vents. Combining the DNA-stable isotope probing technique and subsequent metagenomics, we identified active chemolithoautotrophs under different temperature and pH conditions and analyzed their specific metabolic mechanisms. RESULTS We found that the carbon fixation activities of Nautiliales in vent fluids were significantly increased from 45 to 65 °C under moderately acidic condition, while their heat tolerance was reduced under extremely acidic conditions. In contrast, Campylobacterales actively fixed carbon under both moderately and extremely acidic conditions under 30 - 45 °C. Compared to Campylobacterales, Nautiliales were found to lack the Sox sulfur oxidation system and instead use NAD(H)-linked glutamate dehydrogenase to boost the reverse tricarboxylic acid (rTCA) cycle. Additionally, they exhibit a high genetic potential for high activity of cytochrome bd ubiquinol oxidase in oxygen respiration and hydrogen oxidation at high temperatures. In terms of high-temperature adaption, the rgy gene plays a critical role in Nautiliales by maintaining DNA stability at high temperature. Genes encoding proteins involved in proton export, including the membrane arm subunits of proton-pumping NADH: ubiquinone oxidoreductase, K+ accumulation, selective transport of charged molecules, permease regulation, and formation of the permeability barrier of bacterial outer membranes, play essential roles in enabling Campylobacterales to adapt to extremely acidic conditions. CONCLUSIONS Our study provides in-depth insights into how high temperature and low pH impact the metabolic processes of energy and main elements in chemolithoautotrophs living in hydrothermal ecosystems, as well as the mechanisms they use to adapt to the extreme hydrothermal conditions. Video Abstract.
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Affiliation(s)
- Wenchao Deng
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, 361101, China.
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.
| | - Zihao Zhao
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Yufang Li
- Fisheries College, Jimei University, Xiamen, 361021, China
| | - Rongguang Cao
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, 361101, China
| | - Mingming Chen
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, 361101, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, 361101, China
| | - Deli Wang
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, 361101, China
| | - Wei Fan
- Ocean College, Zhejiang University, Zhoushan, 316000, China
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Guangcheng Chen
- Key Laboratory of Marine Ecological Conservation and Restoration, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Chen-Tung Arthur Chen
- Department of Oceanography, National Sun Yat-Sen University, Kaohsiung Taiwan, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Sciences, Xiamen University, Xiamen, 361101, China.
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Nie L, Wan W. Nutrient-cycling functional gene diversity mirrors phosphorus transformation during chicken manure composting. BIORESOURCE TECHNOLOGY 2023; 386:129504. [PMID: 37468004 DOI: 10.1016/j.biortech.2023.129504] [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: 06/12/2023] [Revised: 07/12/2023] [Accepted: 07/16/2023] [Indexed: 07/21/2023]
Abstract
Elucidating ecological mechanism underlying phosphorus transformation mediated by phosphate-solubilizing bacteria (PSB) during manure composting is an important but rarely investigated subject. The research objective is to disentangle ecological functions of the inoculation of PSB Pseudomonas sp. WWJ-22 during chicken manure composting based on gene quantification and amplicon sequencing. There are large dynamic changes in phosphorus fractions, gene abundances, and bacterial community structure. The PSB addition notably increased available phosphorus from 0.29-0.89 g kg-1 to 0.49-1.39 g kg-1 and significantly affected phosphorus fractionation. The PSB inoculation significantly affected composition of nutrient-cycling functional genes (NCFGs), and notably influenced bacterial community composition and function. Compost bacteria showed significant phylogenetic signals in response to phosphorus fractions, and stochastic processes dominated bacterial community assembly. Results emphasized that PSB addition increased functional redundancy, phylogenetic conservatism, and stochasticity-dominated assembly of bacterial community. Overall, findings highlight NCFG diversity can be a bio-indicator to mirror phosphorus transformation.
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Affiliation(s)
- Liang Nie
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Wenjie Wan
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, PR China.
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5
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Arcadi E, Buschi E, Rastelli E, Tangherlini M, De Luca P, Esposito V, Calogero R, Andaloro F, Romeo T, Danovaro R. Novel Insights on the Bacterial and Archaeal Diversity of the Panarea Shallow-Water Hydrothermal Vent Field. Microorganisms 2023; 11:2464. [PMID: 37894122 PMCID: PMC10608945 DOI: 10.3390/microorganisms11102464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/18/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Current knowledge of the microbial diversity of shallow-water hydrothermal vents is still limited. Recent evidence suggests that these peculiar and heterogeneous systems might host highly diversified microbial assemblages with novel or poorly characterized lineages. In the present work, we used 16S rRNA gene metabarcoding to provide novel insights into the diversity of the bacterial and archaeal assemblages in seawater and sediments of three shallow-water hydrothermal systems of Panarea Island (Tyrrhenian Sea). The three areas were characterized by hot, cold, or intermediate temperatures and related venting activities. Microbial biodiversity in seawater largely differed from the benthic one, both in α-diversity (i.e., richness of amplicon sequence variants-ASVs) and in prokaryotic assemblage composition. Furthermore, at the class level, the pelagic prokaryotic assemblages were very similar among sites, whereas the benthic microbial assemblages differed markedly, reflecting the distinct features of the hydrothermal activities at the three sites we investigated. Our results show that ongoing high-temperature emissions can influence prokaryotic α-diversity at the seafloor, increasing turnover (β-)diversity, and that the intermediate-temperature-venting spot that experienced a violent gas explosion 20 years ago now displays the highest benthic prokaryotic diversity. Overall, our results suggest that hydrothermal vent dynamics around Panarea Island can contribute to an increase in the local heterogeneity of physical-chemical conditions, especially at the seafloor, in turn boosting the overall microbial (γ-)diversity of this peculiar hydrothermal system.
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Affiliation(s)
- Erika Arcadi
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Contrada Porticatello, 29, 98167 Messina, Italy; (E.A.); (R.C.); (F.A.)
| | - Emanuela Buschi
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Fano Marine Centre, Viale Adriatico 1-N, 61032 Fano, Italy;
| | - Eugenio Rastelli
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Fano Marine Centre, Viale Adriatico 1-N, 61032 Fano, Italy;
| | - Michael Tangherlini
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Fano Marine Centre, Viale Adriatico 1-N, 61032 Fano, Italy
| | - Pasquale De Luca
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy;
| | - Valentina Esposito
- Istituto Nazionale di Oceanografia e di Geofisica Sperimentale—OGS Borgo Grotta Gigante 42/C, 34010 Sgonico, Italy;
| | - Rosario Calogero
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Contrada Porticatello, 29, 98167 Messina, Italy; (E.A.); (R.C.); (F.A.)
| | - Franco Andaloro
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Contrada Porticatello, 29, 98167 Messina, Italy; (E.A.); (R.C.); (F.A.)
| | - Teresa Romeo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Via dei Mille 46, 98057 Milazzo, Italy
- National Institute for Environmental Protection and Research, Via dei Mille 46, 98057 Milazzo, Italy
| | - Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy;
- National Biodiversity Future Centre (NBFC), 90133 Palermo, Italy
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Arcadi E, Rizzo C, Calogero R, Sciutteri V, Fabiano F, Consoli P, Andaloro F, Romeo T. Microbial communities inhabiting shallow hydrothermal vents as sentinels of acidification processes. Front Microbiol 2023; 14:1233893. [PMID: 37727286 PMCID: PMC10505797 DOI: 10.3389/fmicb.2023.1233893] [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: 06/02/2023] [Accepted: 08/09/2023] [Indexed: 09/21/2023] Open
Abstract
Introduction Shallow hydrothermal vents are considered natural laboratories to study the effects of acidification on biota, due to the consistent CO2 emissions with a consequent decrease in the local pH. Methods Here the microbial communities of water and sediment samples from Levante Bay (Vulcano Island) with different pH and redox conditions were explored by Next Generation Sequencing techniques. The taxonomic structure was elucidated and compared with previous studies from the same area in the last decades. Results and discussion The results revealed substantial shifts in the taxonomic structure of both bacterial and archaeal communities, with special relevance in the sediment samples, where the effects of external parameters probably act for a long time. The study demonstrates that microbial communities could be used as indicators of acidification processes, by shaping the entire biogeochemical balance of the ecosystem in response to stress factors. The study contributes to understanding how much these communities can tell us about future changes in marine ecosystems.
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Affiliation(s)
- Erika Arcadi
- Department of Biology and Evolution of Marine Organism, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
| | - Carmen Rizzo
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn–, Sicily Marine Centre, Messina, Italy
- Institute of Polar Sciences, National Research Council (CNR-ISP), Messina, Italy
| | - Rosario Calogero
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
| | - Valentina Sciutteri
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
| | - Francesco Fabiano
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn–, Sicily Marine Centre, Messina, Italy
| | - Pierpaolo Consoli
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
| | - Franco Andaloro
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
| | - Teresa Romeo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy
- National Institute for Environmental Protection and Research, Milazzo, Italy
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Cheng Y, Wan W. Strong linkage between nutrient-cycling functional gene diversity and ecosystem multifunctionality during winter composting with pig manure and fallen leaves. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 867:161529. [PMID: 36634774 DOI: 10.1016/j.scitotenv.2023.161529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 01/04/2023] [Accepted: 01/07/2023] [Indexed: 06/17/2023]
Abstract
Microorganisms play important roles in element transformation and display distinct compositional changes during composting. However, little is known about the linkage between nutrient-cycling functional gene diversity and compost ecosystem multifunctionality (EMF). This study performed winter composting with pig manure and fallen leaves and evaluated the distribution patterns and ecological roles of multiple functional genes involved in nutrient cycles. Physicochemical properties and enzyme activities presented large fluctuations during composting. Absolute abundance, composition, and diversity of functional genes participating in carbon, nitrogen, phosphorus, and sulfur cycles presented distinct dynamic changes. Stronger linkage was found between enzyme activities and temperature than other physicochemical factors, whereas total nitrogen rather than other physicochemical factors displayed closer linkage with functional gene composition and diversity. EMF targeting key nutrient (i.e., carbon, nitrogen, phosphorus, and sulfur) cycles was significantly positively correlated with temperature and notably negatively correlated with functional gene diversity. Enzyme activities rather than functional gene diversity showed a greater potential effect on phosphorus availability. Consequently, the available phosphorus (AP) content increased from initial 0.50 g/kg to final 1.43 g/kg. To our knowledge, this is the first study that deciphered ecological roles of nutrient-cycling functional gene diversity during composting, and the final compost can serve as a potential phosphorus fertilizer.
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Affiliation(s)
- Yarui Cheng
- College of Chemistry and Environmental Engineering, Hanjiang Normal University, Shiyan 442000, PR China
| | - Wenjie Wan
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430074, PR China.
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8
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Wu Q, Wan W. Insight into application of phosphate-solubilizing bacteria promoting phosphorus availability during chicken manure composting. BIORESOURCE TECHNOLOGY 2023; 373:128707. [PMID: 36746213 DOI: 10.1016/j.biortech.2023.128707] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Understanding ecological roles of phosphate-solubilizing bacteria (PSB) is important to optimize composting systems. Illumina MiSeq sequencing, gene quantitation, and statistical analyses were employed to explore ecological mechanisms underlying available phosphorus (AP) facilitation during composting with the inoculation of PSB Pseudomonas sp. WWJ-22. Results displayed that the inoculation of PSB significantly increased AP from 0.83 to 1.23 g kg-1, and notably increased abundances of phosphorus-cycling genes as well as numbers of PSB mineralizing phytate and lecithin. The PSB addition significantly affected compost bacterial community composition, and phosphorus factions and phosphorus-cycling genes independently explained 25.4 % and 25.0 % bacterial compositional dissimilarity. Stochastic and homogenizing processes affected more on bacterial community assembly, and rare bacteria potentially mediated organic phosphorus mineralization. These results emphasized that phosphorus fractions, PSB number, phosphorus-cycling gene abundance, and bacterial community composition contributed differently to phosphorus availability. Findings highlight ecological roles of exogenous PSB during chicken manure composting.
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Affiliation(s)
- Qiusheng Wu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Wenjie Wan
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, PR China.
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9
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Jiang X, Xue Z, Chen W, Xu M, Liu H, Liang J, Zhang L, Sun Y, Liu C, Yang X. Biotransformation kinetics and pathways of typical synthetic progestins in soil microcosms. JOURNAL OF HAZARDOUS MATERIALS 2023; 446:130684. [PMID: 36586332 DOI: 10.1016/j.jhazmat.2022.130684] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/28/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
Gestodene (GES), altrenogest (ALT), and medroxyprogesterone acetate (MPA) are three potent synthetic progestins detected in agricultural soils; however, their biotransformation outcomes in soils remain unclear. This study explored the biotransformation of these progestins in five agricultural soils with different physicochemical properties. The biotransformation data were well-described by a first-order decay model (R2 = 0.83-0.99), with estimated half-lives ranging between 12.1 and 188 h. Amplicon sequencing indicated that the presence of progestins changed the bacterial richness and community structure in the soils. Linear correlation, canonical correlation, and two-way correlation network analysis revealed that soil properties can affect biotransformation rates by interfering with progestin-soil interactions or with keystone taxa in soils. The clustermap demonstrated the formation of abundant transformation products (TPs). Isomerization and C4(5) hydrogenation were the major transformation pathways for GES (yields of ∼ 13.7 % and ∼ 10.6 %, respectively). Aromatic dehydrogenation was the major transformation pathway for ALT (yield of ∼ 17.4 %). The C17 hydrolysis with subsequent dehydration and hydrogenation was the major transformation pathway for MPA (yield of ∼ 196 %). In particular, some TPs exhibited progestagenic, androgenic, or estrogenic activity. This study highlights the importance of evaluating the ecotoxicity of progestin and TP mixtures for better understanding their risks in the environment.
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Affiliation(s)
- Xiuping Jiang
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Zhongye Xue
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Weisong Chen
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Manxin Xu
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - He Liu
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Science, Ministry of Ecology and Environment, Guangzhou 510655, PR China
| | - Jiahao Liang
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Science, Ministry of Ecology and Environment, Guangzhou 510655, PR China
| | - Lu Zhang
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China
| | - Yan Sun
- Guangdong Institute of Eco-environmental Science & Technology, Guangzhou, Guangdong 510650, PR China
| | - Churong Liu
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China.
| | - Xingjian Yang
- College of Natural Resources and Environment, Joint Institute for Environment & Education, South China Agricultural University, Guangzhou 510642, PR China.
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Lo LSH, Xu Z, Lee SS, Lau WK, Qiu JW, Liu H, Qian PY, Cheng J. How elevated nitrogen load affects bacterial community structure and nitrogen cycling services in coastal water. Front Microbiol 2022; 13:1062029. [PMID: 36620064 PMCID: PMC9815024 DOI: 10.3389/fmicb.2022.1062029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Nutrient pollution in the coastal environment has been accelerated by progressively intensifying aquaculture activities. Excessive nutrients can lead to coastal eutrophication with serious economic and ecological consequences. In this study, we studied coastal planktonic microbial community over a year to understand the aquaculture impact on coastal water quality and function. We observed increased total inorganic nitrogen concentrations in active fish farms to favor the diverse Alpha- and Gammaproteobacteria. Bacterial community alpha diversity in fish farms was positively correlated with total inorganic nitrogen, and active fish farming co-influenced the bacterial structural composition and regional beta diversity. By analyzing the nitrogen cycle-related functional compositions and pathways using PICRUSt2 prediction on inferred genomes, we identified the contribution of over 600 bacterial species to four major pathways. Enhanced nitrogen load in active fish farms was positively correlated with elevated dissimilatory nitrate reduction and denitrification pathway abundances. Fallowed fish farms were characterized by a predicted high abundance of nirA and narB genes contributing to assimilatory nitrate reduction pathway due to the prevalence of Cyanobacteria. Overall, these results suggested active operation and short hiatus in coastal aquaculture practices could rapidly impact planktonic bacterial communities and further influence nitrogen cycling and associated processes. These findings will improve the understanding of the responses and interactions between microbiome and aquaculture activities. In a world of increasing aquaculture demands, this work has important implications for sustainable water resource management and development.
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Affiliation(s)
- Linus Shing Him Lo
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China,The Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhimeng Xu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China,The Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Sangwook Scott Lee
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China,The Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Wing Keung Lau
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Jian-Wen Qiu
- The Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China,Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Hongbin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China,The Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China,*Correspondence: Hongbin Liu,
| | - Pei-Yuan Qian
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China,The Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China,Pei-Yuan Qian,
| | - Jinping Cheng
- The Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China,Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, Hong Kong SAR, China,Jinping Cheng,
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11
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Zhao L, Shao H, Zhang L, Panno SV, Kelly WR, Lin TY, Liu WT, Flynn TM, Berger P. Impact of salinity origin on microbial communities in saline springs within the Illinois Basin, USA. Environ Microbiol 2022; 24:6112-6127. [PMID: 36222141 PMCID: PMC10099389 DOI: 10.1111/1462-2920.16241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 10/10/2022] [Indexed: 01/12/2023]
Abstract
Saline springs within the Illinois Basin result from the discharge of deep-seated evaporated seawater (brine) and likely contain diverse and complex microbial communities that are poorly understood. In this study, seven saline/mineral springs with different geochemical characteristics and salinity origins were investigated using geochemical and molecular microbiological analyses to reveal the composition of microbial communities inhabiting springs and their key controlling factors. The 16S rRNA sequencing results demonstrated that each spring harbours a unique microbial community influenced by its geochemical properties and subsurface conditions. The microbial communities in springs that originated from Cambrian/Ordovician strata, which are deep confined units that have limited recharge from overlying formations, share a greater similarity in community composition and have a higher species richness and more overlapped taxa than those that originated from shallower Pennsylvanian strata, which are subject to extensive regional surface and groundwater recharge. The microbial distribution along the spring flow paths at the surface indicates that 59.8%-94.2% of total sequences in sedimentary samples originated from spring water, highlighting the role of springs in influencing microbiota in the immediate terrestrial environment. The results indicate that the springs introduce microbiota with a high biodiversity into surface terrestrial or aquatic ecosystems, potentially affecting microbial reservoirs in downstream ecosystems.
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Affiliation(s)
- Linduo Zhao
- Illinois Sustainable Technology Center, Illinois, USA.,Illinois State Water Survey, Illinois, USA
| | - Hongbo Shao
- Illinois State Geology Survey, Illinois, USA
| | - Li Zhang
- Illinois Sustainable Technology Center, Illinois, USA
| | | | | | - Tzu-Yu Lin
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Theodore M Flynn
- California Department of Water Resources, West Sacramento, California, USA
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12
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Wang L, Shen Z, Cheng X, Hwang JS, Guo Y, Sun M, Cao J, Liu R, Fang J. Metagenomic insights into the functions of microbial communities in sulfur-rich sediment of a shallow-water hydrothermal vent off Kueishan Island. Front Microbiol 2022; 13:992034. [DOI: 10.3389/fmicb.2022.992034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/31/2022] [Indexed: 12/05/2022] Open
Abstract
Hydrothermal vent (HTV) systems are important habitats for understanding the biological processes of extremophiles on Earth and their relative contributions to material and energy cycles in the ocean. Current understanding on hydrothermal systems have been primarily focused on deep-sea HTVs, and little is known about the functions and metabolisms of microorganisms in shallow-water HTVs (SW-HTVs), which are distinguished from deep-sea HTVs by a depth limit of 200 m. In this study, we analyzed metagenomes of sulfur-rich sediment samples collected from a SW-HTV of Kueishan Island, located in a marginal sea of the western Pacific Ocean. Comparing with a previously published report of pelagic samples from the nearby sampling site, microbial communities in the SW-HTV sediments enriching with genes of both aerobic and anaerobic respiration inferred variable environments in the tested sediments. Abundant genes of energy metabolism encoding sulfur oxidation, H2 oxidation, and carbon fixation were detected from the sediment samples. Sixty-eight metagenome-assembled-genomes (MAGs) were reconstructed to further understand the metabolism and potential interactions between different microbial taxa in the SW-HTVs sediment. MAGs with the highest abundant were chemolithotrophic sulfur-oxidization bacteria, including Sulfurovum represented Campylobacteria involved sox multienzyme, sulfide oxidation genes and rTCA cycle, and Gammaproteobacteria involved dsr gene and CBB cycle. In addition, Desulfobacterota with the potential to participate in sulfur-disproportionating processes also had higher abundance than the sample’s overall mean value. The interaction of these bacterial groups allows the microbial communities to efficiently metabolize a large variety of sulfur compounds. In addition, the potential to use simple organic carbon, such as acetate, was found in chemolithotrophic Campylobacterial MAGs. Collectively, our results revealed the complexity of environmental conditions of the vent sediment and highlight the interactive relationships of the dominant microbial populations in driving sulfur cycles in the SW-HTV sediments off Kueishan Island.
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13
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Chen X, Tang K, Zhang M, Liu S, Chen M, Zhan P, Fan W, Chen CTA, Zhang Y. Genome-centric insight into metabolically active microbial population in shallow-sea hydrothermal vents. MICROBIOME 2022; 10:170. [PMID: 36242065 PMCID: PMC9563475 DOI: 10.1186/s40168-022-01351-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/22/2022] [Indexed: 05/20/2023]
Abstract
BACKGROUND Geothermal systems have contributed greatly to both our understanding of the functions of extreme life and the evolutionary history of life itself. Shallow-sea hydrothermal systems are ecological intermediates of deep-sea systems and terrestrial springs, harboring unique and complexed ecosystems, which are well-lit and present physicochemical gradients. The microbial communities of deep-sea and terrestrial geothermal systems have been well-studied at the population genome level, yet little is known about the communities inhabiting the shallow-sea hydrothermal systems and how they compare to those inhabiting other geothermal systems. RESULTS Here, we used genome-resolved metagenomic and metaproteomic approaches to probe into the genetic potential and protein expression of microorganisms from the shallow-sea vent fluids off Kueishantao Island. The families Nautiliaceae and Campylobacteraceae within the Epsilonbacteraeota and the Thiomicrospiraceae within the Gammaproteobacteria were prevalent in vent fluids over a 3-year sampling period. We successfully reconstructed the in situ metabolic modules of the predominant populations within the Epsilonbacteraeota and Gammaproteobacteria by mapping the metaproteomic data back to metagenome-assembled genomes. Those active bacteria could use the reductive tricarboxylic acid cycle or Calvin-Benson-Bassham cycle for autotrophic carbon fixation, with the ability to use reduced sulfur species, hydrogen or formate as electron donors, and oxygen as a terminal electron acceptor via cytochrome bd oxidase or cytochrome bb3 oxidase. Comparative metagenomic and genomic analyses revealed dramatic differences between submarine and terrestrial geothermal systems, including microbial functional potentials for carbon fixation and energy conversion. Furthermore, shallow-sea hydrothermal systems shared many of the major microbial genera that were first isolated from deep-sea and terrestrial geothermal systems, while deep-sea and terrestrial geothermal systems shared few genera. CONCLUSIONS The metabolic machinery of the active populations within Epsilonbacteraeota and Gammaproteobacteria at shallow-sea vents can mirror those living at deep-sea vents. With respect to specific taxa and metabolic potentials, the microbial realm in the shallow-sea hydrothermal system presented ecological linkage to both deep-sea and terrestrial geothermal systems. Video Abstract.
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Affiliation(s)
- Xiaofeng Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China.
| | - Mu Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Shujing Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Mingming Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Peiwen Zhan
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
| | - Wei Fan
- Ocean College, Zhejiang University, Zhoushan, China
| | - Chen-Tung Arthur Chen
- Institute of Marine Geology and Chemistry, National Sun Yat-Sen University, Taiwan, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen, China
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14
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Wang Q, Huang Q, Liu Y, Khan MA, Guo G, Lu W, Li X, Hu S, Wang J. Temporal variation of the coupling relationship between methanogens and biogeochemical process in soil-microbes-rice system. CHEMOSPHERE 2022; 303:135099. [PMID: 35618072 DOI: 10.1016/j.chemosphere.2022.135099] [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: 04/01/2022] [Revised: 05/11/2022] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
Microbial community were most resilient option for methane associated mitigation strategies. Biogas slurry provides plant nutrition and affects microbial community. However, little is known about the changes of the functional guilds (methanogen and methanotroph) in the geochemical context after addition biogas slurry. For this purpose, a pot experiment was conducted. Six treatment groups were included in this study, four with biogas slurry: water ratio (1:4, T02; 2:3, T04; 3:2, T06; 4:1, T08), one with a chemical fertilizer (F), and a control (CK). The effective tiller and biomass significantly increased by 1.9 times and 2.1 times in T02 relative to CK. The relative abundance of Bacteroidetes in the biogas slurry treatments was 31.5%, while that in CK was 11.4%. The dominant methanogens in CK, F and treatments were different at heading and mature stages. CK and F were hydrogenotrophs with relative abundance of 0.09% and 0.06%, and the treatment group was acetotrophs with mean value of 1.21% at heading stage. Compared with CK, the number of methanotrophs in the treatments at heading stage increased by 4.1 times, while that at mature increased by 10.3 times. The methanogenic community in the treatments may be shaped by the amount of biogas slurry applied rather than by biogeochemical processes at heading stage. Nevertheless, there may be existed synergistic interaction in the soil-microbes-rice system at mature stage. These findings may provide a better understanding of regulating soil respiration in agricultural land.
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Affiliation(s)
- Qingqing Wang
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province/Center for Eco-Environmental Restoration Engineering of Hainan Province/College of Ecology & Environment/State Key Laboratory of Marine Resource Utilization in South China Sea/Key Laboratory for Environmental Toxicology of Haikou, Haikou, Hainan University, Hainan, 570228, China
| | - Qing Huang
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province/Center for Eco-Environmental Restoration Engineering of Hainan Province/College of Ecology & Environment/State Key Laboratory of Marine Resource Utilization in South China Sea/Key Laboratory for Environmental Toxicology of Haikou, Haikou, Hainan University, Hainan, 570228, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
| | - Yin Liu
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province/Center for Eco-Environmental Restoration Engineering of Hainan Province/College of Ecology & Environment/State Key Laboratory of Marine Resource Utilization in South China Sea/Key Laboratory for Environmental Toxicology of Haikou, Haikou, Hainan University, Hainan, 570228, China
| | - Muhammad Amjad Khan
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province/Center for Eco-Environmental Restoration Engineering of Hainan Province/College of Ecology & Environment/State Key Laboratory of Marine Resource Utilization in South China Sea/Key Laboratory for Environmental Toxicology of Haikou, Haikou, Hainan University, Hainan, 570228, China
| | - Genmao Guo
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province/Center for Eco-Environmental Restoration Engineering of Hainan Province/College of Ecology & Environment/State Key Laboratory of Marine Resource Utilization in South China Sea/Key Laboratory for Environmental Toxicology of Haikou, Haikou, Hainan University, Hainan, 570228, China
| | - Wenkang Lu
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province/Center for Eco-Environmental Restoration Engineering of Hainan Province/College of Ecology & Environment/State Key Laboratory of Marine Resource Utilization in South China Sea/Key Laboratory for Environmental Toxicology of Haikou, Haikou, Hainan University, Hainan, 570228, China
| | - Xiaohui Li
- Hainan Inspection and Detection Center for Modern Agriculture, Haikou, Hainan, 570100, China
| | - Shan Hu
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province/Center for Eco-Environmental Restoration Engineering of Hainan Province/College of Ecology & Environment/State Key Laboratory of Marine Resource Utilization in South China Sea/Key Laboratory for Environmental Toxicology of Haikou, Haikou, Hainan University, Hainan, 570228, China
| | - Junfeng Wang
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province/Center for Eco-Environmental Restoration Engineering of Hainan Province/College of Ecology & Environment/State Key Laboratory of Marine Resource Utilization in South China Sea/Key Laboratory for Environmental Toxicology of Haikou, Haikou, Hainan University, Hainan, 570228, China
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15
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Ravin NV, Rossetti S, Beletsky AV, Kadnikov VV, Rudenko TS, Smolyakov DD, Moskvitina MI, Gureeva MV, Mardanov AV, Grabovich MY. Two New Species of Filamentous Sulfur Bacteria of the Genus Thiothrix, Thiothrix winogradskyi sp. nov. and ‘Candidatus Thiothrix sulfatifontis’ sp. nov. Microorganisms 2022; 10:microorganisms10071300. [PMID: 35889019 PMCID: PMC9319827 DOI: 10.3390/microorganisms10071300] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/22/2022] [Accepted: 06/24/2022] [Indexed: 01/27/2023] Open
Abstract
The metagenome of foulings from sulfidic spring “Serovodorodny” (Tatarstan, Russia), where members of the genus Thiothrix was observed, was sequenced. Representatives of the phyla Gammaproteobacteria, Cyanobacteria and Campilobacteriota dominated in the microbial community. The complete genome of Thiothrix sp. KT was assembled from the metagenome. It displayed 93.93–99.72% 16S rRNA gene sequence identity to other Thiothrix species. The average nucleotide identity (ANI) и digital DNA-DNA hybridization (dDDH) showed that the genome designated KT represents a new species within the genus Thiothrix, ‘Candidatus Thiothrix sulfatifontis’ sp. nov. KT. The taxonomic status has been determined of the strain Thiothrix sp. CT3, isolated about 30 years ago and not assigned to any of Thiothrix species due to high 16S rRNA gene sequence identity with related species (i.e., 98.8–99.4%). The complete genome sequence of strain CT3 was determined. The ANI between CT3 and other Thiothrix species was below 82%, and the dDDH values were less than 40%, indicating that strain CT3 belongs to a novel species, Thiothrix winogradskyi sp. nov. A genome analysis showed that both strains are chemo-organoheterotrophs, chemolithotrophs (in the presence of hydrogen sulfide and thiosulfate) and chemoautotrophs. For the first time, representatives of Thiothrix showed anaerobic growth in the presence of thiosulfate.
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Affiliation(s)
- Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (N.V.R.); (A.V.B.); (V.V.K.); (A.V.M.)
| | - Simona Rossetti
- Water Research Institute, IRSA-CNR, Monterotondo, 00185 Rome, Italy;
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (N.V.R.); (A.V.B.); (V.V.K.); (A.V.M.)
| | - Vitaly V. Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (N.V.R.); (A.V.B.); (V.V.K.); (A.V.M.)
| | - Tatyana S. Rudenko
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (T.S.R.); (D.D.S.); (M.I.M.); (M.V.G.)
| | - Dmitry D. Smolyakov
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (T.S.R.); (D.D.S.); (M.I.M.); (M.V.G.)
| | - Marina I. Moskvitina
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (T.S.R.); (D.D.S.); (M.I.M.); (M.V.G.)
| | - Maria V. Gureeva
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (T.S.R.); (D.D.S.); (M.I.M.); (M.V.G.)
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (N.V.R.); (A.V.B.); (V.V.K.); (A.V.M.)
| | - Margarita Yu. Grabovich
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (T.S.R.); (D.D.S.); (M.I.M.); (M.V.G.)
- Correspondence: ; Tel.: +7-473-2208877
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16
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Du R, Gao D, Wang Y, Liu L, Cheng J, Liu J, Zhang XH, Yu M. Heterotrophic Sulfur Oxidation of Halomonas titanicae SOB56 and Its Habitat Adaptation to the Hydrothermal Environment. Front Microbiol 2022; 13:888833. [PMID: 35774465 PMCID: PMC9237845 DOI: 10.3389/fmicb.2022.888833] [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: 03/03/2022] [Accepted: 05/24/2022] [Indexed: 11/23/2022] Open
Abstract
Halomonas bacteria are ubiquitous in global marine environments, however, their sulfur-oxidizing abilities and survival adaptations in hydrothermal environments are not well understood. In this study, we characterized the sulfur oxidation ability and metabolic mechanisms of Halomonas titanicae SOB56, which was isolated from the sediment of the Tangyin hydrothermal field in the Southern Okinawa Trough. Physiological characterizations showed that it is a heterotrophic sulfur-oxidizing bacterium that can oxidize thiosulfate to tetrathionate, with the Na2S2O3 degradation reaching 94.86%. Two potential thiosulfate dehydrogenase-related genes, tsdA and tsdB, were identified as encoding key catalytic enzymes, and their expression levels in strain SOB56 were significantly upregulated. Nine of fifteen examined Halomonas genomes possess TsdA- and TsdB-homologous proteins, whose amino acid sequences have two typical Cys-X2-Cys-His heme-binding regions. Moreover, the thiosulfate oxidation process in H. titanicae SOB56 might be regulated by quorum sensing, and autoinducer-2 synthesis protein LuxS was identified in its genome. Regarding the mechanisms underlying adaptation to hydrothermal environment, strain SOB56 was capable of forming biofilms and producing EPS. In addition, genes related to complete flagellum assembly system, various signal transduction histidine kinases, heavy metal transporters, anaerobic respiration, and variable osmotic stress regulation were also identified. Our results shed light on the potential functions of heterotrophic Halomonas bacteria in hydrothermal sulfur cycle and revealed possible adaptations for living at deep-sea hydrothermal fields by H. titanicae SOB56.
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Affiliation(s)
- Rui Du
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Di Gao
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Yiting Wang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Lijun Liu
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Jingguang Cheng
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Jiwen Liu
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Min Yu
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- *Correspondence: Min Yu,
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Fang J, Jiang W, Meng S, He W, Wang G, Guo E, Yan Y. Polychaete Bioturbation Alters the Taxonomic Structure, Co-occurrence Network, and Functional Groups of Bacterial Communities in the Intertidal Flat. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02036-2. [PMID: 35604433 DOI: 10.1007/s00248-022-02036-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Polychaetes are important benthic macrofauna that lives in sediments, usually in intertidal flats with high organic content and high sulfide. It has been suggested that polychaete bioturbation could perform environmental remediation. During the process, the microbial community plays important roles. Here, we used high-throughput sequencing technology to study the bioturbation effects on the bacterial community in the polychaete (Perinereis aibuhitensis) burrows at different tidal positions in intertidal flat. The results showed that the bacterial communities were dramatically influenced by the polychaete bioturbation. The ACE, Chao, and Shannon indices of the polychaete burrows increased in summer. Dominant phyla in the polychaete burrows were Proteobacteria, Campilobacterota, Desulfobacterota, Chloroflexi, and Bacteroidota, and the dominant bacterial families were Sulfurvaceae, Flavobacteriaceae, Rhodobacteraceae, Woeseiaceae, Desulfobulbaceae, and Sulfurimonadaceae. Results of linear discriminant analysis effect size (LEfSe) showed that groups that include organic matter degraders, such as Bacteroidota, Flavobacteriaceae, Rhodobacteraceae, Woeseiaceae, and groups that include sulfur oxidizers, such as Campilobacterota, Sulfurovaceae, Rhodobacteraceae, Desulfobulbaceae, and Sulfurimonadaceae, were significantly increased due to the polychaete bioturbation. The polychaete bioturbation reduced the complexity of the bacterial co-occurrence network while increased its modularity and homogeneity. The polychaete bioturbation also changed the functional groups, which significantly enhanced in functional groups of aerobic nitrite oxidation, nitration, dark thiosulfate oxidation, dark sulfur oxidation, and dark sulfite oxidation, while nitrogen respiration and nitrate respiration decreased. These results provide insight into the impact of bacterial communities under the intertidal polychaete bioturbation.
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Affiliation(s)
- Jinghui Fang
- Laboratory for Marine Fisheries Science and Food Production Processes, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, People's Republic of China
| | - Wenwen Jiang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China.
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangdong, 510275, People's Republic of China.
| | - Shan Meng
- Laboratory for Marine Fisheries Science and Food Production Processes, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, People's Republic of China
- China Ocean Press, Beijing, 100081, People's Republic of China
| | - Wei He
- Laboratory for Marine Fisheries Science and Food Production Processes, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, People's Republic of China
| | - Guodong Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China
- Homey Group Co. Ltd, Rongcheng, 264306, People's Republic of China
| | - Enmian Guo
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China
| | - Yisu Yan
- Qingdao Dagang Customs, Qingdao, 266011, People's Republic of China
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Lifestyles Shape the Cytochrome P450 Repertoire of the Bacterial Phylum Proteobacteria. Int J Mol Sci 2022; 23:ijms23105821. [PMID: 35628630 PMCID: PMC9148083 DOI: 10.3390/ijms23105821] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/27/2022] [Accepted: 05/07/2022] [Indexed: 02/06/2023] Open
Abstract
For the last six decades, cytochrome P450 monooxygenases (CYPs/P450s), heme thiolate proteins, have been under the spotlight due to their regio- and stereo-selective oxidation activities, which has led to the exploration of their applications in almost all known areas of biology. The availability of many genome sequences allows us to understand the evolution of P450s in different organisms, especially in the Bacteria domain. The phenomenon that “P450s play a key role in organisms’ adaptation vis a vis lifestyle of organisms impacts P450 content in their genome” was proposed based on studies on a handful of individual bacterial groups. To have conclusive evidence, one must analyze P450s and their role in secondary metabolism in species with diverse lifestyles but that belong to the same category. We selected species of the phylum Proteobacteria classes, Alpha, Beta, Gamma, Delta, and Epsilon, to address this research gap due to their diverse lifestyle and ancient nature. The study identified that the lifestyle of alpha-, beta-, gamma-, delta-, and epsilon-proteobacterial species profoundly affected P450 profiles in their genomes. The study determined that irrespective of the species associated with different proteobacterial classes, pathogenic species or species adapted to a simple lifestyle lost or had few P450s in their genomes. On the contrary, species with saprophytic or complex lifestyles had many P450s and secondary metabolite biosynthetic gene clusters. The study findings prove that the phenomenon mentioned above is factual, and there is no link between the number and diversity of P450s and the age of the bacteria.
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Lin G, Huang J, Luo K, Lin X, Su M, Lu J. Bacterial, archaeal, and fungal community structure and interrelationships of deep-sea shrimp intestine and the surrounding sediment. ENVIRONMENTAL RESEARCH 2022; 205:112461. [PMID: 34863691 DOI: 10.1016/j.envres.2021.112461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/09/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
Invertebrate shrimp are one of the dominant benthic macrofaunae in the deep-sea environment. The microbiota of shrimp intestine can contribute to the adaptation of their host. The impact of surrounding sediment on intestinal microbiota has been observed in cultured shrimp species, but needs to be further investigated in deep-sea shrimp. The characterization of bacterial, archaeal, and fungal community structure and their interrelationships is also limited. In this study, wild-type deep-sea shrimp and the surrounding sediment were sampled. Shrimp individuals incubated in a sediment-absent environment were also used in this study. Microbial community structure of the shrimp intestine and sediment was investigated through amplicon sequencing targeting bacterial 16S rRNA genes, archaeal 16S rRNA genes, and fungal ITS genes. The results demonstrate distinct differences in community structure between shrimp intestine and the surrounding sediment and between surface and deep (5 mbsf) sediment. The composition of the intestinal microbiota in shrimp living without sediment was different from that of wild-type shrimp, indicating that the presence or absence of sediment could influence the shrimp intestinal microbiota. Carbohydrate metabolism, energy metabolism (carbon fixation, methane metabolism, nitrogen metabolism, and sulfur metabolism), amino acid metabolism, and xenobiotic biodegradation were the most commonly predicted microbial functionalities and they interacted closely with one another. Overall, this study provided comprehensive insights into bacterial, archaeal, and fungal community structure of deep-sea shrimp intestine as well as potential ecological interactions with the surrounding sediment. This study could update our understanding of the microbiota characteristics in shrimp and sediment in deep-sea ecosystems.
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Affiliation(s)
- Genmei Lin
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519080, Guangdong, China
| | - Junrou Huang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Kunwen Luo
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Xianbiao Lin
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Ming Su
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519080, Guangdong, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, 510275, Guangdong, China; Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, 519000, Guangdong, China
| | - Jianguo Lu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519080, Guangdong, China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, 510275, Guangdong, China; Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, 519000, Guangdong, China.
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20
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A Comprehensive Profile of Antibiotic Resistance Genes in the Water Column of a Shallow-Sea Hydrothermal Vent Ecosystem. SUSTAINABILITY 2022. [DOI: 10.3390/su14031776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Antibiotic resistance genes (ARGs) became an emerging contaminant, and were found to accumulate in natural and man-made environments. A comprehensive understanding of the diversity and abundance of ARGs in pristine environments is critical for defining the baseline levels of environmental ARGs. However, there is limited information available on the ARG profiles of pristine environments, especially for shallow-sea hydrothermal vents ecosystems. Here, we combined 16S rRNA gene full-length amplicon sequencing and high-throughput quantitative PCR (HT-qPCR) to study the bacterial communities, and ARG abundance and diversity in the shallow-sea hydrothermal vent ecosystem of the Kueishantao Islet. The results of the 16S rRNA gene amplicon sequencing showed that several sulfur-cycling related bacterial genera, including Thiomicrorhabdus, Thioreductor, Sulfurovum, Sulfurimonas and Lebetimonas, dominated in the water column of the shallow-sea system. Temperature was the significant factor shaping the bacterial communities. The results of HT-qPCR analysis showed that the Kueishantao shallow-sea system harbored the lowest diversity (average 10 ARG subtypes) and abundance (average 1.0 × 10−3 copy per bacterial cell) of ARGs compared with other pristine (i.e., Tibet lake sediments, marine water and sediments) and anthropogenic-disturbed (i.e., drinking water reservoirs, urban ponds and wastewater treatment plants) environments. Procrustes analysis demonstrated a concordant pattern between the compositions of bacterial communities and ARGs in the shallow-sea system, while variation partition analysis revealed that the shared effects of physicochemical and bacterial communities explained >80% of the variation in the composition of ARGs. These results suggest that the vent bacterial communities and local environmental factors played an important role in shaping the distribution of the ARG profiles. Our study provides the first comprehensive overview of the background level of ARGs in a shallow-sea hydrothermal vent ecosystem.
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21
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Transformation, Fluxes and Impacts of Dissolved Metals from Shallow Water Hydrothermal Vents on Nearby Ecosystem Offshore of Kueishantao (NE Taiwan). SUSTAINABILITY 2022. [DOI: 10.3390/su14031754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Hydrothermal vents are one of the important sources of major or trace elements in the ocean. The elemental fluxes, however, may be dynamic due to coastal processes and hydrothermal plumes, especially in shallow-water hydrothermal vents. We collected water samples by using the trace-metal clean technique inside and outside two shallow-water hydrothermal vents (white vent: low temperature, high pH; and yellow vent: high temperature, low pH) off Kueishantao Islet, Taiwan, China via SCUBA divers. We analyzed these samples for their hydro-chemical parameters and dissolved elements (Fe, Mn, Mg, V, Cu, and Mo) thereafter. Our results show that dissolved metals’ concentrations were significantly different between the two vents, with higher Mn and Fe in the White Vent than in the Yellow Vent, likely due to the decreased affinity of the dissolved metals for particles in the white vent. We estimated the plume fluxes of dissolved metals from the hydrothermal mouth by multiplying in situ hydrothermal discharge flowrates with metals’ concentrations inside the vents, which were: 1.09~7.02 × 104 kg Mg, 0.10~1.23 kg Fe, 0.08~28 kg Mn, 33.4~306 g V, 2.89~77.7 g Cu, and 54.3~664 g Mo, annually. The results further indicate that such plumes probably have impacted nearby seawater due to coastal currents and particle desorption during transport. Furthermore, the concentrations of biogenic elements could be further modified in seawater, and potentially impact nearby ecosystems on a larger scale. Our study provides information with which to further understand metal redeployment in submarine shallow nearby ecosystems.
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22
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Ravin NV, Rudenko TS, Smolyakov DD, Beletsky AV, Rakitin AL, Markov ND, Fomenkov A, Sun L, Roberts RJ, Novikov AA, Karnachuk OV, Grabovich MY. Comparative Genome Analysis of the Genus Thiothrix Involving Three Novel Species, Thiothrix subterranea sp. nov. Ku-5, Thiothrix litoralis sp. nov. AS and " Candidatus Thiothrix anitrata" sp. nov. A52, Revealed the Conservation of the Pathways of Dissimilatory Sulfur Metabolism and Variations in the Genetic Inventory for Nitrogen Metabolism and Autotrophic Carbon Fixation. Front Microbiol 2021; 12:760289. [PMID: 34745068 PMCID: PMC8570282 DOI: 10.3389/fmicb.2021.760289] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/28/2021] [Indexed: 11/24/2022] Open
Abstract
Two strains of filamentous, colorless sulfur bacteria were isolated from bacterial fouling in the outflow of hydrogen sulfide-containing waters from a coal mine (Thiothrix sp. Ku-5) and on the seashore of the White Sea (Thiothrix sp. AS). Metagenome-assembled genome (MAG) A52 was obtained from a sulfidic spring in the Volgograd region, Russia. Phylogenetic analysis based on the 16S rRNA gene sequences showed that all genomes represented the genus Thiothrix. Based on their average nucleotide identity and digital DNA-DNA hybridization data these new isolates and the MAG represent three species within the genus Thiothrix with the proposed names Thiothrix subterranea sp. nov. Ku-5T, Thiothrix litoralis sp. nov. AST, and “Candidatus Thiothrix anitrata” sp. nov. A52. The complete genome sequences of Thiothrix fructosivorans QT and Thiothrix unzii A1T were determined. Complete genomes of seven Thiothrix isolates, as well as two MAGs, were used for pangenome analysis. The Thiothrix core genome consisted of 1,355 genes, including ones for the glycolysis, the tricarboxylic acid cycle, the aerobic respiratory chain, and the Calvin cycle of carbon fixation. Genes for dissimilatory oxidation of reduced sulfur compounds, namely the branched SOX system (SoxAXBYZ), direct (soeABC) and indirect (aprAB, sat) pathways of sulfite oxidation, sulfur oxidation complex Dsr (dsrABEFHCEMKLJONR), sulfide oxidation systems SQR (sqrA, sqrF), and FCSD (fccAB) were found in the core genome. Genomes differ in the set of genes for dissimilatory reduction of nitrogen compounds, nitrogen fixation, and the presence of various types of RuBisCO.
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Affiliation(s)
- Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Tatyana S Rudenko
- Department of Biochemistry and Cell Physiology, Voronezh State University, Voronezh, Russia
| | - Dmitry D Smolyakov
- Department of Biochemistry and Cell Physiology, Voronezh State University, Voronezh, Russia
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Andrey L Rakitin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Nikita D Markov
- Department of Biochemistry and Cell Physiology, Voronezh State University, Voronezh, Russia
| | | | - Luo Sun
- New England Biolabs, Ipswich, MA, United States
| | | | - Andrey A Novikov
- Department of Physical and Colloid Chemistry, Gubkin Russian State University of Oil and Gas, Moscow, Russia
| | - Olga V Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Margarita Y Grabovich
- Department of Biochemistry and Cell Physiology, Voronezh State University, Voronezh, Russia
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23
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Phylogenetic and Phenogenetic Diversity of Synechococcus along a Yellow Sea Section Reveal Its Environmental Dependent Distribution and Co-Occurrence Microbial Pattern. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2021. [DOI: 10.3390/jmse9091018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Synechococcus is a dominant genus of the coastal phytoplankton with an effective contribution to primary productivity. Here, the phylogenetic and phenogenetic composition of Synechococcus in the coastal Yellow Sea was addressed by sequencing marker gene methods. Meanwhile, its co-occurrence pattern with bacterial and eukaryotic microbes was further investigated based on the construction of networks. The result revealed that Synechococcus abundance ranged from 9.8 × 102 cells mL−1 to 1.6 × 105 cells mL−1, which was significantly correlated to sampling depth and nutrient contents of nitrite, ammonia, and dissolved silicon. A total of eight Synechococcus phylogenetic lineages were detected, of which clade III was dominant in most of the samples. Meanwhile, clade I increased along the water column and even reached a maximum value of 76.13% at 20 m of station B. Phenogenetically, Synechococcus PT3 was always the predominant pigment type across the whole study zone. Only salinity was significantly correlated to the phenogenetic constitution. The networks revealed that Synechococcus co-occurred with 159 prokaryotes, as well as 102 eukaryotes including such possible grazers as Gymnodinium clades and Alveolata. Potential function prediction further showed that microbes co-occurring with Synechococcus were associated with diverse element cycles, but the exact mechanism needed further experimentation to verify. This research promotes exploring regularity in the genomic composition and niche position of Synechococcus in the coastal ecosystem and is significant to further discuss its potential participation in materials circulation and bottom-up effects in microbial food webs.
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24
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Yadav N, Govindwar SP, Rane N, Ahn HJ, Xiong JQ, Jang M, Kim SH, Jeon BH. Insights on the role of periphytic biofilm in synergism with Iris pseudacorus for removing mixture of pharmaceutical contaminants from wastewater. JOURNAL OF HAZARDOUS MATERIALS 2021; 418:126349. [PMID: 34118536 DOI: 10.1016/j.jhazmat.2021.126349] [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: 03/08/2021] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 06/12/2023]
Abstract
The potential of Iris pseudacorus and the associated periphytic biofilm for biodegradation of two common pharmaceutical contaminants (PCs) in urban wastewater was assessed individually and in consortium. An enhanced removal for sulfamethoxazole (SMX) was achieved in consortium (59%) compared to individual sets of I. pseudacorus (50%) and periphytic biofilm (7%) at concentration of 5 mg L-1. Conversely, individual sets of periphytic biofilm (77%) outperformed removal of doxylamine succinate (DOX) compared to individual sets of I. pseudacorus (59%) and consortium (67%) at concentration of 1 mg L-1. Enhanced relative abundance of microflora containing microalgae (Sellaphora, Achnanthidium), rhizobacteria (Acidibacter, Azoarcus, Thioalkalivibrio), and fungi (Serendipita) in periphytic biofilm was observed after treatment. SMX treatment for five days elevated cytochrome P450 enzymes' expressions, including aniline hydroxylase (48%) and aminopyrine N-demethylase (54%) in the periphytic biofilm. Nevertheless, I. pseudacorus showed 175% elevation of aniline hydroxylase along with other biotransformation enzymes, such as peroxidase (629%), glutathione S-transferase (514%), and dichloroindophenol reductase (840%). A floating bed phytoreactor planted with I. pseudacorus and the periphytic biofilm consortium removed 67% SMX and 72% DOX in secondary wastewater effluent. Thus, the implementation of this strategy in constructed wetland-based treatment could be beneficial for managing effluents containing PCs.
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Affiliation(s)
- Nikita Yadav
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Sanjay P Govindwar
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Niraj Rane
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Hyun-Jo Ahn
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Jiu-Qiang Xiong
- College of Marine Life Sciences, Ocean University of China, 5 Rushan, Qingdao, Shandong, China
| | - Min Jang
- Department of Environmental Engineering, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Sang Hyoun Kim
- School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea.
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25
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Soil Redox Controls CO 2, CH 4 and N 2O Efflux from White-Rot Fungi in Temperate Forest Ecosystems. J Fungi (Basel) 2021; 7:jof7080621. [PMID: 34436159 PMCID: PMC8398011 DOI: 10.3390/jof7080621] [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: 06/15/2021] [Revised: 07/14/2021] [Accepted: 07/26/2021] [Indexed: 11/17/2022] Open
Abstract
Microaerophilic white-rot fungi (WRF) are impacted by oxygen depletion because of fluctuating redox occurrence in southern temperate forest soils of Chile (1500-5000 mm year-1). How these conditions influence WRF survival has been scarcely examined. We explored the contributions of WRF to greenhouse gas (GHG) emissions of N2O and CH4 and soil organic C oxidation (CO2) in five sterilized and inoculated forest soils derived from various parent materials and climates. The soil was incubated for 20 days following (i) oxic, (ii) anoxic, and (iii) fluctuating redox conditions. Fungi contributed to 45% of the total GHG under redox fluctuating conditions, including the contribution of bacteria, while the opposite (26%) was valid for oxic treatment. On average, the highest gas emission (62%) was N2O for WRF under redox treatment, followed by anoxic (22%) and oxic (16%) treatments, while CO2 and CH4 emissions followed oxic > redox > anoxic. These data suggest that indigenous microbial WRF communities are well adapted to fluctuating redox milieu with a significant release of GHG emissions in humid temperate forests of the southern cone.
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26
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Zeng X, Alain K, Shao Z. Microorganisms from deep-sea hydrothermal vents. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:204-230. [PMID: 37073341 PMCID: PMC10077256 DOI: 10.1007/s42995-020-00086-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/17/2020] [Indexed: 05/03/2023]
Abstract
With a rich variety of chemical energy sources and steep physical and chemical gradients, hydrothermal vent systems offer a range of habitats to support microbial life. Cultivation-dependent and independent studies have led to an emerging view that diverse microorganisms in deep-sea hydrothermal vents live their chemolithoautotrophic, heterotrophic, or mixotrophic life with versatile metabolic strategies. Biogeochemical processes are mediated by microorganisms, and notably, processes involving or coupling the carbon, sulfur, hydrogen, nitrogen, and metal cycles in these unique ecosystems. Here, we review the taxonomic and physiological diversity of microbial prokaryotic life from cosmopolitan to endemic taxa and emphasize their significant roles in the biogeochemical processes in deep-sea hydrothermal vents. According to the physiology of the targeted taxa and their needs inferred from meta-omics data, the media for selective cultivation can be designed with a wide range of physicochemical conditions such as temperature, pH, hydrostatic pressure, electron donors and acceptors, carbon sources, nitrogen sources, and growth factors. The application of novel cultivation techniques with real-time monitoring of microbial diversity and metabolic substrates and products are also recommended. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-020-00086-4.
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Affiliation(s)
- Xiang Zeng
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005 China
- LIA/IRP 1211 MicrobSea, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Plouzané, France
| | - Karine Alain
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E UMR6197, Univ Brest, CNRS, IFREMER, F-29280 Plouzané, France
- LIA/IRP 1211 MicrobSea, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Plouzané, France
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005 China
- LIA/IRP 1211 MicrobSea, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Plouzané, France
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Ma X, Li X, Li J, Ren J, Chi L, Cheng X. Iron-carbon could enhance nitrogen removal in Sesuvium portulacastrum constructed wetlands for treating mariculture effluents. BIORESOURCE TECHNOLOGY 2021; 325:124602. [PMID: 33486413 DOI: 10.1016/j.biortech.2020.124602] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/16/2020] [Accepted: 12/19/2020] [Indexed: 06/12/2023]
Abstract
This study investigated an Iron-carbon (Fe-C) micro-electrolysis method to enhance nitrogen removal of Sesuvium portulacastrum constructed wetlands (CWs) when treating mariculture effluents. The main objective was to investigate the effects of Fe-C on nitrogen purification performance and microbial characteristics of Sesuvium portulacastrum CWs. Results showed that the presence of Fe-C and Sesuvium portulacastrum could improve nitrogen removal efficiency by 20-30% and 15-30%, respectively. CWs with 33% v/v Fe-C addition performed well on nitrogen removal: TAN, 41.49 ± 13.64%; NO2--N, 13.32%; NO3--N, 60.02 ± 6.17%; TIN, 63.40 ± 12.11%. Microbial analysis revealed that Fe-C altered the microbial communities, and improved the abundance of denitrification related genera. Based on microbial enzyme activities and genes abundance, the anammox and denitrification processes were promoted by Fe-C in CWs. These findings indicate that Sesuvium portulacastrum CWs with 33% v/v Fe-C represents an effective nitrogen removal for mariculture wastewater with insufficient carbon source.
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Affiliation(s)
- Xiaona Ma
- The Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Xian Li
- The Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Jun Li
- The Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China.
| | - Jilong Ren
- School of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China
| | - Liang Chi
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266071, China
| | - Xuewen Cheng
- School of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China
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28
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In silico determination of nitrogen metabolism in microbes from extreme conditions using metagenomics. Arch Microbiol 2021; 203:2521-2540. [PMID: 33677634 DOI: 10.1007/s00203-021-02227-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/21/2020] [Accepted: 02/11/2021] [Indexed: 10/22/2022]
Abstract
The acid ponds of the Danakil Depression in northern Ethiopia are polyextreme environments that exceed the normal physicochemical limits of pH, salinity, ion content, and temperature. We tested for the occurrence of DNA-based life in this environment using Metagenomic Shotgun DNA sequencing approaches. The obtained sequences were examined by the bioinformatic tools MetaSpades, DIAMOND and MEGAN 6-CE, and we were able to bin more than 90% of the metagenomics contigs of Dallol and Black Water to the Bacteria domain, and to the Proteobacteria phylum. Predictions of gene function based on SEED disclosed the presence of different nutrient cycles in the acid ponds. For this study, we focused on partial or completely sequenced genes involved in nitrogen metabolism. The KEGG nitrogen metabolism pathway mapping results for both acid ponds showed that all the predicted genes are involved directly or indirectly in the assimilation of ammonia and no dissimilation or nitrification process was identified. Furthermore, the deduced nitrogen fixation in the two acid ponds based on SEED classification indicated the presence of different sets of nitrogen fixing (nif) genes for biosynthesis and maturation of nitrogenase. Based on the in silico analysis, the predicted proteins involved in nitrogen fixation, especially the cysteine desulfurase and [4Fe-4S] ferredoxin, from both acid ponds are unique with less than 80% sequence similarity to the next closest protein sequence. Considering the extremity of the environmental conditions of the two acid ponds in the Danakil depression, this metagenomics dataset can add to the study of unique gene functions in nitrogen metabolism that enable thriving biocommunities in hypersaline and highly acidic conditions.
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29
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Hou L, Zhang L, Li F, Huang S, Yang J, Ma C, Zhang D, Yu CP, Hu A. Urban ponds as hotspots of antibiotic resistome in the urban environment. JOURNAL OF HAZARDOUS MATERIALS 2021; 403:124008. [PMID: 33265037 DOI: 10.1016/j.jhazmat.2020.124008] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/04/2020] [Accepted: 09/14/2020] [Indexed: 06/12/2023]
Abstract
The occurrence, dissemination and assembly processes of antibiotic resistance genes (ARGs) in urban water ecosystems are far from being understood. Here, we examined the diversity and abundance of ARGs in urban water ecosystems including landscape ponds, drinking water reservoirs, influents (IFs) and effluents (EFs) of wastewater treatment plants of a coastal city, China through high-throughput quantitative PCR. A total of 237 ARGs were identified, where multidrug, aminoglycoside and beta-lactamase resistance genes were the most abundant. Urban ponds had a comparatively high diversity and large numbers of shared ARGs with IFs and EFs. The average absolute abundance of ARGs (1.38 × 107 copies/mL) and mobile genetic elements (MGEs) (4.19 × 106 copies/mL) in ponds were only one order of magnitude lower than those of IFs, but higher than those of EFs and reservoirs. Stochastic processes dominated the ARG community assembly in IFs and ponds due to the random horizontal gene transfer caused by MGEs. These results imply that urban ponds are hotspots of ARGs. We further identified 25, 3, and 11 indicator ARGs for tracing the ARG contamination from IFs, EFs and ponds, respectively. Our study represents the first to highlight the role of urban ponds in the dissemination of ARGs.
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Affiliation(s)
- Liyuan Hou
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Department of Chemistry, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| | - Lanping Zhang
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Furun Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sijun Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Jun Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Cong Ma
- Xiamen Municipal Environment Technology Co., Ltd., Xiamen 361001, China
| | - Duanxin Zhang
- General Water of Xiamen Sewage Co., Ltd., Xiamen 361001, China
| | - Chang-Ping Yu
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Graduate Institute of Environmental Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Anyi Hu
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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Sabu EA, Gonsalves MJ, Sreepada RA, Shivaramu MS, Ramaiah N. Evaluation of the Physiological Bacterial Groups in a Tropical Biosecured, Zero-Exchange System Growing Whiteleg Shrimp, Litopenaeus vannamei. MICROBIAL ECOLOGY 2021; 81:335-346. [PMID: 32880700 DOI: 10.1007/s00248-020-01575-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 08/10/2020] [Indexed: 06/11/2023]
Abstract
To elucidate the individual and multiple roles of physiological bacterial groups involved in biogeochemical cycles of carbon, nitrogen, phosphorus and sulfur, the changes in the abundance of aerobic bacteria (heterotrophs, methane oxidizers, ammonia oxidizers, sulfur oxidizers, phosphate solubilizers, phosphate accumulators) and anaerobic bacteria (total anaerobes, nitrate reducers, denitrifiers and sulfate reducers) were investigated in a biosecured, zero-exchange system stocked with whiteleg shrimp, Litopenaeus vannamei for one production cycle. Key water quality parameters during the 96-day production cycle fell within the normal range for L. vannamei culture. Results of Spearman's correlation matrix revealed that different sets of variables correlated at varying levels of significance of the interrelationships between bacterial abundances and water quality parameters. The three nitrogenous species (ammonia, nitrite and nitrate) strongly influenced the physiological bacterial groups' abundance. The strong relationship of bacterial groups with phytoplankton biomass and abundance clearly showed the trophic interconnections in nutrient exchange/recycling. Canonical correspondence analysis performed to assess the total variation revealed that the three dissolved nitrogen species followed by salinity, temperature, phytoplankton biomass and pH collectively accounted for as much as 82% of the total variation. In conclusion, the results of the study revealed that the major drivers that interweaved biogeochemical cycles are the three dissolved nitrogen species, which microbially mediated various aerobic-anaerobic assimilation/dissimilation processes in the pond ecosystem. Considering the pond microbial ecology becoming an important management tool where applied research could improve the economic and environmental sustainability of the aquaculture industry, the findings of the present study are practically relevant.
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Affiliation(s)
- Elaine A Sabu
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403 004, India
- School of Earth, Ocean and Atmospheric Sciences, Goa University, Taleigao Plateau, Goa, 403 206, India
| | - Maria Judith Gonsalves
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403 004, India.
| | - R A Sreepada
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403 004, India
| | - Mamatha S Shivaramu
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403 004, India
- Department of Food Protectants & Infestation Control, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka, 570 020, India
| | - N Ramaiah
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403 004, India
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DeCastro ME, Doane MP, Dinsdale EA, Rodríguez-Belmonte E, González-Siso MI. Exploring the taxonomical and functional profile of As Burgas hot spring focusing on thermostable β-galactosidases. Sci Rep 2021; 11:101. [PMID: 33420292 PMCID: PMC7794327 DOI: 10.1038/s41598-020-80489-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/17/2020] [Indexed: 01/29/2023] Open
Abstract
In the present study we investigate the microbial community inhabiting As Burgas geothermal spring, located in Ourense (Galicia, Spain). The approximately 23 Gbp of Illumina sequences generated for each replicate revealed a complex microbial community dominated by Bacteria in which Proteobacteria and Aquificae were the two prevalent phyla. An association between the two most prevalent genera, Thermus and Hydrogenobacter, was suggested by the relationship of their metabolism. The high relative abundance of sequences involved in the Calvin-Benson cycle and the reductive TCA cycle unveils the dominance of an autotrophic population. Important pathways from the nitrogen and sulfur cycle are potentially taking place in As Burgas hot spring. In the assembled reads, two complete ORFs matching GH2 beta-galactosidases were found. To assess their functional characterization, the two ORFs were cloned and overexpressed in E. coli. The pTsbg enzyme had activity towards o-Nitrophenyl-β-D-galactopyranoside (ONPG) and p-Nitrophenyl-β-D-fucopyranoside, with high thermal stability and showing maximal activity at 85 °C and pH 6, nevertheless the enzyme failed to hydrolyze lactose. The other enzyme, Tsbg, was unable to hydrolyze even ONPG or lactose. This finding highlights the challenge of finding novel active enzymes based only on their sequence.
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Affiliation(s)
- María-Eugenia DeCastro
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Facultade de Ciencias, Universidade da Coruña, A Coruña, Spain
| | - Michael P Doane
- Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
- Syndey Institute of Marine Science, 19 Chowder Bay Rd, Mosman, NSW, 2088, Australia
| | - Elizabeth Ann Dinsdale
- Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
- College of Science and Engineering, Flinders University, Sturt Rd, Bedford Park, SA, 5042, Australia
| | - Esther Rodríguez-Belmonte
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Facultade de Ciencias, Universidade da Coruña, A Coruña, Spain
| | - María-Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Facultade de Ciencias, Universidade da Coruña, A Coruña, Spain.
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Lin YS, Lin HT, Wang BS, Huang WJ, Lin LH, Tsai AY. Intense but variable autotrophic activity in a rapidly flushed shallow-water hydrothermal plume (Kueishantao Islet, Taiwan). GEOBIOLOGY 2021; 19:87-101. [PMID: 33043601 DOI: 10.1111/gbi.12418] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 09/11/2020] [Accepted: 09/20/2020] [Indexed: 06/11/2023]
Abstract
Shallow-water hydrothermal plumes concomitantly host both photosynthetic and chemoautotrophic organisms in a single biotope. Yet, rate measurements to quantify the contributions of different autotrophic activity types are scarce. Herein, we measured the light and dark dissolved inorganic carbon (DIC) uptake rates in the plume water of the Kueishantao hydrothermal field using the 13 C-labeling approach. Seventy percent of the plume-water samples had chemoautotrophy as the dominant mode of carbon fixation, with the dark DIC uptake rates (up to 18.6 mg C/m3 /h) within the range of the primary production in productive inner-shelf waters. When considered alongside the geochemical and microbiological observations, the rate data reveal the distribution of different trophic activities in the hydrothermal plume. The autotrophic activity at the initial phase of plume dispersal is low. This is explained by the short response time the chemoautotrophs have to the stimulation from vent-fluid discharge, and the harmful effects of hydrothermal substances on phytoplankton. As plume dispersal and mixing continue, chemoautotrophic activities begin to rise and peak in waters that have low-to-moderate Si(OH)4 content. Toward the plume margin, chemoautotrophy declines to background levels, whereas photosynthesis by phytoplankton regains importance. Our results also provide preliminary indication to the loci of enhanced heterotrophy in the plume. Results of artificial mixing experiments suggest that previously formed plume water is the primary source of microbial inoculum for new plume water. This self-inoculation mechanism, in combination with the intense DIC uptake, helps to sustain a distinct planktonic autotrophic community in this rapidly flushed hydrothermal plume.
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Affiliation(s)
- Yu-Shih Lin
- Department of Oceanography, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Huei-Ting Lin
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Bo-Shian Wang
- Taiwan Ocean Research Institute, National Applied Research Laboratories, Kaohsiung, Taiwan
- National Academy of Marine Research, Kaohsiung, Taiwan
| | - Wei-Jen Huang
- Department of Oceanography, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Li-Hung Lin
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
- Research Center for Future Earth, National Taiwan University, Taipei, Taiwan
| | - An-Yi Tsai
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
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Ruan Y, Wang T, Guo S, Ling N, Shen Q. Plant Grafting Shapes Complexity and Co-occurrence of Rhizobacterial Assemblages. MICROBIAL ECOLOGY 2020; 80:643-655. [PMID: 32514604 DOI: 10.1007/s00248-020-01532-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 05/25/2020] [Indexed: 06/11/2023]
Abstract
Grafting is a basic technique which is widely used to increase yield and enhance biotic and abiotic stress tolerance in plant production. The diversity and interactions of rhizobacterial assemblages shaped by grafting are important for the growth of their hosts but remain poorly understood. To test the hypothesis that plant grafting shapes complexity and co-occurrence of rhizobacterial assemblage, four types of plants, including ungrafted bottle gourd (B), ungrafted watermelon (W), grafted watermelon with bottle gourd rootstock (W/B), and grafted bottle gourd with watermelon rootstock (B/W), were cultivated in two soil types in a greenhouse, and the rhizosphere bacterial communities were analyzed by 16S rRNA gene high-throughput sequencing. Both the soil type and grafting significantly influenced the bacterial community composition. Grafting increased bacterial within-sample diversity in both soils. Core enriched operational taxonomic units (OTUs) in the W/B rhizosphere compared with the other three treatments (B, W, and B/W) were mainly affiliated with Alphaproteobacteria, Deltaproteobacteria, and Bacteroidetes, which are likely related to methanol oxidation, methylotrophy, fermentation, and ureolysis. Co-occurrence network analysis proved that grafting increased network complexity, including the number of nodes, edges, and modules. Moreover, grafting strengthened the structural robustness of the network in the rhizosphere, while ungrafted watermelon had the lowest network robustness. Homogeneous selection played a predominant role in bacterial community assembly, and the contribution of dispersal limitation was increased in grafted watermelon with bottle gourd rootstock. Grafting increased the diversity and transformed the network topology of the bacterial community, which indicated that grafting could improve species coexistence in the watermelon rhizosphere.
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Affiliation(s)
- Yang Ruan
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tingting Wang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shiwei Guo
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ning Ling
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
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Chang M, Wang Y, Zhong R, Zhang K, Pan Y, Lyu L, Zhu T. Performance of HABR + MSABP system for the treatment of dairy wastewater and analyses of microbial community structure and low excess sludge production. BIORESOURCE TECHNOLOGY 2020; 311:123576. [PMID: 32470867 DOI: 10.1016/j.biortech.2020.123576] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 05/12/2023]
Abstract
The potential of the system, a hybrid anaerobic baffled reactor (HABR) coupled with a multi-stage active biological process (MSABP) reactor, for simulated dairy wastewater at various temperature, hydraulic retention time (HRT), and pH was investigated. Percentage removals of chemical oxygen demand (COD) and NH4+ were optimized using response surface methodology. Under optimized conditions (temperature, 33 °C; HRT, 24 h; pH, 7.35), the removal efficiencies of COD and NH4+ were 99.89% and 97.83%, respectively. Miseq sequencing analysis exhibited that the anaerobic segment of the system was dominated by fermentation and acetogenic bacteria, and in the aerobic segment, microorganisms involved in the nitrogen cycle were significantly enriched. Meanwhile, it could be found that the excess sludge production of the process was much lower than that of other bio-processes. The average excess sludge production rate was 0.025-0.05 g SS/g COD removed under different organic loadings.
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Affiliation(s)
- Mingdong Chang
- School of Mechanical Engineering and Automation, Northeastern University, 3-11, Wenhua Road, Heping District, Shenyang 110819, China
| | - Youzhao Wang
- School of Mechanical Engineering and Automation, Northeastern University, 3-11, Wenhua Road, Heping District, Shenyang 110819, China
| | - Rui Zhong
- School of Mechanical Engineering and Automation, Northeastern University, 3-11, Wenhua Road, Heping District, Shenyang 110819, China
| | - Kuo Zhang
- School of Mechanical Engineering and Automation, Northeastern University, 3-11, Wenhua Road, Heping District, Shenyang 110819, China
| | - Yuan Pan
- School of Mechanical Engineering and Automation, Northeastern University, 3-11, Wenhua Road, Heping District, Shenyang 110819, China
| | - Liting Lyu
- School of Mechanical Engineering and Automation, Northeastern University, 3-11, Wenhua Road, Heping District, Shenyang 110819, China
| | - Tong Zhu
- School of Mechanical Engineering and Automation, Northeastern University, 3-11, Wenhua Road, Heping District, Shenyang 110819, China.
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Сhaіka OM, Peretyatko TB. Effect of abiotic factors on sulfidogenic activity of bacteria Desulfuromonas sp. REGULATORY MECHANISMS IN BIOSYSTEMS 2020. [DOI: 10.15421/022025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Sulfur-reducing bacteria are promising agents for the development of new methods of wastewater treatment with the removal of ions of heavy metals and organic compounds. Study of the effect of various environmental factors on the growth and sulfidogenic activity of sulfur-reducing bacteria allows one to investigate the adaptability of these microorganisms to stress factors. The paper deals with the effect of рН, different concentrations of elemental sulfur, hydrogen sulfide and presence of various electron acceptors on the growth and sulfidogenic activity of bacteria Desulfuromonas sp. YSDS-3. The calculation of C/S ratio for sulfur-reducing bacteria Desulfuromonas sp. YSDS-3 was made, with the comparison with similar parameters of sulfate-reducing bacteria. In the medium with elemental sulfur, concentration of hydrogen sulfide increased with the concentration of elemental sulfur. Bacteria Desulfuromonas sp. YSDS-3 accumulated their biomass in the most effective way at the concentration of elemental sulfur of 10–100 mM. In the medium with polysulfide form of sulfur at the neutral pH, bacteria produced hydrogen sulfide and accumulated biomass the best. Hydrogen sulfide at the concentration of 3 mM did not inhibit the bacterial growth, but further increase in the hydrogen sulfide concentration inhibited the growth of bacteria. The bacteria did not grow at the hydrogen sulfide concentration of 25 mM and above. As the concentration of elemental sulfur and cell density increases, sulfidogenic activity of the bacteria grows. Presence of two electron acceptors (S and K2Cr2O7, S and MnO2, S and Fe (III)) did not affect the accumulation of biomass of the bacteria Desulfuromonas sp. YSDS-3. However, under such conditions the bacteria accumulated 1.5–2.5 times less hydrogen sulfide than in the test medium. After 12–24 h of cultivation, different concentrations of elemental sulfur had a significant effect on the sulfidogenic activity. However, during 3–16 days of cultivation, the percentage of effect of elemental sulfur concentration decreased to 31%, while the percentage of effect of cell density increased threefold. Presence in the medium of the electron acceptors (Cr (VI), MnO2, Fe (III)) alternative to elemental sulfur led to a significant decrease in the content of hydrogen sulfide produced by sulfur-reducing bacteria.
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Effects of Hydraulic Retention Time and Influent Nitrate-N Concentration on Nitrogen Removal and the Microbial Community of an Aerobic Denitrification Reactor Treating Recirculating Marine Aquaculture System Effluent. WATER 2020. [DOI: 10.3390/w12030650] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The effects of hydraulic retention time (HRT) and influent nitrate-N concentration on nitrogen removal and the microbial community composition of an aerobic denitrification reactor treating recirculating marine aquaculture system effluent were evaluated. Results showed that over 98% of nitrogen was removed and ammonia-N and nitrite-N levels were below 1 mg/L when influent nitrate-N was below 150 mg/L and HRT over 5 h. The maximum nitrogen removal efficiency and nitrogen removal rate were observed at HRT of 6 or 7 h when influent nitrate-N was 150 mg/L. High-throughput DNA sequencing analysis revealed that the microbial phyla Proteobacteria and Bacteroidetes were predominant in the reactor, with an average relative total abundance above 70%. The relative abundance of denitrifying bacteria of genera Halomonas and Denitratisoma within the reactor decreased with increasing influent nitrate-N concentrations. Our results show the presence of an aerobically denitrifying microbial consortium with both expected and unexpected members, many of them relatively new to science. Our findings provide insights into the biological workings and inform the design and operation of denitrifying reactors for marine aquaculture systems.
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Liu D, Zhang J, Lü C, Xia Y, Liu H, Jiao N, Xun L, Liu J. Synechococcus sp. Strain PCC7002 Uses Sulfide:Quinone Oxidoreductase To Detoxify Exogenous Sulfide and To Convert Endogenous Sulfide to Cellular Sulfane Sulfur. mBio 2020; 11:e03420-19. [PMID: 32098824 PMCID: PMC7042703 DOI: 10.1128/mbio.03420-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 01/17/2020] [Indexed: 12/19/2022] Open
Abstract
Eutrophication and deoxygenation possibly occur in coastal waters due to excessive nutrients from agricultural and aquacultural activities, leading to sulfide accumulation. Cyanobacteria, as photosynthetic prokaryotes, play significant roles in carbon fixation in the ocean. Although some cyanobacteria can use sulfide as the electron donor for photosynthesis under anaerobic conditions, little is known on how they interact with sulfide under aerobic conditions. In this study, we report that Synechococcus sp. strain PCC7002 (PCC7002), harboring an sqr gene encoding sulfide:quinone oxidoreductase (SQR), oxidized self-produced sulfide to S0, present as persulfide and polysulfide in the cell. The Δsqr mutant contained less cellular S0 and had increased expression of key genes involved in photosynthesis, but it was less competitive than the wild type in cocultures. Further, PCC7002 with SQR and persulfide dioxygenase (PDO) oxidized exogenous sulfide to tolerate high sulfide levels. Thus, SQR offers some benefits to cyanobacteria even under aerobic conditions, explaining the common presence of SQR in cyanobacteria.IMPORTANCE Cyanobacteria are a major force for primary production via oxygenic photosynthesis in the ocean. A marine cyanobacterium, PCC7002, is actively involved in sulfide metabolism. It uses SQR to detoxify exogenous sulfide, enabling it to survive better than its Δsqr mutant in sulfide-rich environments. PCC7002 also uses SQR to oxidize endogenously generated sulfide to S0, which is required for the proper expression of key genes involved in photosynthesis. Thus, SQR has at least two physiological functions in PCC7002. The observation provides a new perspective for the interplays of C and S cycles.
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Affiliation(s)
- Daixi Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China
| | - Jiajie Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China
| | - Chuanjuan Lü
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yongzhen Xia
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Huaiwei Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Nianzhi Jiao
- Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China
- Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Luying Xun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- School of Molecular Biosciences, Washington State University, Pullman, Washington, USA
| | - Jihua Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China
- Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
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Procópio L. The era of 'omics' technologies in the study of microbiologically influenced corrosion. Biotechnol Lett 2020; 42:341-356. [PMID: 31897850 DOI: 10.1007/s10529-019-02789-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/30/2019] [Indexed: 12/28/2022]
Abstract
Efforts to elucidate the relationships between microorganisms and metal corrosion were mainly directed to understanding the formation of biofilm structures grown on corroded surfaces. The emergence of high throughput DNA sequencing techniques has helped in the description of microbial species involved directly and indirectly in the corrosion processes of alloys. Coupled with sequencing from environmental samples, other methodologies such as metatranscriptome, metaproteomics and metabolomics have allowed a new horizon to be opened on the understanding of the role of corrosive microbial biofilm. Several groups of bacteria and archaea were identified, showing the dominance of Proteobacteria in several samples analyzed and members of groups that previously received less attention, such as Firmicutes and Bacteroidetes. Our research also shows that metagenomic studies describe the presence of various Archaea domain thermophilic and methanogenic groups associated with metal corrosion. Thus, opening the prospect of describing new microbial groups as possible participants in this current global concern.
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Affiliation(s)
- Luciano Procópio
- Industrial Microbiology and Bioremediation Department, Federal University of Rio de Janeiro (UFRJ), Caxias - Rio de Janeiro, Brazil.
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D'Angeli IM, Ghezzi D, Leuko S, Firrincieli A, Parise M, Fiorucci A, Vigna B, Addesso R, Baldantoni D, Carbone C, Miller AZ, Jurado V, Saiz-Jimenez C, De Waele J, Cappelletti M. Geomicrobiology of a seawater-influenced active sulfuric acid cave. PLoS One 2019; 14:e0220706. [PMID: 31393920 PMCID: PMC6687129 DOI: 10.1371/journal.pone.0220706] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 07/22/2019] [Indexed: 12/16/2022] Open
Abstract
Fetida Cave is an active sulfuric acid cave influenced by seawater, showing abundant microbial communities that organize themselves under three main different morphologies: water filaments, vermiculations and moonmilk deposits. These biofilms/deposits have different cave distribution, pH, macro- and microelement and mineralogical composition, carbon and nitrogen content. In particular, water filaments and vermiculations had circumneutral and slightly acidic pH, respectively, both had abundant organic carbon and high microbial diversity. They were rich in macro- and microelements, deriving from mineral dissolution, and, in the case of water filaments, from seawater composition. Vermiculations had different color, partly associated with their mineralogy, and unusual minerals probably due to trapping capacities. Moonmilk was composed of gypsum, poor in organic matter, had an extremely low pH (0-1) and low microbial diversity. Based on 16S rRNA gene analysis, the microbial composition of the biofilms/deposits included autotrophic taxa associated with sulfur and nitrogen cycles and biomineralization processes. In particular, water filaments communities were characterized by bacterial taxa involved in sulfur oxidation and reduction in aquatic, aphotic, microaerophilic/anoxic environments (Campylobacterales, Thiotrichales, Arenicellales, Desulfobacterales, Desulforomonadales) and in chemolithotrophy in marine habitats (Oceanospirillales, Chromatiales). Their biodiversity was linked to the morphology of the water filaments and their collection site. Microbial communities within vermiculations were partly related to their color and showed high abundance of unclassified Betaproteobacteria and sulfur-oxidizing Hydrogenophilales (including Sulfuriferula), and Acidiferrobacterales (including Sulfurifustis), sulfur-reducing Desulfurellales, and ammonia-oxidizing Planctomycetes and Nitrospirae. The microbial community associated with gypsum moonmilk showed the strong dominance (>60%) of the archaeal genus Thermoplasma and lower abundance of chemolithotrophic Acidithiobacillus, metal-oxidizing Metallibacterium, Sulfobacillus, and Acidibacillus. This study describes the geomicrobiology of water filaments, vermiculations and gypsum moonmilk from Fetida Cave, providing insights into the microbial taxa that characterize each morphology and contribute to biogeochemical cycles and speleogenesis of this peculiar seawater-influenced sulfuric acid cave.
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Affiliation(s)
- Ilenia M D'Angeli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Daniele Ghezzi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Stefan Leuko
- DLR Institute of Aerospace Medicine, Radiation Biology, Köln, Germany
| | - Andrea Firrincieli
- School of Environmental and Forest Science, University of Washington, Seattle, WA, United States of America
| | - Mario Parise
- Department of Geological and Environmental Sciences, University of Bari "Aldo Moro", Bari, Italy
| | - Adriano Fiorucci
- Department of Environment, Land and Infrastructure Engineering, Polytechnic University of Turin, Torino, Italy
| | - Bartolomeo Vigna
- Department of Environment, Land and Infrastructure Engineering, Polytechnic University of Turin, Torino, Italy
| | - Rosangela Addesso
- Department of Chemistry and Biology "Adolfo Zambelli", University of Salerno, Fisciano (SA), Italy
| | - Daniela Baldantoni
- Department of Chemistry and Biology "Adolfo Zambelli", University of Salerno, Fisciano (SA), Italy
| | - Cristina Carbone
- DISTAV, Department of Geological, Environmental and Biological Sciences, University of Genoa, Genoa, Italy
| | | | - Valme Jurado
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Sevilla, Spain
| | | | - Jo De Waele
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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