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Chi Y, Ma X, Zhang X, Wang R, Zhang D, Chu S, Zhao T, Zhou P, Zhang D. Plant growth promoting endophyte modulates soil ecological characteristics during the enhancement process of cadmium phytoremediation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 369:122206. [PMID: 39197342 DOI: 10.1016/j.jenvman.2024.122206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 08/06/2024] [Accepted: 08/11/2024] [Indexed: 09/01/2024]
Abstract
Endophyte assisted phytoremediation of cadmium (Cd) contaminated soil represents a promising strategy. However, the precise soil ecological regulatory mechanisms by which endophyte enhance the Cd phytoextraction remain unclear. Here, we employed the plant growth promoting endophyte (PGPE) Pseudomonas sp. E3, which has been validated to effectively enhance Cd extraction in Solanum nigrum L., to investigate its regulatory mechanism on soil ecology. The results demonstrated that while PGPE inoculation resulted in minimal alterations to the physicochemical properties of the bulk soil, it led to a notable increase in acid phosphatase activity by 17.86% and urease activity by 24.85% in the rhizosphere soil. This, in turn, significantly raised the available nitrogen and phosphorus contents by 16.93% and 21.27%, respectively, in the rhizosphere soil. Additionally, PGPE inoculation effectively replenished the bioavailable fractions of Fe and Cd, which had been depleted due to root uptake. Importantly, the inoculation specifically augmented the abundance of biomarkers p_Patescibacteria, f_Saccharimonadales, and g_Saccharimonadales in the rhizosphere soil. These biomarkers exhibited a significant positive correlation with the available nutrient and metal element contents. Moreover, the co-occurrence network analysis demonstrated that the inoculation resulted in a simplified bacterial community network, which may have facilitated community synergism by displacing bacteria with a negative association. This regulation appears to occur independently of PGPE colonization. Overall, our findings suggested that PGPE also exerts a regulatory influence on soil ecological features, significantly aiding hyperaccumulators in nutrient acquisition and heavy metal accumulation.
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Affiliation(s)
- Yaowei Chi
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240, China; Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs, Shanghai, 200240, China; Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, Shanghai, 200240, China; Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, Shanghai, 200240, China; Bor S. Luh Food Safety Research Center, Shanghai, 200240, China; Yunnan Dali Research Institute, Shanghai Jiaotong University, Shanghai, 200240, China.
| | - Xianzhong Ma
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240, China; Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs, Shanghai, 200240, China; Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, Shanghai, 200240, China; Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, Shanghai, 200240, China; Bor S. Luh Food Safety Research Center, Shanghai, 200240, China; Yunnan Dali Research Institute, Shanghai Jiaotong University, Shanghai, 200240, China
| | - Xia Zhang
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240, China; Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs, Shanghai, 200240, China; Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, Shanghai, 200240, China; Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, Shanghai, 200240, China; Bor S. Luh Food Safety Research Center, Shanghai, 200240, China; Yunnan Dali Research Institute, Shanghai Jiaotong University, Shanghai, 200240, China
| | - Renyuan Wang
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240, China; Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs, Shanghai, 200240, China; Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, Shanghai, 200240, China; Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, Shanghai, 200240, China; Bor S. Luh Food Safety Research Center, Shanghai, 200240, China; Yunnan Dali Research Institute, Shanghai Jiaotong University, Shanghai, 200240, China
| | - Dongwei Zhang
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240, China; Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs, Shanghai, 200240, China; Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, Shanghai, 200240, China; Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, Shanghai, 200240, China; Bor S. Luh Food Safety Research Center, Shanghai, 200240, China; Yunnan Dali Research Institute, Shanghai Jiaotong University, Shanghai, 200240, China
| | - Shaohua Chu
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240, China; Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs, Shanghai, 200240, China; Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, Shanghai, 200240, China; Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, Shanghai, 200240, China; Bor S. Luh Food Safety Research Center, Shanghai, 200240, China; Yunnan Dali Research Institute, Shanghai Jiaotong University, Shanghai, 200240, China
| | - Ting Zhao
- Yunnan Dali Research Institute, Shanghai Jiaotong University, Shanghai, 200240, China
| | - Pei Zhou
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240, China; Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs, Shanghai, 200240, China; Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, Shanghai, 200240, China; Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, Shanghai, 200240, China; Bor S. Luh Food Safety Research Center, Shanghai, 200240, China; Yunnan Dali Research Institute, Shanghai Jiaotong University, Shanghai, 200240, China
| | - Dan Zhang
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240, China; Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs, Shanghai, 200240, China; Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, Shanghai, 200240, China; Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, Shanghai, 200240, China; Bor S. Luh Food Safety Research Center, Shanghai, 200240, China; Yunnan Dali Research Institute, Shanghai Jiaotong University, Shanghai, 200240, China.
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Gekenidis MT, Vollenweider V, Joyce A, Murphy S, Walser JC, Ju F, Bürgmann H, Hummerjohann J, Walsh F, Drissner D. Unde venis? Bacterial resistance from environmental reservoirs to lettuce: tracking microbiome and resistome over a growth period. FEMS Microbiol Ecol 2024; 100:fiae118. [PMID: 39216995 PMCID: PMC11418651 DOI: 10.1093/femsec/fiae118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/05/2024] [Accepted: 08/30/2024] [Indexed: 09/04/2024] Open
Abstract
Fresh produce is suggested to contribute highly to shaping the gut resistome. We investigated the impact of pig manure and irrigation water quality on microbiome and resistome of field-grown lettuce over an entire growth period. Lettuce was grown under four regimes, combining soil amendment with manure (with/without) with sprinkler irrigation using river water with an upstream wastewater input, disinfected by UV (with/without). Lettuce leaves, soil, and water samples were collected weekly and analysed by bacterial cultivation, 16S rRNA gene amplicon sequencing, and shotgun metagenomics from total community DNA. Cultivation yielded only few clinically relevant antibiotic-resistant bacteria (ARB), but numbers of ARB on lettuce increased over time, while no treatment-dependent changes were observed. Microbiome analysis confirmed a temporal trend. Antibiotic resistance genes (ARGs) unique to lettuce and water included multidrug and β-lactam ARGs, whereas lettuce and soil uniquely shared mainly glycopeptide and tetracycline ARGs. Surface water carried clinically relevant ARB (e.g. ESBL-producing Escherichia coli or Serratia fonticola) without affecting the overall lettuce resistome significantly. Resistance markers including biocide and metal resistance were increased in lettuce grown with manure, especially young lettuce (increased soil contact). Overall, while all investigated environments had their share as sources of the lettuce resistome, manure was the main source especially on young plants. We therefore suggest minimizing soil-vegetable contact to minimize resistance markers on fresh produce.
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Affiliation(s)
| | - Vera Vollenweider
- Department of Quantitative Biomedicine, University of Zurich, 8057 Zurich, Switzerland
| | - Aoife Joyce
- Department of Biology, Maynooth University, W23 F2H6 Maynooth, Ireland
| | - Sinéad Murphy
- Department of Biology, Maynooth University, W23 F2H6 Maynooth, Ireland
| | - Jean-Claude Walser
- Genetic Diversity Centre (GDC), Department of Environmental System Sciences (D-USYS), Swiss Federal Institute of Technology (ETH), 8092 Zurich, Switzerland
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Helmut Bürgmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
| | | | - Fiona Walsh
- Department of Biology, Maynooth University, W23 F2H6 Maynooth, Ireland
| | - David Drissner
- Department of Life Sciences, Albstadt-Sigmaringen University, 72488 Sigmaringen, Germany
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Wasmund K, Singleton C, Dahl Dueholm MK, Wagner M, Nielsen PH. The predicted secreted proteome of activated sludge microorganisms indicates distinct nutrient niches. mSystems 2024:e0030124. [PMID: 39254351 DOI: 10.1128/msystems.00301-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 08/08/2024] [Indexed: 09/11/2024] Open
Abstract
In wastewater treatment plants (WWTPs), complex microbial communities process diverse chemical compounds from sewage. Secreted proteins are critical because many are the first to interact with or degrade external (macro)molecules. To better understand microbial functions in WWTPs, we predicted secreted proteomes of WWTP microbiota from more than 1,000 high-quality metagenome-assembled genomes (MAGs) from 23 Danish WWTPs with biological nutrient removal. Focus was placed on examining secreted catabolic exoenzymes that target major classes of macromolecules. We demonstrate that Bacteroidota has a high potential to digest complex polysaccharides, but also proteins and nucleic acids. Poorly understood activated sludge members of Acidobacteriota and Gemmatimonadota also have high capacities for extracellular polysaccharide digestion. Secreted nucleases are encoded by 61% of MAGs indicating an importance for extracellular DNA and/or RNA digestion in WWTPs. Secreted lipases were the least common macromolecule-targeting enzymes predicted, encoded mainly by Gammaproteobacteria and Myxococcota. In contrast, diverse taxa encode extracellular peptidases, indicating that proteins are widely used nutrients. Diverse secreted multi-heme cytochromes suggest capabilities for extracellular electron transfer by various taxa, including some Bacteroidota that encode undescribed cytochromes with >100 heme-binding motifs. Myxococcota have exceptionally large secreted protein complements, probably related to predatory lifestyles and/or complex cell cycles. Many Gammaproteobacteria MAGs (mostly former Betaproteobacteria) encode few or no secreted hydrolases, but many periplasmic substrate-binding proteins and ABC- and TRAP-transporters, suggesting they are mostly sustained by small molecules. Together, this study provides a comprehensive overview of how WWTPs microorganisms interact with the environment, providing new insights into their functioning and niche partitioning.IMPORTANCEWastewater treatment plants (WWTPs) are critical biotechnological systems that clean wastewater, allowing the water to reenter the environment and limit eutrophication and pollution. They are also increasingly important for the recovery of resources. They function primarily by the activity of microorganisms, which act as a "living sponge," taking up and transforming nutrients, organic material, and pollutants. Despite much research, many microorganisms in WWTPs are uncultivated and poorly characterized, limiting our understanding of their functioning. Here, we analyzed a large collection of high-quality metagenome-assembled genomes from WWTPs for encoded secreted enzymes and proteins, with special emphasis on those used to degrade organic material. This analysis showed highly distinct secreted proteome profiles among different major phylogenetic groups of microorganisms, thereby providing new insights into how different groups function and co-exist in activated sludge. This knowledge will contribute to a better understanding of how to efficiently manage and exploit WWTP microbiomes.
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Affiliation(s)
- Kenneth Wasmund
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- School of Biological Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | - Caitlin Singleton
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morten Kam Dahl Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Michael Wagner
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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Ai C, Cui P, Liu C, Wu J, Xu Y, Liang X, Yang QE, Tang X, Zhou S, Liao H, Friman VP. Viral and thermal lysis facilitates transmission of antibiotic resistance genes during composting. Appl Environ Microbiol 2024; 90:e0069524. [PMID: 39078126 PMCID: PMC11337816 DOI: 10.1128/aem.00695-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 06/06/2024] [Indexed: 07/31/2024] Open
Abstract
While the distribution of extracellular ARGs (eARGs) in the environment has been widely reported, the factors governing their release remain poorly understood. Here, we combined multi-omics and direct experimentation to test whether the release and transmission of eARGs are associated with viral lysis and heat during cow manure composting. Our results reveal that the proportion of eARGs increased 2.7-fold during composting, despite a significant and concomitant reduction in intracellular ARG abundances. This relative increase of eARGs was driven by composting temperature and viral lysis of ARG-carrying bacteria based on metagenome-assembled genome (MAG) analysis. Notably, thermal lysis of mesophilic bacteria carrying ARGs was a key factor in releasing eARGs at the thermophilic phase, while viral lysis played a relatively stronger role during the non-thermal phase of composting. Furthermore, MAG-based tracking of ARGs in combination with direct transformation experiments demonstrated that eARGs released during composting pose a potential transmission risk. Our study provides bioinformatic and experimental evidence of the undiscovered role of temperature and viral lysis in co-driving the spread of ARGs in compost microbiomes via the horizontal transfer of environmentally released DNA. IMPORTANCE The spread of antibiotic resistance genes (ARGs) is a critical global health concern. Understanding the factors influencing the release of extracellular ARGs (eARGs) is essential for developing effective strategies. In this study, we investigated the association between viral lysis, heat, and eARG release during composting. Our findings revealed a substantial increase in eARGs despite reduced intracellular ARG abundance. Composting temperature and viral lysis were identified as key drivers, with thermal lysis predominant during the thermophilic phase and viral lysis during non-thermal phases. Moreover, eARGs released during composting posed a transmission risk through horizontal gene transfer. This study highlights the significance of temperature and phage lysis in ARG spread, providing valuable insights for mitigating antibiotic resistance threats.
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Affiliation(s)
- Chaofan Ai
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Peng Cui
- Guangdong Provincial Engineering and Technology Research Center for Agricultural Land Pollution Prevention and Control, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Chen Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiawei Wu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan Xu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaolong Liang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, China
| | - Qiu-e Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiang Tang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hanpeng Liao
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
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Majeed A, Liu J, Knight AJ, Pajerowska-Mukhtar KM, Mukhtar MS. Bacterial Communities Associated with the Leaves and the Roots of Salt Marsh Plants of Bayfront Beach, Mobile, Alabama, USA. Microorganisms 2024; 12:1595. [PMID: 39203436 PMCID: PMC11356468 DOI: 10.3390/microorganisms12081595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 07/23/2024] [Accepted: 08/01/2024] [Indexed: 09/03/2024] Open
Abstract
Salt marshes are highly dynamic and biologically diverse ecosystems that serve as natural habitats for numerous salt-tolerant plants (halophytes). We investigated the bacterial communities associated with the roots and leaves of plants growing in the coastal salt marshes of the Bayfront Beach, located in Mobile, Alabama, United States. We compared external (epiphytic) and internal (endophytic) communities of both leaf and root plant organs. Using 16S rDNA amplicon sequencing methods, we identified 10 bacterial phyla and 59 different amplicon sequence variants (ASVs) at the genus level. Bacterial strains belonging to the phyla Proteobacteria, Bacteroidetes, and Firmicutes were highly abundant in both leaf and root samples. At the genus level, sequences of the genus Pseudomonas were common across all four sample types, with the highest abundance found in the leaf endophytic community. Additionally, Pantoea was found to be dominant in leaf tissue compared to roots. Our study revealed that plant habitat (internal vs. external for leaves and roots) was a determinant of the bacterial community structure. Co-occurrence network analyses enabled us to discern the intricate characteristics of bacterial taxa. Our network analysis revealed varied levels of ASV complexity in the epiphytic networks of roots and leaves compared to the endophytic networks. Overall, this study advances our understanding of the intricate composition of the bacterial microbiota in habitats (epiphytic and endophytic) and organs (leaf and root) of coastal salt marsh plants and suggests that plants might recruit habitat- and organ-specific bacteria to enhance their tolerance to salt stress.
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Affiliation(s)
- Aqsa Majeed
- Department of Biology, University of Alabama at Birmingham, 3100 East Science Hall, 902 14th Street South, Birmingham, AL 35294, USA; (A.M.); (J.L.); (A.J.K.); (K.M.P.-M.)
- Department of Genetics & Biochemistry, Biosystems Research Complex, Clemson University, 105 Collings St., Clemson, SC 29634, USA
| | - Jinbao Liu
- Department of Biology, University of Alabama at Birmingham, 3100 East Science Hall, 902 14th Street South, Birmingham, AL 35294, USA; (A.M.); (J.L.); (A.J.K.); (K.M.P.-M.)
| | - Adelle J. Knight
- Department of Biology, University of Alabama at Birmingham, 3100 East Science Hall, 902 14th Street South, Birmingham, AL 35294, USA; (A.M.); (J.L.); (A.J.K.); (K.M.P.-M.)
| | - Karolina M. Pajerowska-Mukhtar
- Department of Biology, University of Alabama at Birmingham, 3100 East Science Hall, 902 14th Street South, Birmingham, AL 35294, USA; (A.M.); (J.L.); (A.J.K.); (K.M.P.-M.)
- Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC 29634, USA
| | - M. Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, 3100 East Science Hall, 902 14th Street South, Birmingham, AL 35294, USA; (A.M.); (J.L.); (A.J.K.); (K.M.P.-M.)
- Department of Genetics & Biochemistry, Biosystems Research Complex, Clemson University, 105 Collings St., Clemson, SC 29634, USA
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Yang L, Chen Q, Wei J, Fan T, Kong L, Long T, Zhang S, Deng S. Response of microbial communities in aquifers with multiple organic solvent contamination: Implications for MNA remedy. JOURNAL OF HAZARDOUS MATERIALS 2024; 474:134798. [PMID: 38843633 DOI: 10.1016/j.jhazmat.2024.134798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/07/2024] [Accepted: 06/01/2024] [Indexed: 06/26/2024]
Abstract
The application of Monitored Natural Attenuation (MNA) technology has been widespread, while there is a paucity of data on groundwater with multiple co-contaminants. This study focused on high permeability, low hydraulic gradient groundwater with co-contamination of benzene, toluene, ethylbenzene, and xylenes (BTEX), chlorinated aliphatic hydrocarbons (CAHs), and chlorinated aromatic hydrocarbons (CPs). The objective was to investigate the responses of microbial communities during natural attenuation processes. Results revealed greater horizontal variation in groundwater microbial community composition compared to vertical variation. The variation was strongly correlated with the total contaminant quantity (r = 0.722, p < 0.001) rather than individual contaminants. BTEX exerted a more significant influence on community diversity than other contaminants. The assembly of groundwater microbial communities was primarily governed by deterministic processes (βNTI < -2) in high contaminant concentration zones, while stochastic processes (|βNTI| < 2) dominated in low-concentration zones. Moreover, the microbial interactions shifted at different depths indicating the degradation rate variation in the vertical. This study makes fundamental contribution to the understanding for the effects of groundwater flow and material fields on indigenous microbial communities, which will provide a scientific basis for more precise adoption of microbial stimulation/augmentation to accelerate the rate of contaminant removal.
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Affiliation(s)
- Lu Yang
- State Environmental Protection Key Laboratory of Soil Environmental Management and Pollution Control, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing 210042, China
| | - Qiang Chen
- State Environmental Protection Key Laboratory of Soil Environmental Management and Pollution Control, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing 210042, China
| | - Jing Wei
- State Environmental Protection Key Laboratory of Soil Environmental Management and Pollution Control, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing 210042, China
| | - Tingting Fan
- State Environmental Protection Key Laboratory of Soil Environmental Management and Pollution Control, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing 210042, China
| | - Lingya Kong
- State Environmental Protection Key Laboratory of Soil Environmental Management and Pollution Control, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing 210042, China.
| | - Tao Long
- State Environmental Protection Key Laboratory of Soil Environmental Management and Pollution Control, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing 210042, China
| | - Shengtian Zhang
- State Environmental Protection Key Laboratory of Soil Environmental Management and Pollution Control, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing 210042, China
| | - Shaopo Deng
- State Environmental Protection Key Laboratory of Soil Environmental Management and Pollution Control, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing 210042, China.
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Litti Y, Elcheninov A, Botchkova E, Chernyh N, Merkel A, Vishnyakova A, Popova N, Zhang Y, Safonov A. Metagenomic evidence of a novel anammox community in a cold aquifer with high nitrogen pollution. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 365:121629. [PMID: 38944958 DOI: 10.1016/j.jenvman.2024.121629] [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: 01/10/2024] [Revised: 06/06/2024] [Accepted: 06/26/2024] [Indexed: 07/02/2024]
Abstract
The process of anaerobic ammonium oxidation by nitrite (anammox) is a globally essential part of N cycle. To date, 8 Candidatus genera and more than 22 species of anammox bacteria have been discovered in various anthropogenic and natural habitats, including nitrogen-polluted aquifers. In this work, anammox bacteria were detected for the first time in the groundwater ecosystem with high anthropogenic nitrogen pollution (up to 1760 mg NO3--N/L and 280 mg NH4+-N/L) and low year-round temperature (7-8 °C) in the zone of a uranium sludge repository. Further metagenomic analysis resulted in retrieval of metagenome-assembled genomes of 4 distinct anammox bacteria: a new genus named Ca. Frigussubterria, new species in Ca. Kuenenia, and two strains of a new species in Ca. Scalindua. Analysis of the genomes revealed essential genes involved in anammox metabolism. Both strains of Ca. Scalindua chemeplantae had a high copy number of genes encoding the cold shock proteins CspA/B, which can also function as an antifreeze protein (CspB). Ca. Kuenenia glazoviensis and Ca. Frigussubterria udmurtiae were abundant in less N-polluted site, while Ca. Scalindua chemeplantae inhabited both sites. Genes for urea utilization, reduction of insoluble Fe2O3 or MnO2, assimilatory sulfate reduction, reactive oxygen detoxification, nitrate reduction to ammonium, and putatively arsenate respiration were found. These findings enrich knowledge of the functional and phylogenetic diversity of anammox bacteria and improve understanding of the nitrogen cycle in polluted aquifers.
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Affiliation(s)
- Yuriy Litti
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312, Moscow, Russia.
| | - Alexander Elcheninov
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312, Moscow, Russia.
| | - Ekaterina Botchkova
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312, Moscow, Russia.
| | - Nikolay Chernyh
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312, Moscow, Russia.
| | - Alexander Merkel
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312, Moscow, Russia.
| | - Anastasia Vishnyakova
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312, Moscow, Russia.
| | - Nadezhda Popova
- Frumkin Institute of Physical Chemistry and Electrochemistry RAS, 31, bld.4, Leninsky Prospect, 119071, Moscow, Russia.
| | - Yaobin Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China.
| | - Alexey Safonov
- Frumkin Institute of Physical Chemistry and Electrochemistry RAS, 31, bld.4, Leninsky Prospect, 119071, Moscow, Russia.
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Hao H, Yue Y, Wang Q, Xiao T, Zhao Z, Zhang J, Chen H. Effects of the rice-mushroom rotation pattern on soil properties and microbial community succession in paddy fields. Front Microbiol 2024; 15:1449922. [PMID: 39113843 PMCID: PMC11303333 DOI: 10.3389/fmicb.2024.1449922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024] Open
Abstract
Introduction Currently, straw biodegradation and soil improvement in rice-mushroom rotation systems have attracted much attention. However, there is still a lack of studies on the effects of rice-mushroom rotation on yield, soil properties and microbial succession. Methods In this study, no treatment (CK), green manure return (GM) and rice straw return (RS) were used as controls to fully evaluate the effect of Stropharia rugosoannulata cultivation substrate return (SRS) on soil properties and microorganisms. Results The results indicated that rice yield, soil nutrient (organic matter, organic carbon, total nitrogen, available nitrogen and available potassium) and soil enzyme (urease, saccharase, lignin peroxidase and laccase) activities had positive responses to the rice-mushroom rotation. At the interannual level, microbial diversity varied significantly among treatments, with the rice-mushroom rotation significantly increasing the relative alpha diversity index of soil bacteria and enriching beneficial microbial communities such as Rhizobium, Bacillus and Trichoderma for rice growth. Soil nutrients and enzymatic activities were significantly correlated with microbial communities during rice-mushroom rotation. The fungal-bacterial co-occurrence networks were modular, and Latescibacterota, Chloroflexi, Gemmatimonadota and Patescibacteria were closely related to the accumulation of nutrients in the soil. The structural equation model (SEM) showed that fungal diversity responded more to changes in soil nutrients than did bacterial diversity. Discussion Overall, the rice-mushroom rotation model improved soil nutrients and rice yields, enriched beneficial microorganisms and maintained microbial diversity. This study provides new insights into the use of S. rugosoannulata cultivation substrates in the sustainable development of agroecosystems.
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Affiliation(s)
- Haibo Hao
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
- State Key Laboratory of Genetic Engineering and Fudan Center for Genetic Diversity and Designing Agriculture, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yihong Yue
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Qian Wang
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Tingting Xiao
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Zelong Zhao
- Shanghai Biozeron Biotechnology Co., Ltd., Shanghai, China
| | - Jinjing Zhang
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Hui Chen
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
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9
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Dong Y, Chen R, Graham EB, Yu B, Bao Y, Li X, You X, Feng Y. Eco-evolutionary strategies for relieving carbon limitation under salt stress differ across microbial clades. Nat Commun 2024; 15:6013. [PMID: 39019914 PMCID: PMC11255312 DOI: 10.1038/s41467-024-50368-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 07/09/2024] [Indexed: 07/19/2024] Open
Abstract
With the continuous expansion of saline soils under climate change, understanding the eco-evolutionary tradeoff between the microbial mitigation of carbon limitation and the maintenance of functional traits in saline soils represents a significant knowledge gap in predicting future soil health and ecological function. Through shotgun metagenomic sequencing of coastal soils along a salinity gradient, we show contrasting eco-evolutionary directions of soil bacteria and archaea that manifest in changes to genome size and the functional potential of the soil microbiome. In salt environments with high carbon requirements, bacteria exhibit reduced genome sizes associated with a depletion of metabolic genes, while archaea display larger genomes and enrichment of salt-resistance, metabolic, and carbon-acquisition genes. This suggests that bacteria conserve energy through genome streamlining when facing salt stress, while archaea invest in carbon-acquisition pathways to broaden their resource usage. These findings suggest divergent directions in eco-evolutionary adaptations to soil saline stress amongst microbial clades and serve as a foundation for understanding the response of soil microbiomes to escalating climate change.
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Affiliation(s)
- Yang Dong
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Ruirui Chen
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China.
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Emily B Graham
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA, 99352, USA.
- School of Biological Sciences, Washington State University, P.O. Box 645910, Pullman, WA, 99164, USA.
| | - Bingqian Yu
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yuanyuan Bao
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xin Li
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiangwei You
- Marine Agriculture Research Center, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Youzhi Feng
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing, 210095, China
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10
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Gladkov GV, Kimeklis AK, Tembotov RK, Ivanov MN, Andronov EE, Abakumov EV. Linking the composition of cryoconite prokaryotic communities in the Arctic, Antarctic, and Central Caucasus with their chemical characteristics. Sci Rep 2024; 14:15838. [PMID: 38982048 PMCID: PMC11233692 DOI: 10.1038/s41598-024-64452-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 06/10/2024] [Indexed: 07/11/2024] Open
Abstract
Cryoconites are the deposits on the surface of glaciers that create specific ecological niches for the development of microorganism communities. The sediment material can vary in origin, structure, and nutrient content, creating local variations in the growth conditions. An additional factor of variability is the location of the glaciers, as they are found in different climatic zones in the high mountain regions and closer to the poles. Here, using the analysis of amplicon sequencing of the 16S rRNA gene, we studied the taxonomic composition of the prokaryotic communities from glaciers from remote regions, including the Arctic (Mushketova on the Severnaya Zemlya, IGAN in Polar Ural), Antarctic (Pimpirev on the Livingstone Island) and Central Caucasus (Skhelda and Garabashi) and connected it with the variation of the physicochemical characteristics of the substrate: pH, carbon, nitrogen, macro- and microelements. The cryoconite microbiomes were comprised of specific for this environment phyla (mostly Pseudomonadota, Cyanobacteria, Bacteroidota, Acidobacteriota, and Actinobacteriota), but each glacier had a unique taxonomic imprint. The core microbiome between regions was composed of only a few ASVs, among which the most likely globally distributed ones attributed to Polaromonas sp., Rhodoferax sp., Cryobacterium sp., and Hymenobacter frigidus. The WGSNA defined clusters of co-occurring ASVs between microbiomes, that significantly change their abundance corresponding with the variation of chemical parameters of cryoconites, but do not fully coincide with their regional separation. Thus, our work demonstrates that the chemical characteristics of the sediment material can explain the variation in the cryoconite prokaryotic community which is not always linked to geographic isolation.
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Affiliation(s)
- Grigory V Gladkov
- Department of Applied Ecology, St. Petersburg State University, Saint-Petersburg, Russia, 199034
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia, 196608
| | - Anastasiia K Kimeklis
- Department of Applied Ecology, St. Petersburg State University, Saint-Petersburg, Russia, 199034
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia, 196608
| | - Rustam Kh Tembotov
- Department of Applied Ecology, St. Petersburg State University, Saint-Petersburg, Russia, 199034
- Tembotov Institute of Ecology of Mountain Territories, Russian Academy of Sciences, Nalchik, Russia, 360051
| | - Mikhail N Ivanov
- Department of Cryolithology and Glaciology, Lomonosov Moscow State University, GSP-1, Leninskie Gory, Moscow, Russia, 119991
| | - Evgeny E Andronov
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia, 196608
- V.V. Dokuchaev Soil Science Institute, Moscow, Russia, 119017
| | - Evgeny V Abakumov
- Department of Applied Ecology, St. Petersburg State University, Saint-Petersburg, Russia, 199034.
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia, 196608.
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11
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Liu X, Wu M, Guo J. Coupling Nitrate-Dependent Anaerobic Ethane Degradation with Anaerobic Ammonium Oxidation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:11525-11533. [PMID: 38898713 DOI: 10.1021/acs.est.4c00488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The microbial oxidation of short-chain gaseous alkanes (SCGAs, consisting of ethane, propane, and butane) serves as an efficient sink to mitigate these gases' emission to the atmosphere, thus reducing their negative impacts on air quality and climate. "Candidatus Alkanivorans nitratireducens" are recently found to mediate nitrate-dependent anaerobic ethane oxidation (n-DAEO). In natural ecosystems, anaerobic ammonium-oxidizing (anammox) bacteria may consume nitrite generated from nitrate reduction by "Ca. A. nitratireducens", thereby alleviating the inhibition caused by nitrite accumulation on the metabolism of "Ca. A. nitratireducens". Here, we demonstrate the coupling of n-DAEO with anammox in a laboratory-scale model system to prevent nitrite accumulation. Our results suggest that a high concentration of ethane (6.9-7.9%) has acute inhibition on anammox activities, thus making the coupling process a significant challenge. By maintaining ethane concentrations within the range of 1.7-5.5%, stable ethane and ammonium oxidation, nitrate reduction, and dinitrogen gas generation without nitrite accumulation were finally achieved. After the accomplished coupling of n-DAEO with anammox, nitrate reduction rates increased by 8.1 times compared to the rate observed with n-DAEO alone. Microbial community profiling via 16S rRNA gene amplicon sequencing showed "Ca. A. nitratireducens" (6.6-12.9%) and anammox bacteria "Candidatus Kuenenia" (3.4-5.6%) were both dominant in the system, indicating they potentially form a syntrophic partnership to jointly contribute to nitrogen removal. Our findings offer insights into the cross-feeding interaction between "Ca. A. nitratireducens" and anammox bacteria in anoxic environments.
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Affiliation(s)
- Xiawei Liu
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Mengxiong Wu
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
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12
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Yang J, Ouyang L, Chen S, Zhang C, Zheng J, He S. Amendments affect the community assembly and co-occurrence network of microorganisms in Cd and Pb tailings of the Eucalyptus camaldulensis rhizosphere. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172365. [PMID: 38641118 DOI: 10.1016/j.scitotenv.2024.172365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 04/08/2024] [Accepted: 04/08/2024] [Indexed: 04/21/2024]
Abstract
Mining tailings containing large amounts of Pb and Cd cause severe regional ecosystem pollution. Soil microorganisms play a regulatory role in the restoration of degraded ecosystems. The remediation of heavy metal-contaminated tailings with amendments and economically valuable Eucalyptus camaldulensis is a research hotspot due to its cost-effectiveness and sustainability. However, the succession and co-occurrence patterns of these microbial communities in this context remain unclear. Tailing samples of five kinds of Cd and Pb were collected in E. camaldulensis restoration models. Physicochemical properties, the proportions of different Cd and Pb forms, microbial community structure, and the co-occurrence network of rhizosphere tailings during different restoration process (organic bacterial manure, organic manure, inorganic fertilizer, bacterial agent) were considered. Organic and organic bacterial manures significantly increased pH, cation exchange capacity, and the proportion of residual Pb. Still, there was a significant decrease in the proportion of reducible Pb. The changes in microbial communities were related to physicochemical properties and the types of amendments. Organic and organic bacterium manures decreased the relative abundance of oligotrophic groups and increased the relative abundance of syntrophic groups. Inorganic fertilizers and bacterial agents decreased the relative abundance of saprophytic fungi. B. subtilis would play a better role in the environment improved by organic manure, increasing the relative abundance of beneficial microorganism and reducing the relative abundance of pathogenic microorganism. pH, cation exchange capacity, and the proportion of different forms of Pb were the main factors affecting the bacterial and fungi variation. All four amendments transformed the main critical groups of the microbial network structure from acidophilus and pathogenic microorganisms to beneficial microorganisms. Heavy metal-resistant microorganisms, stress-resistant microorganisms, beneficial microorganisms that promote nutrient cycling, and copiotrophic groups have become critical to building stable rhizosphere microbial communities. The topological properties and stability of the rhizosphere co-occurrence network were also enhanced. Adding organic and organic bacterium manures combined with E. camaldulensis to repair Cd and Pb tailings improved (1) pH and cation exchange capacity, (2) reduced the biological toxicity of Pb, (3) enhanced the stability of microbial networks, and (4) improved ecological network relationships. These positive changes are conducive to the restoration of the ecological functions of tailings.
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Affiliation(s)
- Jiaqi Yang
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, State Key Laboratory of Efficient Production of Forest Resources, Zhanjiang 524022, China
| | - Linnan Ouyang
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, State Key Laboratory of Efficient Production of Forest Resources, Zhanjiang 524022, China.
| | - Shaoxiong Chen
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, State Key Laboratory of Efficient Production of Forest Resources, Zhanjiang 524022, China
| | - Cheng Zhang
- Experimental Forest Farm of Qingyuan County,Qingyuan 323800, China
| | - Jiaqi Zheng
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, State Key Laboratory of Efficient Production of Forest Resources, Zhanjiang 524022, China
| | - Shae He
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, State Key Laboratory of Efficient Production of Forest Resources, Zhanjiang 524022, China
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13
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Wang Q, Yu J, Li X, Zhang Y, Zhang J, Wang J, Mu J, Yu X, Hui R. Seasonal and anthropogenic influences on bacterioplankton communities: ecological impacts in the coastal waters of Qinhuangdao, Northern China. Front Microbiol 2024; 15:1431548. [PMID: 38962120 PMCID: PMC11220261 DOI: 10.3389/fmicb.2024.1431548] [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: 05/12/2024] [Accepted: 06/06/2024] [Indexed: 07/05/2024] Open
Abstract
Marine bacterioplankton play a crucial role in the cycling of carbon, nitrogen, and phosphorus in coastal waters. And the impact of environmental factors on bacterial community structure and ecological functions is a dynamic ongoing process. To systematically assess the relationship between environmental changes and bacterioplankton communities, this study delved into the spatiotemporal distribution and predicted metabolic characteristics of bacterioplankton communities at two estuarine beaches in Northern China. Coastal water samples were collected regularly in spring, summer, and autumn, and were analyzed in combination with environmental parameters and bacterioplankton community. Results indicated significant seasonal variations in bacterioplankton communities as Bacteroidetes and Actinobacteria were enriched in spring, Cyanobacteria proliferated in summer. While Pseudomonadota and microorganisms associated with organic matter decomposition prevailed in autumn, closely linked to seasonal variation of temperature, light and nutrients such as nitrogen and phosphorus. Particularly in summer, increased tourism activities and riverine inputs significantly raised nutrient levels, promoting the proliferation of specific photosynthetic microorganisms, potentially linked to the occurrence of phytoplankton blooms. Spearman correlation analysis further revealed significant correlations between bacterioplankton communities and environmental factors such as salinity, chlorophyll a, and total dissolved phosphorus (TDP). Additionally, the metabolic features of the spring bacterioplankton community were primarily characterized by enhanced activities in the prokaryotic carbon fixation pathways, reflecting rapid adaptation to increased light and temperature, as well as significant contributions to primary productivity. In summer, the bacterial communities were involved in enhanced glycolysis and biosynthetic pathways, reflecting high energy metabolism and responses to increased light and biomass. In autumn, microorganisms adapted to the accelerated decomposition of organic matter and the seasonal changes in environmental conditions through enhanced amino acid metabolism and material cycling pathways. These findings demonstrate that seasonal changes and human activities significantly influence the structure and function of bacterioplankton communities by altering nutrient dynamics and physical environmental conditions. This study provides important scientific insights into the marine biological responses under global change.
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Affiliation(s)
- Qiuzhen Wang
- Ocean College, Hebei Agricultural University, Qinhuangdao, China
- Hebei Key Laboratory of Nutrition Regulation and Disease Control for Aquaculture, Qinhuangdao, China
| | - Jia Yu
- Ocean College, Hebei Agricultural University, Qinhuangdao, China
| | - Xiaofang Li
- Ocean College, Hebei Agricultural University, Qinhuangdao, China
| | - Yong Zhang
- Department of Ocean Survey, Qinhuangdao Marine Center of the Ministry of Natural Resources, Qinhuangdao, China
| | - Jianle Zhang
- Department of Ocean Survey, Qinhuangdao Marine Center of the Ministry of Natural Resources, Qinhuangdao, China
| | - Jianyan Wang
- Department of Life Sciences, National Natural History Museum of China, Beijing, China
| | - Jiandong Mu
- Ecological Environment Research Department, Hebei Ocean and Fisheries Science Research Institute, Qinhuangdao, China
| | - Xinping Yu
- Ocean College, Hebei Agricultural University, Qinhuangdao, China
| | - Ruixue Hui
- Ocean College, Hebei Agricultural University, Qinhuangdao, China
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14
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Gao M, Zhang Q, Wu S, Wu L, Cao P, Zhang Y, Rong L, Fang B, Yuan C, Yao Y, Wang Y, Sun H. Contamination Status of Novel Organophosphate Esters Derived from Organophosphite Antioxidants in Soil and the Effects on Soil Bacterial Communities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:10740-10751. [PMID: 38771797 DOI: 10.1021/acs.est.3c10611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
The contamination status of novel organophosphate esters (NOPEs) and their precursors organophosphite antioxidants (OPAs) and hydroxylated/diester transformation products (OH-OPEs/di-OPEs) in soils across a large-scale area in China were investigated. The total concentrations of the three test NOPEs in soil were 82.4-716 ng g-1, which were considerably higher than those of traditional OPEs (4.50-430 ng g-1), OPAs (n.d.-30.8 ng g-1), OH-OPEs (n.d.-0.49 ng g-1), and di-OPEs (0.57-21.1 ng g-1). One NOPE compound, i.e., tris(2,4-di-tert-butylphenyl) phosphate (AO168 = O) contributed over 65% of the concentrations of the studied OPE-associated contaminants. A 30-day soil incubation experiment was performed to confirm the influence of AO168 = O on soil bacterial communities. Specific genera belonging to Proteobacteria, such as Lysobacter and Ensifer, were enriched in AO168 = O-contaminated soils. Moreover, the ecological function of methylotrophy was observed to be significantly enhanced (t-test, p < 0.01) in soil treated with AO168 = O, while nitrogen fixation was significantly inhibited (t-test, p < 0.01). These findings comprehensively revealed the contamination status of OPE-associated contaminants in the soil environment and provided the first evidence of the effects of NOPEs on soil microbial communities.
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Affiliation(s)
- Meng Gao
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Qiuyue Zhang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Shanxing Wu
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Lina Wu
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Peiyu Cao
- Department of Global Development, College of Agriculture and Life Science, and Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, New York 14850, United States
| | - Yaozhi Zhang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Lili Rong
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Bo Fang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Chaolei Yuan
- School of Agriculture, Sun Yat-sen University, Shenzhen 518107, China
| | - Yiming Yao
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Yu Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Hongwen Sun
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
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15
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Robins K, O'Donnell G, Neumann A, Schmidt W, Hart A, Graham DW. Antimicrobial resistance in rural rivers: Comparative study of the Coquet (Northumberland) and Eden (Cumbria) River catchments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172348. [PMID: 38614353 DOI: 10.1016/j.scitotenv.2024.172348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/15/2024]
Abstract
Many studies have characterised resistomes in river microbial communities. However, few have compared resistomes in parallel rural catchments that have few point-source inputs of antimicrobial genes (ARGs) and organisms (i.e., AMR) - catchments where one can contrast more nebulous drivers of AMR in rural rivers. Here, we used quantitative microbial profiling (QMP) to compare resistomes and microbiomes in two rural river catchments in Northern England, the Coquet and Eden in Northumberland and Cumbria, respectively, with different hydrological and geographical conditions. The Eden has higher flow rates, higher annual surface runoff, and longer periods of soil saturation, whereas the Coquet is drier and has lower flowrates. QMP analysis showed the Eden contained significantly more abundant microbes associated with soil sources, animal faeces, and wastewater than the Coquet, which had microbiomes like less polluted rivers (Wilcoxon test, p < 0.01). The Eden also had greater ARG abundances and resistome diversity (Kruskal Wallis, p < 0.05), and higher levels of potentially clinically relevant ARGs. The Eden catchment had greater and flashier runoff and more extensive agricultural land use in its middle reach, which explains higher levels of AMR in the river. Hydrological and geographic factors drive AMR in rural rivers, which must be considered in environmental monitoring programmes.
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Affiliation(s)
- Katie Robins
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Greg O'Donnell
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Anke Neumann
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Wiebke Schmidt
- Chief Scientists Group, Environment Agency, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Alwyn Hart
- Chief Scientists Group, Environment Agency, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
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16
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Wang YC, Fu HM, Shen Y, Wang J, Wang N, Chen YP, Yan P. Biosynthetic potential of uncultured anammox community bacteria revealed through multi-omics analysis. BIORESOURCE TECHNOLOGY 2024; 401:130740. [PMID: 38677385 DOI: 10.1016/j.biortech.2024.130740] [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: 01/29/2024] [Revised: 03/11/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024]
Abstract
Microbial secondary metabolites (SMs) and their derivatives have been widely used in medicine, agriculture, and energy. Growing needs for renewable energy and the challenges posed by antibiotic resistance, cancer, and pesticides emphasize the crucial hunt for new SMs. Anaerobic ammonium-oxidation (anammox) systems harbor many uncultured or underexplored bacteria, representing potential resources for discovering novel SMs. Leveraging HiFi long-read metagenomic sequencing, 1,040 biosynthetic gene clusters (BGCs) were unearthed from the anammox microbiome with 58% being complete and showcasing rich diversity. Most of them showed distant relations to known BGCs, implying novelty. Members of the underexplored lineages (Chloroflexota and Planctomycetota) and Proteobacteria contained lots of BGCs, showcasing substantial biosynthetic potential. Metaproteomic results indicated that Planctomycetota members harbored the most active BGCs, particularly those involved in producing potential biofuel-ladderane. Overall, these findings underscore that anammox microbiomes could serve as valuable resources for mining novel BGCs and discovering new SMs for practical application.
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Affiliation(s)
- Yi-Cheng Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Hui-Min Fu
- National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing 400067, China
| | - Yu Shen
- National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing 400067, China
| | - Jin Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Nuo Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - You-Peng Chen
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Peng Yan
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China.
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Fu S, Xie Z, Feng K, Zou H, Guo R, Lian S. Energetic utilization of corn stalk and elimination of methyl orange in ECMO-like integrated reactor: Co-occurrence of anaerobic digestion and aerobic treatment. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 360:121139. [PMID: 38744212 DOI: 10.1016/j.jenvman.2024.121139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 04/29/2024] [Accepted: 05/09/2024] [Indexed: 05/16/2024]
Abstract
For the simultaneous energetic utilization of corn stalk and azo-dye contaminated wastewater, an ECMO-like integrated reactor was come up to achieve the biogas production and azo-dye degradation during anaerobic digestion (AD). Methyl orange (MO) was selected as the model compound for azo-dye. The ECMO-like reactor included AD main reactor with a spray device and solid-liquid separation components, integrated with an aeration reactor for biogas slurry. Methane yields of corn stalks (100.82 mL/g VS) were highest in the ECMO-like reactor, compared with reactors without aeration. As a stable metabolite, 4-aminobenzenesulfonic acid (4-ABA) was detected in AD, while it was assumed that the metabolites can be further transformed in the ECMO-like reactor (R3), due to the 4-ABA removal efficiency as 92.87 % after 35 days' digestion. Class Alphaproteobacteria and Clostridia were assumed as functional microbes responding to aeration. Overall, this ECMO-like integrated reactor provided a novel biotechnology strategy for agricultural and azo dye waste treatment.
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Affiliation(s)
- Shanfei Fu
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, NO. 189 Songling Road, Qingdao, 266101, PR China; Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, NO.1800 Lihu Avenue, Wuxi, Jiangsu Province, 214122, PR China; Shandong Energy Institute, NO. 189 Songling Road, Qingdao, 266101, PR China; Qingdao New Energy Shandong Laboratory, NO. 189 Songling Road, Qingdao, 266101, PR China; Dalian National Laboratory for Clean Energy, Dalian, 116023, PR China.
| | - Zhong Xie
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, NO.1800 Lihu Avenue, Wuxi, Jiangsu Province, 214122, PR China.
| | - Kai Feng
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, NO.1800 Lihu Avenue, Wuxi, Jiangsu Province, 214122, PR China.
| | - Hua Zou
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, NO.1800 Lihu Avenue, Wuxi, Jiangsu Province, 214122, PR China.
| | - Rongbo Guo
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, NO. 189 Songling Road, Qingdao, 266101, PR China; Shandong Energy Institute, NO. 189 Songling Road, Qingdao, 266101, PR China; Qingdao New Energy Shandong Laboratory, NO. 189 Songling Road, Qingdao, 266101, PR China; Dalian National Laboratory for Clean Energy, Dalian, 116023, PR China.
| | - Shujuan Lian
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, NO. 189 Songling Road, Qingdao, 266101, PR China; Shandong Energy Institute, NO. 189 Songling Road, Qingdao, 266101, PR China; Qingdao New Energy Shandong Laboratory, NO. 189 Songling Road, Qingdao, 266101, PR China.
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18
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Barco RA, Merino N, Lam B, Budnik B, Kaplan M, Wu F, Amend JP, Nealson KH, Emerson D. Comparative proteomics of a versatile, marine, iron-oxidizing chemolithoautotroph. Environ Microbiol 2024; 26:e16632. [PMID: 38861374 DOI: 10.1111/1462-2920.16632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/20/2024] [Indexed: 06/13/2024]
Abstract
This study conducted a comparative proteomic analysis to identify potential genetic markers for the biological function of chemolithoautotrophic iron oxidation in the marine bacterium Ghiorsea bivora. To date, this is the only characterized species in the class Zetaproteobacteria that is not an obligate iron-oxidizer, providing a unique opportunity to investigate differential protein expression to identify key genes involved in iron-oxidation at circumneutral pH. Over 1000 proteins were identified under both iron- and hydrogen-oxidizing conditions, with differentially expressed proteins found in both treatments. Notably, a gene cluster upregulated during iron oxidation was identified. This cluster contains genes encoding for cytochromes that share sequence similarity with the known iron-oxidase, Cyc2. Interestingly, these cytochromes, conserved in both Bacteria and Archaea, do not exhibit the typical β-barrel structure of Cyc2. This cluster potentially encodes a biological nanowire-like transmembrane complex containing multiple redox proteins spanning the inner membrane, periplasm, outer membrane, and extracellular space. The upregulation of key genes associated with this complex during iron-oxidizing conditions was confirmed by quantitative reverse transcription-PCR. These findings were further supported by electromicrobiological methods, which demonstrated negative current production by G. bivora in a three-electrode system poised at a cathodic potential. This research provides significant insights into the biological function of chemolithoautotrophic iron oxidation.
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Affiliation(s)
- Roman A Barco
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
| | - N Merino
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Lawrence Livermore National Lab, Biosciences and Biotechnology Division, Livermore, California, USA
| | - B Lam
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - B Budnik
- Mass Spectrometry and Proteomics Resource Laboratory, Harvard University, Cambridge, Massachusetts, USA
| | - M Kaplan
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - F Wu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, Zhejiang, China
| | - J P Amend
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - K H Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - D Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
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19
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Hu X, Zhang S, Liu G, Wang J, Wang Y. Promoting mechanism of nitrogen removal by Fe 3O 4 magnetic particles during the start-up phase in sequencing batch reactor. Bioprocess Biosyst Eng 2024; 47:851-862. [PMID: 38676738 DOI: 10.1007/s00449-024-03006-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 03/20/2024] [Indexed: 04/29/2024]
Abstract
In this paper, a magnetic sequencing batch reactor (SBR) was constructed, and the influence rule of magnetic particle dosing performance of denitrification was investigated. The diversity, structure, and potential functions of the microbial community were comprehensively explored. The results showed that the particle size and the dosage of Fe3O4 magnetic particles were the main parameters affecting the sedimentation performance of activated sludge. The start-up phase of the SBR reactor with Fe3O4 magnetic particles was 5 days less than the control. Moreover, total nitrogen removal efficiency during the start-up phase was improved, with the maximum value reaching 91.93%, surpassing the control by 9.7% with the Fe3O4 dosage of 1.2 g L-1. In addition, the activated sludge concentration and dehydrogenase activity were improved, compared to the control. High-throughput sequencing showed that the denitrifying bacterium Saccharimonadales dominated the reactor and was enriched by magnetic particles. According to predicted functions, the abundance of genes for denitrification increased with the addition of magnetic particles, suggesting the capacity of nitrogen removal was enhanced in the microbial community. Overall, the Fe3O4 magnetic particles provide great potential for enhanced wastewater nitrogen removal.
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Affiliation(s)
- Xiaoyu Hu
- School of Civil Engineering and Architecture, University of Jinan, Jinan, 250022, China
| | - Shuai Zhang
- School of Civil Engineering and Architecture, University of Jinan, Jinan, 250022, China
| | - Guicai Liu
- School of Civil Engineering and Architecture, University of Jinan, Jinan, 250022, China
| | - Jiabin Wang
- School of Civil Engineering and Architecture, University of Jinan, Jinan, 250022, China.
| | - Yue Wang
- Shuifa Water Holding Group Limited, Jinan, 250000, China
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20
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Cataruci ACS, Kawamoto D, Shimabukuro N, Ishikawa KH, Ando-Suguimoto ES, Ribeiro RA, Nicastro GG, Albuquerque-Souza E, de Souza RF, Mayer MPA. Oral Administration of Lactobacillus acidophilus LA5 Prevents Alveolar Bone Loss and Alters Oral and Gut Microbiomes in a Murine Periodontitis Experimental Model. Microorganisms 2024; 12:1057. [PMID: 38930439 PMCID: PMC11205731 DOI: 10.3390/microorganisms12061057] [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: 04/02/2024] [Revised: 05/09/2024] [Accepted: 05/15/2024] [Indexed: 06/28/2024] Open
Abstract
Periodontitis is a destructive inflammatory response triggered by dysbiosis. Lactobacillus acidophilus LA5 (LA5) may impair microbial colonization and alter the host. Thus, we evaluated the effect of LA5 on alveolar bone loss in a periodontitis murine model and investigated its effect on the oral and gut microbiomes. Porphyromonas gingivalis, Prevotella intermedia, Fusobacterium nucleatum, and Streptococcus gordonii were inoculated in C57BL/6 mice (P+), with LA5 (L+). SHAM infected controls (P- and/or L- groups) were also evaluated. After 45 days, alveolar bone loss in the maxilla and oral and gut microbiomes were determined. The administration of LA5 controlled the microbial consortium-induced alveolar bone loss. Periodontopathogens infection resulted in shifts in the oral and gut microbiomes consistent with dysbiosis, and LA5 reshaped these changes. The oral microbiome of P+L- group showed the increased abundance of Enterococaccea, Streptoccocaceae, Staphylococcaceae, Moraxellaceae, and Pseudomonadaceae, which were attenuated by the administration of LA5 to the infected group (P+L+). The administration of LA5 to otherwise non-infected mice resulted in the increased abundance of the superphylum Patescibacteria and the family Saccharamonadaceae in the gut. These data indicate L. acidophilus LA5 as a candidate probiotic for the control of periodontitis.
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Affiliation(s)
- Amalia C. S. Cataruci
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-220, SP, Brazil; (A.C.S.C.); (D.K.); (N.S.); (K.H.I.); (R.A.R.); (G.G.N.); (E.A.-S.); (R.F.d.S.); (M.P.A.M.)
- Division of Periodontics, Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo 05508-220, SP, Brazil
| | - Dione Kawamoto
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-220, SP, Brazil; (A.C.S.C.); (D.K.); (N.S.); (K.H.I.); (R.A.R.); (G.G.N.); (E.A.-S.); (R.F.d.S.); (M.P.A.M.)
| | - Natali Shimabukuro
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-220, SP, Brazil; (A.C.S.C.); (D.K.); (N.S.); (K.H.I.); (R.A.R.); (G.G.N.); (E.A.-S.); (R.F.d.S.); (M.P.A.M.)
- Division of Periodontics, Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo 05508-220, SP, Brazil
| | - Karin H. Ishikawa
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-220, SP, Brazil; (A.C.S.C.); (D.K.); (N.S.); (K.H.I.); (R.A.R.); (G.G.N.); (E.A.-S.); (R.F.d.S.); (M.P.A.M.)
| | - Ellen S. Ando-Suguimoto
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-220, SP, Brazil; (A.C.S.C.); (D.K.); (N.S.); (K.H.I.); (R.A.R.); (G.G.N.); (E.A.-S.); (R.F.d.S.); (M.P.A.M.)
| | - Rodolfo A. Ribeiro
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-220, SP, Brazil; (A.C.S.C.); (D.K.); (N.S.); (K.H.I.); (R.A.R.); (G.G.N.); (E.A.-S.); (R.F.d.S.); (M.P.A.M.)
| | - Gianlucca G. Nicastro
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-220, SP, Brazil; (A.C.S.C.); (D.K.); (N.S.); (K.H.I.); (R.A.R.); (G.G.N.); (E.A.-S.); (R.F.d.S.); (M.P.A.M.)
| | - Emanuel Albuquerque-Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-220, SP, Brazil; (A.C.S.C.); (D.K.); (N.S.); (K.H.I.); (R.A.R.); (G.G.N.); (E.A.-S.); (R.F.d.S.); (M.P.A.M.)
- Division of Periodontics, Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo 05508-220, SP, Brazil
- William Harvey Research Institute, Queen Mary University of London, London E1 2AT, UK
| | - Robson F. de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-220, SP, Brazil; (A.C.S.C.); (D.K.); (N.S.); (K.H.I.); (R.A.R.); (G.G.N.); (E.A.-S.); (R.F.d.S.); (M.P.A.M.)
| | - Marcia P. A. Mayer
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-220, SP, Brazil; (A.C.S.C.); (D.K.); (N.S.); (K.H.I.); (R.A.R.); (G.G.N.); (E.A.-S.); (R.F.d.S.); (M.P.A.M.)
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21
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Wang YC, Mao Y, Fu HM, Wang J, Weng X, Liu ZH, Xu XW, Yan P, Fang F, Guo JS, Shen Y, Chen YP. New insights into functional divergence and adaptive evolution of uncultured bacteria in anammox community by complete genome-centric analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171530. [PMID: 38453092 DOI: 10.1016/j.scitotenv.2024.171530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/13/2023] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
Anaerobic ammonium-oxidation (anammox) bacteria play a crucial role in global nitrogen cycling and wastewater nitrogen removal, but they share symbiotic relationships with various other microorganisms. Functional divergence and adaptive evolution of uncultured bacteria in anammox community remain underexplored. Although shotgun metagenomics based on short reads has been widely used in anammox research, metagenome-assembled genomes (MAGs) are often discontinuous and highly contaminated, which limits in-depth analyses of anammox communities. Here, for the first time, we performed Pacific Biosciences high-fidelity (HiFi) long-read sequencing on the anammox granule sludge sample from a lab-scale bioreactor, and obtained 30 accurate and complete metagenome-assembled genomes (cMAGs). These cMAGs were obtained by selecting high-quality circular contigs from initial assemblies of long reads generated by HiFi sequencing, eliminating the need for Illumina short reads, binning, and reassembly. One new anammox species affiliated with Candidatus Jettenia and three species affiliated with novel families were found in this anammox community. cMAG-centric analysis revealed functional divergence in general and nitrogen metabolism among the anammox community members, and they might adopt a cross-feeding strategy in organic matter, cofactors, and vitamins. Furthermore, we identified 63 mobile genetic elements (MGEs) and 50 putative horizontal gene transfer (HGT) events within these cMAGs. The results suggest that HGT events and MGEs related to phage and integration or excision, particularly transposons containing tnpA in anammox bacteria, might play important roles in the adaptive evolution of this anammox community. The cMAGs generated in the present study could be used to establish of a comprehensive database for anammox bacteria and associated microorganisms. These findings highlight the advantages of HiFi sequencing for the studies of complex mixed cultures and advance the understanding of anammox communities.
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Affiliation(s)
- Yi-Cheng Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Yanping Mao
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518071, Guangdong, China
| | - Hui-Min Fu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China; National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing 400067, China
| | - Jin Wang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Xun Weng
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Zi-Hao Liu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Xiao-Wei Xu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Peng Yan
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Fang Fang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Jin-Song Guo
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - Yu Shen
- National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing 400067, China
| | - You-Peng Chen
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China.
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22
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Geng H, Wang F, Wu H, Qin Q, Ma S, Chen H, Zhou B, Yuan R, Luo S, Sun K. Biochar and nano-hydroxyapatite combined remediation of soil surrounding tailings area: Multi-metal(loid)s fixation and soybean rhizosphere soil microbial improvement. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133817. [PMID: 38422730 DOI: 10.1016/j.jhazmat.2024.133817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 02/11/2024] [Accepted: 02/15/2024] [Indexed: 03/02/2024]
Abstract
The soil near tailings areas is relatively barren and contaminated by multi-metal(loid)s, seriously threatening the safety of crop production. Here, biochar and nano-hydroxyapatite (nHAP) were combined to improve the sterilized and unsterilized polymetallic contaminated soil, and soil incubation and soybean pot experiments were designed. Results showed that biochar and nHAP not only increased soil C, N, and P but also effectively reduced multi-metal bioavailability, wherein the combined application of the two amendments had the best effect on metal immobilization. The synergistic effect of the two amendments decreased the acid-soluble contents of Co, Cu, Fe, and Pb in rhizosphere soils up to 86.75%, 80.69%, 89.09%, and 96.70%, respectively. The ameliorant reduced the accumulation of metal(loid)s in soybean plants, and rhizosphere microorganisms inhibited the migration of soil metals to plants. Additionally, biochar and nHAP regulated the rhizosphere soil microbial community. The rhizosphere soil of the sterilization group tended to prioritize the restoration of the original dominant bacteria. As, Pb, Fe, Urease, OM, TN, and TP were the critical environmental variables affecting rhizosphere soil bacterial communities. Therefore, combining biochar and nHAP is an environmentally friendly strategy to reduce polymetallic mobility in tailings soil and crops and improve soil microbial community structure.
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Affiliation(s)
- Huanhuan Geng
- School of Environment, Beijing Normal University, No.19, Xinjiekouwai St, Haidian District, Beijing 100875, PR China; School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Fei Wang
- School of Environment, Beijing Normal University, No.19, Xinjiekouwai St, Haidian District, Beijing 100875, PR China.
| | - Haoming Wu
- School of Environment, Beijing Normal University, No.19, Xinjiekouwai St, Haidian District, Beijing 100875, PR China
| | - Qizheng Qin
- School of Chemical & Environmental Engineering, China University of Mining & Technology (Beijing), D11 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Shuai Ma
- School of Environment, Beijing Normal University, No.19, Xinjiekouwai St, Haidian District, Beijing 100875, PR China
| | - Huilun Chen
- School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Beihai Zhou
- School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Rongfang Yuan
- School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Shuai Luo
- School of Energy & Environmental Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Ke Sun
- School of Environment, Beijing Normal University, No.19, Xinjiekouwai St, Haidian District, Beijing 100875, PR China
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23
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Gago JF, Viver T, Urdiain M, Ferreira E, Robledo P, Rossello-Mora R. Metagenomics of two aquifers with thermal anomalies in Mallorca Island, and proposal of new uncultivated taxa named following the rules of SeqCode. Syst Appl Microbiol 2024; 47:126506. [PMID: 38640749 DOI: 10.1016/j.syapm.2024.126506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/27/2024] [Accepted: 04/04/2024] [Indexed: 04/21/2024]
Abstract
Groundwater offers an intriguing blend of distinctive physical and chemical conditions, constituting a challenge for microbial life. In Mallorca, the largest island of Balearic archipelago, harbours a variety of thermal anomalies (i.e., geothermal manifestation where surface aquifers exhibiting temperatures exceeding the regional average). The metagenomes of two aquifers in the centre and southern of the island showed Pseudomonadota to be the most represented phylum when using extracted 16S rRNA gene sequences. However, the microbial structures within and between aquifers were remarkably diverse but similar in their metabolic profiles as revealed by the metagenome-assembled genomes (MAGs) pointing to a prevalence of aerobic chemolithoautotrophic and heterotrophic metabolisms, especially in the Llucmajor aquifer. Also, some evidences of anaerobic lifestyles were detected, which would indicate that these environments either could suffer episodes of oxygen depletion or the anaerobes had been transported from deeper waters. We believe that the local environmental factors (temperature, external inputs or chemistry) seem to be more relevant than the connection and, eventually, transport of microbial cells within the aquifer in determining the highly divergent structures. Notably, most of the reconstructed genomes belonged to undescribed bacterial lineages and from them two high-quality MAGs could be classified as novel taxa named following the rules of the Code for Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). Accordingly, we propose the new species and genus Costitxia debesea gen. nov., sp. nov., affiliated with the novel family Costitxiaceae fam. nov., order Costitxiales ord. nov. and class Costitxiia class. nov.; and the new new species and genus Lloretia debesea gen. nov. sp. nov. affiliated with the novel family Lloretiaceae fam. nov.
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Affiliation(s)
- Juan F Gago
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain; The Deep Blue Sea Enterprise S.L., Barcelona, Spain; Lipotrue S.L., Barcelona, Spain.
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain; Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Mercedes Urdiain
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Elaine Ferreira
- The Deep Blue Sea Enterprise S.L., Barcelona, Spain; Lipotrue S.L., Barcelona, Spain
| | - Pedro Robledo
- Unit of Geological and Mining Institute of Spain in Balearic Islands (IGME-CSIC), Palma de Mallorca, Spain
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain.
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24
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Cubillos CF, Aguilar P, Moreira D, Bertolino P, Iniesto M, Dorador C, López-García P. Exploring the prokaryote-eukaryote interplay in microbial mats from an Andean athalassohaline wetland. Microbiol Spectr 2024; 12:e0007224. [PMID: 38456669 PMCID: PMC10986560 DOI: 10.1128/spectrum.00072-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 01/28/2024] [Indexed: 03/09/2024] Open
Abstract
Microbial community assembly results from the interaction between biotic and abiotic factors. However, environmental selection is thought to predominantly shape communities in extreme ecosystems. Salar de Huasco, situated in the high-altitude Andean Altiplano, represents a poly-extreme ecosystem displaying spatial gradients of physicochemical conditions. To disentangle the influence of abiotic and biotic factors, we studied prokaryotic and eukaryotic communities from microbial mats and underlying sediments across contrasting areas of this athalassohaline ecosystem. The prokaryotic communities were primarily composed of bacteria, notably including a significant proportion of photosynthetic organisms like Cyanobacteria and anoxygenic photosynthetic members of Alpha- and Gammaproteobacteria and Chloroflexi. Additionally, Bacteroidetes, Verrucomicrobia, and Deltaproteobacteria were abundantly represented. Among eukaryotes, photosynthetic organisms (Ochrophyta and Archaeplastida) were predominant, alongside relatively abundant ciliates, cercozoans, and flagellated fungi. Salinity emerged as a key driver for the assembly of prokaryotic communities. Collectively, abiotic factors influenced both prokaryotic and eukaryotic communities, particularly those of algae. However, prokaryotic communities strongly correlated with photosynthetic eukaryotes, suggesting a pivotal role of biotic interactions in shaping these communities. Co-occurrence networks suggested potential interactions between different organisms, such as diatoms with specific photosynthetic and heterotrophic bacteria or with protist predators, indicating influences beyond environmental selection. While some associations may be explained by environmental preferences, the robust biotic correlations, alongside insights from other ecosystems and experimental studies, suggest that symbiotic and trophic interactions significantly shape microbial mat and sediment microbial communities in this athalassohaline ecosystem.IMPORTANCEHow biotic and abiotic factors influence microbial community assembly is still poorly defined. Here, we explore their influence on prokaryotic and eukaryotic community assembly within microbial mats and sediments of an Andean high-altitude polyextreme wetland system. We show that, in addition to abiotic elements, mutual interactions exist between prokaryotic and eukaryotic communities. Notably, photosynthetic eukaryotes exhibit a strong correlation with prokaryotic communities, specifically diatoms with certain bacteria and other protists. Our findings underscore the significance of biotic interactions in community assembly and emphasize the necessity of considering the complete microbial community.
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Affiliation(s)
- Carolina F. Cubillos
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Pablo Aguilar
- Laboratorio de Complejidad Microbiana, Instituto Antofagasta and Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
- Millennium Nucleus of Austral Invasive Salmonids - INVASAL, Concepción, Chile
| | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Paola Bertolino
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Miguel Iniesto
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana, Instituto Antofagasta and Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
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Cai Y, Yang J, Ran Z, Bu F, Chen X, Shaaban M, Peng QA. Optimizing Typha biochar with phosphoric acid modification and ferric chloride impregnation for hexavalent chromium remediation in water and soil. CHEMOSPHERE 2024; 354:141739. [PMID: 38503383 DOI: 10.1016/j.chemosphere.2024.141739] [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: 01/22/2024] [Revised: 02/21/2024] [Accepted: 03/15/2024] [Indexed: 03/21/2024]
Abstract
Considering the persistent and covert nature of heavy metal soil contamination, the sustainable development of ecological environments and food safety is at significant risk. Our study focuses on remediating soils contaminated with chromium (Cr); we introduce an advanced remediation material, iron oxide phosphoric acid-loaded activated biochar (HFBC), synthesized through pyrolysis. This HFBC displays greater microporosity, fewer impurities, and enhanced efficiency for the remediation process. Our research utilized a comprehensive set of analytical techniques, including Scanning Electron Microscopy (SEM), Fourier Transform Infrared Spectroscopy (FTIR), and X-ray Photoelectron Spectroscopy (XPS), alongside adsorption studies to elucidate the Cr removal mechanism. The effectiveness of HFBC in remediation was influenced by several factors: the pH level, dosage of HFBC, the initial concentration of Cr, and the ambient temperature. Our results indicated an optimal chromium (VI) adsorption capacity of 55.5 mg/g by HFBC at a pH of 6.0 and a temperature of 25 °C, with the process adhering to the pseudo-second-order kinetic model and the Langmuir adsorption isotherm, thus suggesting spontaneity in the uptake method. Moreover, this mechanism encompasses both adsorption and reduction reactions. Using HFBC in pot experiments with cabbage indicated not only an increase in soil pH and cation exchange capacity (CEC), but also a surge in bacterial community abundance. Significant reductions in bioavailable chromium were also recorded. Interestingly, HFBC addition bolstered the growth of cabbage, while concurrently diminishing chromium accumulation within the plant, particularly notable as the HFBC application rate increased. In summation, the HFBC produced in our study has demonstrated convincing efficacy in removing chromium from aqueous solutions and soil. Moreover, the positive agronomic implications of its use, such as enhanced plant growth and reduced heavy metal uptake by plants, indicate its high potential for operational value in the domain of environmental remediation of heavy metals.
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Affiliation(s)
- Yajun Cai
- College of Environmental Engineering, Wuhan Textile University, Wuhan, 430200, China; Clean Production of Textile Printing and DyeingEngineering Research Center, Ministry of Education, Wuhan, 430200, China.
| | - Jianwei Yang
- College of Environmental Engineering, Wuhan Textile University, Wuhan, 430200, China.
| | - Zhonglyu Ran
- College of Environmental Engineering, Wuhan Textile University, Wuhan, 430200, China.
| | - Fantong Bu
- College of Environmental Engineering, Wuhan Textile University, Wuhan, 430200, China.
| | - Xu Chen
- College of Environmental Engineering, Wuhan Textile University, Wuhan, 430200, China.
| | - Muhammad Shaaban
- College of Agriculture, Henan University of Science and Technology, Luoyang, China.
| | - Qi-An Peng
- College of Environmental Engineering, Wuhan Textile University, Wuhan, 430200, China; Clean Production of Textile Printing and DyeingEngineering Research Center, Ministry of Education, Wuhan, 430200, China.
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Macey MC. Genome-resolved metagenomics identifies novel active microbes in biogeochemical cycling within methanol-enriched soil. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13246. [PMID: 38575138 PMCID: PMC10994693 DOI: 10.1111/1758-2229.13246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/15/2024] [Indexed: 04/06/2024]
Abstract
Metagenome assembled genomes (MAGs), generated from sequenced 13C-labelled DNA from 13C-methanol enriched soils, were binned using an ensemble approach. This method produced a significantly larger number of higher-quality MAGs compared to direct binning approaches. These MAGs represent both the primary methanol utilizers and the secondary utilizers labelled via cross-feeding and predation on the labelled methylotrophs, including numerous uncultivated taxa. Analysis of these MAGs enabled the identification of multiple metabolic pathways within these active taxa that have climatic relevance relating to nitrogen, sulfur and trace gas metabolism. This includes denitrification, dissimilatory nitrate reduction to ammonium, ammonia oxidation and metabolism of organic sulfur species. The binning of viral sequence data also yielded extensive viral MAGs, identifying active viral replication by both lytic and lysogenic phages within the methanol-enriched soils. These MAGs represent a valuable resource for characterizing biogeochemical cycling within terrestrial environments.
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Affiliation(s)
- Michael C. Macey
- AstrobiologyOU, Earth, Environment and Ecosystem SciencesThe Open UniversityMilton KeynesUK
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Li Y, Wang J, Liu C, Wang L, Zhang P, Zhao Q, Xiong Z, Zhang G, Zhang W. Remediation of arsenic-contaminated soil using nanoscale schwertmannite synthesized by persulfate oxidation with carboxymethyl cellulose stabilization. ENVIRONMENTAL RESEARCH 2024; 244:117937. [PMID: 38109958 DOI: 10.1016/j.envres.2023.117937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/09/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023]
Abstract
Schwertmannite (SCH) is a promising material for adsorbing inorganic arsenic (As). We synthesized SCH nanoparticles (nano-SCH) via a modified chemical oxidation method and investigated the application of nano-SCH for the remediation of As-contaminated soils. The production of nano-SCH was successfully prepared using the persulfate oxidation method with carboxymethyl cellulose stabilization. The spherical structure of the nano-SCH particles had an average hydrodynamic diameter of 296 nm with high specific surface areas (108.9 m2/g). Compared with SCH synthesized via the H2O2 oxidation method, the percentage of Fe3+ precipitation in nano-SCH synthesis increased from 63.2% to 84.1%. The inorganic As adsorption capacity of nano-SCH improved by 2.27 times at solution pH = 6. After remediation of heavily As-contaminated soils by using 5% nano-SCH, the leachability of inorganic As rapidly decreased to 0.01% in 30 d. Correspondingly, the immobilization efficiencies of inorganic As in soil reached >99.9%. The inorganic As fractions in treated soil shifted from specifically and nonspecifically bound forms to amorphous and crystalline hydrous oxide-bound fractions. After treatment with 5% nano-SCH for 60 d, soil pH slightly decreased from 5.47 to 4.94; by contrast, soil organic matter content increased by 20.9%. Simultaneously, dehydrogenase concentration in soil decreased by 22.4%-34.7% during the remediation process. These changes in soil properties and As immobilization jointly decreased microbial activity and initiated the re-establishment of bacterial communities in the soil. In summary, this study presents a novel and high-productivity technology for nano-SCH synthesis and confirms the high As immobilization effectiveness of nano-SCH in the remediation of As-contaminated soils.
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Affiliation(s)
- Yujie Li
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, People's Republic of China; Institute of Environmental Research at Greater Bay Area, Guangzhou University, Guangzhou, 510006, People's Republic of China
| | - Jia Wang
- College of Environment and Ecology, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Chao Liu
- Institute of Environmental Research at Greater Bay Area, Guangzhou University, Guangzhou, 510006, People's Republic of China
| | - Long Wang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, People's Republic of China
| | - Peng Zhang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, People's Republic of China
| | - Qianyu Zhao
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, People's Republic of China
| | - Zhu Xiong
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, People's Republic of China
| | - Gaosheng Zhang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, People's Republic of China
| | - Wei Zhang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, People's Republic of China.
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Guo T, Wang X, Zhang Q, Jia Y, Wang Y, Wei L, Li N, Xu X, Liu H, Hu L, Zhao N, Xu S. Effects of the alpine meadow in different phenological periods on rumen fermentation and gastrointestinal tract bacteria community in grazing yak on the Qinghai-Tibetan Plateau. BMC Microbiol 2024; 24:62. [PMID: 38373936 PMCID: PMC10875897 DOI: 10.1186/s12866-024-03182-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/05/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND In this study, we investigated the effects of alpine meadow in different phenological periods on ruminal fermentation, serum biochemical indices, and gastrointestinal tract microbes in grazing yak on the Qinghai-Tibetan Plateau. A total of eighteen female freely grazing yaks with an average age of 3 years old and a body weight of 130 ± 19 kg were selected. According to the plant phenological periods, yaks were randomly allocated to one of three treatments: (1) regreen periods group (RP, n = 6); (2) grassy periods group (GP, n = 6); and (3) hay periods group (HP, n = 6). At the end of the experiment, the blood, rumen fluids, and rectal contents were collected to perform further analysis. RESULTS The concentrations of total volatile fatty acid (TVFA), acetate, glucose (GLU), triglyceride (TG), cholesterol (CHO), high density lipoprotein (HDL), and low density lipoprotein (LDL) were higher in the GP group than in the HP group (P < 0.05). However, compared with the RP and GP groups, the HP group had higher concentrations of isobutyrate, isovalerate, valerate, and creatinine (CREA) (P < 0.05). The abundance of Prevotella in the rumen, and the abundances of Rikenellaceae_RC9_gut_group, Eubacterium_coprostanoligenes_group, and Prevotellaceae_UCG-004 in the gut were higher in the GP group compared with the HP group (P < 0.05). The HP had higher abundance of Eubacterium_coprostanoligenes_group in the rumen as well as the abundances of Romboutsia and Arthrobacter in the gut compared with the RP and GP groups (P < 0.05). CONCLUSIONS Based on the results of rumen fermentation, serum biochemical, differential biomarkers, and function prediction, the carbohydrate digestion of grazing yak would be higher with the alpine meadow regreen and grassy due to the gastrointestinal tract microbes. However, the risk of microbe disorders and host inflammation in grazing yak were higher with the alpine meadow wither.
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Affiliation(s)
- Tongqing Guo
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xungang Wang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Qian Zhang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Yuna Jia
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yalin Wang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lin Wei
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Na Li
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xianli Xu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongjin Liu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Linyong Hu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Na Zhao
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Shixiao Xu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China.
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Guo X, Yan Q, Wang F, Wang W, Zhang Z, Liu Y, Liu K. Habitat-specific patterns of bacterial communities in a glacier-fed lake on the Tibetan Plateau. FEMS Microbiol Ecol 2024; 100:fiae018. [PMID: 38378869 PMCID: PMC10903976 DOI: 10.1093/femsec/fiae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/22/2023] [Accepted: 02/19/2024] [Indexed: 02/22/2024] Open
Abstract
Different types of inlet water are expected to affect microbial communities of lake ecosystems due to changing environmental conditions and the dispersal of species. However, knowledge of the effects of changes in environmental conditions and export of microbial assemblages on lake ecosystems is limited, especially for glacier-fed lakes. Here, we collected water samples from the surface water of a glacier-fed lake and its two fed streams on the Tibetan Plateau to investigate the importance of glacial and non-glacial streams as sources of diversity for lake bacterial communities. Results showed that the glacial stream was an important source of microorganisms in the studied lake, contributing 45.53% to the total bacterial community in the lake water, while only 19.14% of bacterial community in the lake water was seeded by the non-glacial stream. Bacterial communities were significantly different between the glacier-fed lake and its two fed streams. pH, conductivity, total dissolved solids, water temperature and total nitrogen had a significant effect on bacterial spatial turnover, and together explained 36.2% of the variation of bacterial distribution among habitats. Moreover, bacterial co-occurrence associations tended to be stronger in the lake water than in stream habitats. Collectively, this study may provide an important reference for assessing the contributions of different inlet water sources to glacier-fed lakes.
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Affiliation(s)
- Xuezi Guo
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Yan
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Feng Wang
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenqiang Wang
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Zhihao Zhang
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
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An Z, Gao X, Shao B, Zhang Q, Ding J, Peng Y. Synchronous Achievement of Advanced Nitrogen Removal and N 2O Reduction in the Anoxic Zone in the AOA Process for Low C/N Municipal Wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:2335-2345. [PMID: 38271692 DOI: 10.1021/acs.est.3c06746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Continuous flow processes for the in situ determination of N2O emissions during low C/N municipal wastewater treatment have rarely been reported. The anaerobic/aerobic/anoxic (AOA) process has recently shown promising potential in energy savings and advanced nitrogen removal, but it still needs to be comprehensively explored in relation to N2O emissions for its carbon reduction advantages. In this study, a novel gas-collecting continuous flow reactor was designed to comprehensively evaluate the emissions of N2O from the gas and liquid phases of the AOA process. Additionally, the measures of enhancing endogenous denitrification (ED) and self-enriching anaerobic ammonium oxidation (Anammox) were employed to optimize nitrogen removal and achieve N2O reduction in the anoxic zone. The results showed that enhanced ED coupled with Anammox led to an increase in the nitrogen removal efficiency (NRE) from 67.65 to 81.96%, an enhancement of the NO3- removal rate from 1.76 mgN/(L h) to 3.99 mgN/(L h), and the N2O emission factor in the anoxic zone decreased from 0.28 to 0.06%. Impressively, ED eliminated 91.46 ± 2.47% of the dissolved N2O from the upstream aerobic zone, and the dissolved N2O in the effluent was reduced to less than 0.01 mg/L. This study provides valuable strategies for fully evaluating N2O emissions and N2O reduction from the AOA process.
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Affiliation(s)
- Zeming An
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, PR China
| | - Xinjie Gao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, PR China
| | - Baishuo Shao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, PR China
| | - Qiong Zhang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, PR China
| | - Jing Ding
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, PR China
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, PR China
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31
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Zhai Y, Guo W, Li D, Chen B, Xu X, Cao X, Zhao L. Size-dependent influences of nanoplastics on microbial consortium differentially inhibiting 2, 4-dichlorophenol biodegradation. WATER RESEARCH 2024; 249:121004. [PMID: 38101052 DOI: 10.1016/j.watres.2023.121004] [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: 09/21/2023] [Revised: 11/22/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]
Abstract
Nanoplastics (NPs), as a type of newly emerging pollutant, are ubiquitous in various environmental systems, one of which is coexistence with organic pollutants in wastewater, potentially influencing the pollutants' biodegradation. A knowledge gap exists regarding the influence of microbial consortium and NPs interactions on biodegradation efficiency. In this work, a 2,4-dichlorophenol (DCP) biodegradation experiment with presence of polystyrene nanoplastics (PS-NPs) with particle sizes of 100 nm (PS100) or 20 nm (PS20) was conducted to verify that PS-NPs had noticeable inhibitory effect on DCP biodegradation in a size-dependent manner. PS100 at 10 mg/L and 100 mg/L both prolonged the microbial stagnation compared to the control without PS-NPs; PS20 exacerbated greater, with PS20 at 100 mg/L causing a noticeable 6-day lag before the start-up of rapid DCP reduction. The ROS level increased to 1.4-fold and 1.8-fold under PS100 and PS20 exposure, respectively, while the elevated LDH under PS20 exposure indicated the mechanical damage to cell membrane by smaller NPs. PS-NPs exposure also resulted in a decrease in microbial diversity and altered the niches of microbial species, e.g., they decreased the abundance of some functional bacteria such as Brevundimonas and Comamonas, while facilitated some minor members to obtain more proliferation. A microbial network with higher complexity and less competition was induced to mediate PS-NPs stress. Functional metabolism responded differentially to PS100 and PS20 exposure. Specifically, PS100 downregulated amino acid metabolism, while PS20 stimulated certain pathways in response to more severe oxidative stress. Our findings give insights into PS-NPs environmental effects concerning microflora and biological degradation.
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Affiliation(s)
- Ying Zhai
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wenbo Guo
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Deping Li
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bo Chen
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoyun Xu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xinde Cao
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China; China-UK Low Carbon College, Shanghai Jiao Tong University, Shanghai 201306, China
| | - Ling Zhao
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China; China-UK Low Carbon College, Shanghai Jiao Tong University, Shanghai 201306, China.
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32
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Rungjaeng C, Ratanatamskul C. Effect of antibiotics addition on nutrient removal stability and microbial community change of the solar-powered oxidation ditch-membrane bioreactor in treating building wastewater. CHEMOSPHERE 2024; 349:140786. [PMID: 38013026 DOI: 10.1016/j.chemosphere.2023.140786] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 10/07/2023] [Accepted: 11/21/2023] [Indexed: 11/29/2023]
Abstract
The solar-powered oxidation ditch-membrane bioreactors (SOD-MBR) system was developed and operated with long solid retention times (SRTs) of 80 and 160 days. The aim was to investigate the effects of using a long SRT and antibiotics in building wastewater on the stability of nutrient removal, as well as membrane fouling. An increase in the SRT from 80 days to 160 days did not significantly affect the performance of the SOD-MBR system. Ciprofloxacin and Sulfamethoxazole removal efficiencies were 94.47 ± 1.54% and 87.54 ± 24.7%. However, the presence of antibiotics resulted in lower removal efficiencies for NH4+-nitrogen and phosphorus and stimulated the production of extracellular polymeric substances (EPS), particularly proteins in L-EPS and T-EPS of the foulant. FTIR and FEEM analysis revealed that the microbial sludge primarily consisted of proteins, carbohydrates, and lipids. Furthermore, the relative abundance analysis of microbial communities identified bacteria associated with nitrogen removal in the SOD-MBR system, including Anammox, AOB (ammonia oxidizing bacteria), DNB (denitrifying bacteria), and NOB (nitrite oxidizing bacteria), with a total of 25 genera. The majority of these bacteria were stimulated by the presence of antibiotics, resulting in higher relative abundance. Finally, the SOD-MBR system achieved energy savings of 97.38% by utilizing photovoltaic (PV) technology.
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Affiliation(s)
- Chanissara Rungjaeng
- Center of Excellence in Innovative Waste Treatment and Water Reuse, Faculty of Engineering, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chavalit Ratanatamskul
- Center of Excellence in Innovative Waste Treatment and Water Reuse, Faculty of Engineering, Chulalongkorn University, Bangkok, 10330, Thailand; Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok, 10330, Thailand.
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Ning D, Wang Y, Fan Y, Wang J, Van Nostrand JD, Wu L, Zhang P, Curtis DJ, Tian R, Lui L, Hazen TC, Alm EJ, Fields MW, Poole F, Adams MWW, Chakraborty R, Stahl DA, Adams PD, Arkin AP, He Z, Zhou J. Environmental stress mediates groundwater microbial community assembly. Nat Microbiol 2024; 9:490-501. [PMID: 38212658 DOI: 10.1038/s41564-023-01573-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 11/28/2023] [Indexed: 01/13/2024]
Abstract
Community assembly describes how different ecological processes shape microbial community composition and structure. How environmental factors impact community assembly remains elusive. Here we sampled microbial communities and >200 biogeochemical variables in groundwater at the Oak Ridge Field Research Center, a former nuclear waste disposal site, and developed a theoretical framework to conceptualize the relationships between community assembly processes and environmental stresses. We found that stochastic assembly processes were critical (>60% on average) in shaping community structure, but their relative importance decreased as stress increased. Dispersal limitation and 'drift' related to random birth and death had negative correlations with stresses, whereas the selection processes leading to dissimilar communities increased with stresses, primarily related to pH, cobalt and molybdenum. Assembly mechanisms also varied greatly among different phylogenetic groups. Our findings highlight the importance of microbial dispersal limitation and environmental heterogeneity in ecosystem restoration and management.
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Affiliation(s)
- Daliang Ning
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Yajiao Wang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Yupeng Fan
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Jianjun Wang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Liyou Wu
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Ping Zhang
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Daniel J Curtis
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Renmao Tian
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Institute for Food Safety and Health, Illinois Institute of Technology, Bedford Park, IL, USA
| | - Lauren Lui
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Terry C Hazen
- Department of Earth and Planetary Sciences, Bredesen Center, Department of Civil and Environmental Sciences, Center for Environmental Biotechnology, and Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Eric J Alm
- Department of Biological Engineering, Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthew W Fields
- Center for Biofilm Engineering and Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Farris Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Romy Chakraborty
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Paul D Adams
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Adam P Arkin
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Zhili He
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA.
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA.
- School of Computer Science, University of Oklahoma, Norman, OK, USA.
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Bai X, Chen X, Zhang D, Liu X, Li J. Targeted phytogenic compounds against Vibrio parahaemolyticus biofilms. Crit Rev Food Sci Nutr 2024:1-12. [PMID: 38189321 DOI: 10.1080/10408398.2023.2299949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
As one of main culprit of seafood-associated human illness, Vibrio parahaemolyticus can readily accumulate on biotic or abiotic surfaces to form biofilms in the seafood processing environment. Biofilm formation on various surfaces can provide a protective barrier for viable bacterial cells that are resistant to most traditional bacteriostatic measures. This underscores the necessity and urgency of developing effective alternative strategies to control V. parahaemolyticus biofilms. Plants have always provided an extensive and infinite source of biologically active compounds for "green" antibiofilm agents. This review summarizes recent developments in promising multitargeted phytogenic compounds against V. parahaemolyticus biofilms. This review provides valuable insights into potential research targets that can be pursued further to identify potent natural antibiofilm agents in the food industry.
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Affiliation(s)
- Xue Bai
- College of Food Science and Engineering, Bohai University, Jinzhou, China
| | - Xiaoli Chen
- College of Food Science and Engineering, Bohai University, Jinzhou, China
| | - Defu Zhang
- College of Food Science and Engineering, Bohai University, Jinzhou, China
| | - Xuefei Liu
- College of Food Science and Engineering, Bohai University, Jinzhou, China
| | - Jianrong Li
- College of Food Science and Engineering, Bohai University, Jinzhou, China
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35
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Zheng Y, Wang B, Gao P, Yang Y, Xu B, Su X, Ning D, Tao Q, Li Q, Zhao F, Wang D, Zhang Y, Li M, Winkler MKH, Ingalls AE, Zhou J, Zhang C, Stahl DA, Jiang J, Martens-Habbena W, Qin W. Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments. THE ISME JOURNAL 2024; 18:wrad002. [PMID: 38365232 PMCID: PMC10811736 DOI: 10.1093/ismejo/wrad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/03/2023] [Accepted: 10/28/2023] [Indexed: 02/18/2024]
Abstract
Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant archaea on Earth, widely distributed in marine, terrestrial, and geothermal ecosystems. However, the genomic diversity, biogeography, and evolutionary process of AOA populations in subsurface environments are vastly understudied compared to those in marine and soil systems. Here, we report a novel AOA order Candidatus (Ca.) Nitrosomirales which forms a sister lineage to the thermophilic Ca. Nitrosocaldales. Metagenomic and 16S rRNA gene-read mapping demonstrates the abundant presence of Nitrosomirales AOA in various groundwater environments and their widespread distribution across a range of geothermal, terrestrial, and marine habitats. Terrestrial Nitrosomirales AOA show the genetic capacity of using formate as a source of reductant and using nitrate as an alternative electron acceptor. Nitrosomirales AOA appear to have acquired key metabolic genes and operons from other mesophilic populations via horizontal gene transfer, including genes encoding urease, nitrite reductase, and V-type ATPase. The additional metabolic versatility conferred by acquired functions may have facilitated their radiation into a variety of subsurface, marine, and soil environments. We also provide evidence that each of the four AOA orders spans both marine and terrestrial habitats, which suggests a more complex evolutionary history for major AOA lineages than previously proposed. Together, these findings establish a robust phylogenomic framework of AOA and provide new insights into the ecology and adaptation of this globally abundant functional guild.
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Affiliation(s)
- Yue Zheng
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Baozhan Wang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ping Gao
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiyan Yang
- National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States
| | - Bu Xu
- Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen 518055, China
- Shanghai Sheshan National Geophysical Observatory , Shanghai 201602, China
| | - Xiaoquan Su
- College of Computer Science and Technology, Qingdao University , Qingdao 266101, China
| | - Daliang Ning
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
| | - Qing Tao
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
| | - Qian Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Feng Zhao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Dazhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Mari-K H Winkler
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, United States
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA 98195, United States
| | - Jizhong Zhou
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK 73019, United States
- Department of Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Chuanlun Zhang
- Department of Ocean Science and Engineering, Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen 518055, China
- Shanghai Sheshan National Geophysical Observatory , Shanghai 201602, China
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, United States
| | - Jiandong Jiang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Willm Martens-Habbena
- Department of Microbiology and Cell Science, Fort Lauderdale Research and Education Center, University of Florida, Davie, FL 33314, United States
| | - Wei Qin
- School of Biological Sciences, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, United States
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Newman-Portela AM, Krawczyk-Bärsch E, Lopez-Fernandez M, Bok F, Kassahun A, Drobot B, Steudtner R, Stumpf T, Raff J, Merroun ML. Biostimulation of indigenous microbes for uranium bioremediation in former U mine water: multidisciplinary approach assessment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:7227-7245. [PMID: 38157180 PMCID: PMC10821841 DOI: 10.1007/s11356-023-31530-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/09/2023] [Indexed: 01/03/2024]
Abstract
Characterizing uranium (U) mine water is necessary to understand and design an effective bioremediation strategy. In this study, water samples from two former U-mines in East Germany were analysed. The U and sulphate (SO42-) concentrations of Schlema-Alberoda mine water (U: 1 mg/L; SO42-: 335 mg/L) were 2 and 3 order of magnitude higher than those of the Pöhla sample (U: 0.01 mg/L; SO42-: 0.5 mg/L). U and SO42- seemed to influence the microbial diversity of the two water samples. Microbial diversity analysis identified U(VI)-reducing bacteria (e.g. Desulfurivibrio) and wood-degrading fungi (e.g. Cadophora) providing as electron donors for the growth of U-reducers. U-bioreduction experiments were performed to screen electron donors (glycerol, vanillic acid, and gluconic acid) for Schlema-Alberoda U-mine water bioremediation purpose. Thermodynamic speciation calculations show that under experimental conditions, U(VI) is not coordinated to the amended electron donors. Glycerol was the best-studied electron donor as it effectively removed 99% of soluble U, 95% of Fe, and 58% of SO42- from the mine water, probably by biostimulation of indigenous microbes. Vanillic acid removed 90% of U, and no U removal occurred using gluconic acid.
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Affiliation(s)
- Antonio M Newman-Portela
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva S/N, 18071, Granada, Spain.
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany.
| | - Evelyn Krawczyk-Bärsch
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Margarita Lopez-Fernandez
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva S/N, 18071, Granada, Spain
| | - Frank Bok
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Andrea Kassahun
- WISMUT GmbH, Jagdschänkenstraße 29, 09117, Chemnitz, Germany
| | - Björn Drobot
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Robin Steudtner
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Thorsten Stumpf
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Johannes Raff
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Mohamed L Merroun
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva S/N, 18071, Granada, Spain
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Goff JL, Lui LM, Nielsen TN, Poole FL, Smith HJ, Walker KF, Hazen TC, Fields MW, Arkin AP, Adams MWW. Mixed waste contamination selects for a mobile genetic element population enriched in multiple heavy metal resistance genes. ISME COMMUNICATIONS 2024; 4:ycae064. [PMID: 38800128 PMCID: PMC11128244 DOI: 10.1093/ismeco/ycae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/11/2024] [Indexed: 05/29/2024]
Abstract
Mobile genetic elements (MGEs) like plasmids, viruses, and transposable elements can provide fitness benefits to their hosts for survival in the presence of environmental stressors. Heavy metal resistance genes (HMRGs) are frequently observed on MGEs, suggesting that MGEs may be an important driver of adaptive evolution in environments contaminated with heavy metals. Here, we report the meta-mobilome of the heavy metal-contaminated regions of the Oak Ridge Reservation subsurface. This meta-mobilome was compared with one derived from samples collected from unimpacted regions of the Oak Ridge Reservation subsurface. We assembled 1615 unique circularized DNA elements that we propose to be MGEs. The circular elements from the highly contaminated subsurface were enriched in HMRG clusters relative to those from the nearby unimpacted regions. Additionally, we found that these HMRGs were associated with Gamma and Betaproteobacteria hosts in the contaminated subsurface and potentially facilitate the persistence and dominance of these taxa in this region. Finally, the HMRGs were associated with conjugative elements, suggesting their potential for future lateral transfer. We demonstrate how our understanding of MGE ecology, evolution, and function can be enhanced through the genomic context provided by completed MGE assemblies.
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Affiliation(s)
- Jennifer L Goff
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY 13210, United States
| | - Lauren M Lui
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Torben N Nielsen
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Farris L Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States
| | - Heidi J Smith
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, United States
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, United States
| | - Kathleen F Walker
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37916, United States
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37916, United States
- Genome Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - Matthew W Fields
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, United States
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, United States
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Department of Bioengineering, University of California, Berkeley, CA 94720, United States
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States
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38
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Chen JS, Hussain B, Tsai HC, Nagarajan V, Kumar RS, Lin IC, Hsu BM. Deciphering microbial communities and their unique metabolic repertoire across rock-soil-plant continuum in the Dayoukeng fumarolic geothermal field of the Tatun Volcano Group. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:7330-7344. [PMID: 38158533 DOI: 10.1007/s11356-023-31313-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024]
Abstract
High temperature and sulfur concentrations in geothermal sulfur fumaroles host unique microbial ecosystems with niche-specific metabolic diversity and physiological functions. In this study, the microbial communities and their functionalities associated with the Dayoukeng geothermal field and the rock-soil-plant continuum were investigated to underpin the microbial modulation at different distances from the fumaroles source. At the phylum level, Bacteroidota, Planctomycetota, Armatimonadota, and Patescibacteria were abundant in plant samples; Elusimicrobiota and Desulfobacterota were in the rock samples while Nitrospirota, Micrarchaeota, and Deinococcota were dominant in the soil samples. Acidophilic thermophiles were enriched in samples within close proximity to the fumaroles, primarily at a distance of 1 m. The sulfur and iron-oxidizing acidophilic bacterial genera such as Acidothiobacillus and Sulfobacillus were abundant in the rock samples. The thermoacidophilic archaeon Acidianus and acidophilic bacteria Acidiphilium were abundant in the soil samples. Additionally, Thermosporothrix and Acidothermus were found abundant in the plant samples. The results of the functional annotation indicated that dark sulfur oxidation, iron oxidation, and hydrogen oxidation pathways were abundant in the soil samples up to 1 m from the fumaroles, while methanogenic and fermentation pathways were more prevalent in the soil samples located 10 m from the fumaroles. Interestingly, the results of this study indicated a higher microbial richness and abundance of acidophilic communities in the soils and plants compared to the rocks of the DYK fumarolic geothermal field.
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Affiliation(s)
- Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Minxiong, Chiayi County, Taiwan
- Department of Biomedical Sciences, National Chung Cheng University, Minxiong, Chiayi County, Taiwan
| | - Hsin-Chi Tsai
- Department of Psychiatry, School of Medicine, Tzu Chi University, Hualien, Taiwan
- Department of Psychiatry, Tzu-Chi General Hospital, Hualien, Taiwan
| | - Viji Nagarajan
- Department of Earth and Environmental Sciences, National Chung Cheng University, Minxiong, Chiayi County, Taiwan
| | - Rajendran Senthil Kumar
- Department of Earth and Environmental Sciences, National Chung Cheng University, Minxiong, Chiayi County, Taiwan
| | - I-Ching Lin
- Department of Family Medicine, Asia University Hospital, Taichung, Taiwan
- Department of Kinesiology, Health and Leisure, Chienkuo Technology University, Chenghua, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Minxiong, Chiayi County, Taiwan.
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39
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Man DKW, Hermans SM, Taubert M, Garcia SL, Hengoju S, Küsel K, Rosenbaum MA. Enrichment of different taxa of the enigmatic candidate phyla radiation bacteria using a novel picolitre droplet technique. ISME COMMUNICATIONS 2024; 4:ycae080. [PMID: 38946848 PMCID: PMC11214157 DOI: 10.1093/ismeco/ycae080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/24/2024] [Accepted: 06/20/2024] [Indexed: 07/02/2024]
Abstract
The candidate phyla radiation (CPR) represents a distinct monophyletic clade and constitutes a major portion of the tree of life. Extensive efforts have focused on deciphering the functional diversity of its members, primarily using sequencing-based techniques. However, cultivation success remains scarce, presenting a significant challenge, particularly in CPR-dominated groundwater microbiomes characterized by low biomass. Here, we employ an advanced high-throughput droplet microfluidics technique to enrich CPR taxa from groundwater. Utilizing a low-volume filtration approach, we successfully harvested a microbiome resembling the original groundwater microbial community. We assessed CPR enrichment in droplet and aqueous bulk cultivation for 30 days using a novel CPR-specific primer to rapidly track the CPR fraction through the cultivation attempts. The combination of soil extract and microbial-derived necromass provided the most supportive conditions for CPR enrichment. Employing these supplemented conditions, droplet cultivation proved superior to bulk cultivation, resulting in up to a 13-fold CPR enrichment compared to a 1- to 2-fold increase in bulk cultivation. Amplicon sequencing revealed 10 significantly enriched CPR orders. The highest enrichment in CPRs was observed for some unknown members of the Parcubacteria order, Cand. Jorgensenbacteria, and unclassified UBA9983. Furthermore, we identified co-enriched putative host taxa, which may guide more targeted CPR isolation approaches in subsequent investigations.
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Affiliation(s)
- DeDe Kwun Wai Man
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), 07745 Jena, Germany
- Balance of the Microverse, Cluster of Excellence, Friedrich Schiller University, 07743 Jena, Germany
| | - Syrie M Hermans
- Balance of the Microverse, Cluster of Excellence, Friedrich Schiller University, 07743 Jena, Germany
- Food Science and Microbiology, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, 1142 Auckland, New Zealand
- Aquatic Geomicrobiology, Institute of Biodiversity, Faculty of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany
| | - Martin Taubert
- Balance of the Microverse, Cluster of Excellence, Friedrich Schiller University, 07743 Jena, Germany
- Aquatic Geomicrobiology, Institute of Biodiversity, Faculty of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany
| | - Sarahi L Garcia
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, 106 91 Stockholm, Sweden
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg, Germany
| | - Sundar Hengoju
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), 07745 Jena, Germany
| | - Kirsten Küsel
- Balance of the Microverse, Cluster of Excellence, Friedrich Schiller University, 07743 Jena, Germany
- Aquatic Geomicrobiology, Institute of Biodiversity, Faculty of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Miriam A Rosenbaum
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), 07745 Jena, Germany
- Balance of the Microverse, Cluster of Excellence, Friedrich Schiller University, 07743 Jena, Germany
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany
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40
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Hoover RL, Keffer JL, Polson SW, Chan CS. Gallionellaceae pangenomic analysis reveals insight into phylogeny, metabolic flexibility, and iron oxidation mechanisms. mSystems 2023; 8:e0003823. [PMID: 37882557 PMCID: PMC10734462 DOI: 10.1128/msystems.00038-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 09/20/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Neutrophilic iron-oxidizing bacteria (FeOB) produce copious iron (oxyhydr)oxides that can profoundly influence biogeochemical cycles, notably the fate of carbon and many metals. To fully understand environmental microbial iron oxidation, we need a thorough accounting of iron oxidation mechanisms. In this study, we show the Gallionellaceae FeOB genomes encode both characterized iron oxidases as well as uncharacterized multiheme cytochromes (MHCs). MHCs are predicted to transfer electrons from extracellular substrates and likely confer metabolic capabilities that help Gallionellaceae occupy a range of different iron- and mineral-rich niches. Gallionellaceae appear to specialize in iron oxidation, so it would be advantageous for them to have multiple mechanisms to oxidize various forms of iron, given the many iron minerals on Earth, as well as the physiological and kinetic challenges faced by FeOB. The multiple iron/mineral oxidation mechanisms may help drive the widespread ecological success of Gallionellaceae.
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Affiliation(s)
- Rene L. Hoover
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Jessica L. Keffer
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Shawn W. Polson
- Department of Computer and Information Sciences, University of Delaware, Newark, Delaware, USA
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA
| | - Clara S. Chan
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
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41
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Pelevina A, Gruzdev E, Berestovskaya Y, Dorofeev A, Nikolaev Y, Kallistova A, Beletsky A, Ravin N, Pimenov N, Mardanov A. New insight into the granule formation in the reactor for enhanced biological phosphorus removal. Front Microbiol 2023; 14:1297694. [PMID: 38163067 PMCID: PMC10755871 DOI: 10.3389/fmicb.2023.1297694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/15/2023] [Indexed: 01/03/2024] Open
Abstract
While granulated activated sludge exhibits high productivity, the processes of granule formation are incompletely studied. The processes of granule formation and succession of communities were investigated in a laboratory sequencing batch reactor (SBR) under conditions for enhanced biological phosphorus removal (EBPR) using microbiological and molecular techniques. Active consumption of acetate, primarily by the phosphate-accumulating organisms (PAO), commenced at day 150 of cultivation. This was indicated by the high ratio of molar P-released/acetate uptake (0.73-0.77 P-mol/C-mol), characteristic of PAO. During this period, two types of granule-like aggregates formed spontaneously out of the activated sludge flocs. The aggregates differed in morphology and microbial taxonomic composition. While both aggregate types contained phosphorus-enriched bacterial cells, PAO prevailed in those of morphotype I, and glycogen-accumulating organisms (GAOs) were predominant in the aggregates of morphotype II. After 250 days, the elimination of the morphotype II aggregates from the reactor was observed. The subsequent selection of the community was associated with the development of the morphotype I aggregates, in which the relative abundance of PAO increased significantly, resulting in higher efficiency of phosphorus removal. Metagenomic analysis revealed a predominance of the organisms closely related to Candidatus Accumulibacter IС and IIС and of Ca. Accumulibacter IIB among the PAO. Based on the content of the genes of the key metabolic pathways, the genomes of potential PAO belonging to the genera Amaricoccus, Azonexus, Thauera, Zoogloea, Pinisolibacter, and Siculibacillus were selected. The patterns of physicochemical processes and the microbiome structure associated with granule formation and succession of the microbial communities were revealed.
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Affiliation(s)
- Anna Pelevina
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Evgeny Gruzdev
- K.G. Skryabin Institute of Bioengineering, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Yulia Berestovskaya
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Dorofeev
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Yury Nikolaev
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Anna Kallistova
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey Beletsky
- K.G. Skryabin Institute of Bioengineering, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nikolai Ravin
- K.G. Skryabin Institute of Bioengineering, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nikolai Pimenov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey Mardanov
- K.G. Skryabin Institute of Bioengineering, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
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42
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Khan T, Song W, Nappi J, Marzinelli EM, Egan S, Thomas T. Functional guilds and drivers of diversity in seaweed-associated bacteria. FEMS MICROBES 2023; 5:xtad023. [PMID: 38213395 PMCID: PMC10781435 DOI: 10.1093/femsmc/xtad023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/21/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024] Open
Abstract
Comparisons of functional and taxonomic profiles from bacterial communities in different habitats have suggested the existence of functional guilds composed of taxonomically or phylogenetically distinct members. Such guild membership is, however, rarely defined and the factors that drive functional diversity in bacteria remain poorly understood. We used seaweed-associated bacteria as a model to shed light on these important aspects of community ecology. Using a large dataset of over 1300 metagenome-assembled genomes from 13 seaweed species we found substantial overlap in the functionality of bacteria coming from distinct taxa, thus supporting the existence of functional guilds. This functional equivalence between different taxa was particularly pronounced when only functions involved in carbohydrate degradation were considered. We further found that bacterial taxonomy is the dominant driver of functional differences between bacteria and that seaweed species or seaweed type (i.e. brown, red and green) had relatively stronger impacts on genome functionality for carbohydrate-degradation functions when compared to all other cellular functions. This study provides new insight into the factors underpinning the functional diversity of bacteria and contributes to our understanding how community function is generated from individual members.
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Affiliation(s)
- Tahsin Khan
- Centre for Marine Science and Innovation & School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Weizhi Song
- Centre for Marine Science and Innovation & School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Jadranka Nappi
- Centre for Marine Science and Innovation & School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Ezequiel M Marzinelli
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Suhelen Egan
- Centre for Marine Science and Innovation & School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation & School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
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43
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Yadav P, Quattrone A, Yang Y, Owens J, Kiat R, Kuppusamy T, Russo SE, Weber KA. Zea mays genotype influences microbial and viral rhizobiome community structure. ISME COMMUNICATIONS 2023; 3:129. [PMID: 38057501 DOI: 10.1038/s43705-023-00335-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 12/08/2023]
Abstract
Plant genotype is recognized to contribute to variations in microbial community structure in the rhizosphere, soil adherent to roots. However, the extent to which the viral community varies has remained poorly understood and has the potential to contribute to variation in soil microbial communities. Here we cultivated replicates of two Zea mays genotypes, parviglumis and B73, in a greenhouse and harvested the rhizobiome (rhizoplane and rhizosphere) to identify the abundance of cells and viruses as well as rhizobiome microbial and viral community using 16S rRNA gene amplicon sequencing and genome resolved metagenomics. Our results demonstrated that viruses exceeded microbial abundance in the rhizobiome of parviglumis and B73 with a significant variation in both the microbial and viral community between the two genotypes. Of the viral contigs identified only 4.5% (n = 7) of total viral contigs were shared between the two genotypes, demonstrating that plants even at the level of genotype can significantly alter the surrounding soil viral community. An auxiliary metabolic gene associated with glycoside hydrolase (GH5) degradation was identified in one viral metagenome-assembled genome (vOTU) identified in the B73 rhizobiome infecting Propionibacteriaceae (Actinobacteriota) further demonstrating the viral contribution in metabolic potential for carbohydrate degradation and carbon cycling in the rhizosphere. This variation demonstrates the potential of plant genotype to contribute to microbial and viral heterogeneity in soil systems and harbors genes capable of contributing to carbon cycling in the rhizosphere.
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Affiliation(s)
- Pooja Yadav
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Amanda Quattrone
- Complex Biosystems, University of Nebraska-Lincoln, Lincoln, NE, USA
- Texas A&M University, College Station, TX, USA
| | - Yuguo Yang
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jacob Owens
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
- University of Nebraska-Medical Center, Omaha, NE, USA
| | - Rebecca Kiat
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | | | - Sabrina E Russo
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Karrie A Weber
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.
- Department of Earth and Atmospheric Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.
- Daugherty Water for Food Global Institute, University of Nebraska, Lincoln, NE, USA.
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44
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Arrington EC, Tarn J, Kittner HE, Kivenson V, Liu RM, Valentine DL. Methylated cycloalkanes fuel a novel genus in the Porticoccaceae family (Ca. Reddybacter gen. nov). Environ Microbiol 2023; 25:2958-2971. [PMID: 37599091 DOI: 10.1111/1462-2920.16474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 07/19/2023] [Indexed: 08/22/2023]
Abstract
Cycloalkanes are abundant and toxic compounds in subsurface petroleum reservoirs and their fate is important to ecosystems impacted by natural oil seeps and spills. This study focuses on the microbial metabolism of methylcyclohexane (MCH) and methylcyclopentane (MCP) in the deep Gulf of Mexico. MCH and MCP are often abundant cycloalkanes observed in petroleum and will dissolve into the water column when introduced at the seafloor via a spill or natural seep. We conducted incubations with deep Gulf of Mexico (GOM) seawater amended with MCH and MCP at four stations. Within incubations with active respiration of MCH and MCP, we found that a novel genus of bacteria belonging to the Porticoccaceae family (Candidatus Reddybacter) dominated the microbial community. Using metagenome-assembled genomes, we reconstructed the central metabolism of Candidatus Reddybacter, identifying a novel clade of the particulate hydrocarbon monooxygenase (pmo) that may play a central role in MCH and MCP metabolism. Through comparative analysis of 174 genomes, we parsed the taxonomy of the Porticoccaceae family and found evidence suggesting the acquisition of pmo and other genes related to the degradation of cyclic and branched hydrophobic compounds were likely key events in the ecology and evolution of this group of organisms.
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Affiliation(s)
- Eleanor C Arrington
- Marine Science Institute, University of California-Santa Barbara, Santa Barbara, California, USA
| | - Jonathan Tarn
- Interdepartmental Graduate Program in Marine Science, University of California-Santa Barbara, Santa Barbara, California, USA
| | - Hailie E Kittner
- Interdepartmental Graduate Program in Marine Science, University of California-Santa Barbara, Santa Barbara, California, USA
| | - Veronika Kivenson
- Innovative Genomics Institute, University of California-Berkeley, Berkeley, California, USA
| | - Rachel M Liu
- School of Oceanography, University of Washington, Seattle, Washington, USA
| | - David L Valentine
- Marine Science Institute, University of California-Santa Barbara, Santa Barbara, California, USA
- Department of Earth Science, University of California-Santa Barbara, Santa Barbara, California, USA
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45
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Zhang H, Zhou X, Li Z, Bartlam M, Wang Y. Anthropogenic original DOM is a critical factor affecting LNA bacterial community assembly. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 902:166169. [PMID: 37562635 DOI: 10.1016/j.scitotenv.2023.166169] [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: 04/25/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/12/2023]
Abstract
We investigated the geographical and environmental distance-decay relationships for both of the two bacteria in the Haihe River, Tianjin, China. HNA bacteria exhibited a stronger geographical variation-dependent pattern while LNA bacteria exhibited a stronger environmental variation-dependent pattern. Variance partition analysis (VPA), Mantel test, and partial mantel test validated the discrepant impacts of geographical distance and environmental factors on their two communities. The heterogeneous selection dominated community assembly of LNA bacteria demonstrates their greater sensitivity to environmental conditions. As the deterministic environmental factor, anthropogenic original dissolved organic matter (DOM) functions exclusively on LNA bacteria, and it is the critical factor leading to the discrepant biogeographical patterns of LNA and HNA bacteria. LNA bacteria interact with HNA bacteria and mediate the DOM driving total bacteria assembly. The LNA keystone taxa, Pseudomonas, Rheinheimera, Candidatus Aquiluna, and hgcl clade are capable to compete with HNA bacteria for anthropogenic original DOM, and are potential indicators of anthropogenic pollution. Our research reveals the non-negligible effect of the LNA bacteria in regulating the ecological response of total bacteria.
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Affiliation(s)
- Hui Zhang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin 300350, China
| | - Xinzhu Zhou
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin 300350, China
| | - Zun Li
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin 300350, China
| | - Mark Bartlam
- College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin 300071, China.
| | - Yingying Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai International Advanced Research Institute (Shenzhen Futian), Nankai University, Tianjin 300350, China.
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46
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Momper L, Casar CP, Osburn MR. A metagenomic view of novel microbial and metabolic diversity found within the deep terrestrial biosphere at DeMMO: A microbial observatory in South Dakota, USA. Environ Microbiol 2023; 25:3719-3737. [PMID: 37964716 DOI: 10.1111/1462-2920.16543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/31/2023] [Indexed: 11/16/2023]
Abstract
The deep terrestrial subsurface is a large and diverse microbial habitat and vast repository of biomass. However, in relation to its size and physical heterogeneity we have limited understanding of taxonomic and metabolic diversity in this realm. Here we present a detailed metagenomic analysis of samples from the Deep Mine Microbial Observatory (DeMMO) spanning depths from the surface to 1.5 km into the crust. From eight geochemically and spatially distinct fluid samples we reconstructed ~600 partial to near-complete metagenome-assembled genomes (MAGs), representing 50 distinct phyla and including 18 candidate phyla. These novel clades include members of the candidate phyla radiation, two new MAGs from OLB16, a phylum originally identified in DeMMO fluids and for which only one other MAG is currently available, and new MAGs from the Eisenbacteria, Omnitrophota, and Edwardsbacteria. We find that microbes spanning this expansive phylogenetic diversity and physical subsurface space gain a competitive edge by maintaining a wide variety of functional pathways, are often capable of numerous dissimilatory energy metabolisms and poised to take advantage of nutrients as they become available in isolated fracture fluids. Our results support and expand on emerging themes of tight nutrient cycling and genomic plasticity in deep subsurface biosphere taxa.
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Affiliation(s)
- Lily Momper
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, Illinois, USA
- Exponent, Inc, Menlo Park, California, USA
| | - Caitlin P Casar
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, Illinois, USA
| | - Magdalena R Osburn
- Department of Earth and Planetary Sciences, Northwestern University, Evanston, Illinois, USA
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47
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Li R, Fu R, Cui ZQ, Guo L, Chen YH, Bai J, Yang JB, Tan QR, Peng ZW. Effects of low-frequency rTMS combined with risperidone on the gut microbiome in hospitalized patients with chronic schizophrenia. Brain Res 2023; 1819:148539. [PMID: 37598899 DOI: 10.1016/j.brainres.2023.148539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/23/2023] [Accepted: 08/17/2023] [Indexed: 08/22/2023]
Abstract
Repetitive transcranial magnetic stimulation (rTMS) has been widely used in treating schizophrenia (SCH). However, the effects of the low frequency of rTMS combined with antipsychotics on the gut microbiome in chronic SCH have been poorly investigated. In the present study, psychiatric symptoms were assessed and the stool samples obtained from 33 adult patients with chronic SCH (at baselinephase), 27 after 2 weeks of treatment (rTMS combined with risperidone, SCH-2W), and 37 healthy controls (HC) were analyzed by 16S rRNA gene sequencing. We found that the reduction of phylum Proteobacteria, family Enterobacteriaceae and genera Escherichia-Shigella as well as the increase of genera norank_f_Lachnospiraceae might be related to the antipsychotic effect of rTMS combined with risperidone. These findings indicate that the brain-gut-microbiota axis might be involved in the therapeutic effect of rTMS combined with antipsychotic drugs.
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Affiliation(s)
- Rui Li
- Department of Psychiatry, Chang'an Hospital, Xi'an 710000, China
| | - Rui Fu
- Department of Psychiatry, Chang'an Hospital, Xi'an 710000, China
| | - Zhi-Quan Cui
- Department of Psychiatry, Chang'an Hospital, Xi'an 710000, China
| | - Lin Guo
- Department of Psychiatry, Chang'an Hospital, Xi'an 710000, China
| | - Yi-Huan Chen
- Department of Psychiatry, Xijing Hospital, Air Force Medical University, Xi'an 710032, China
| | - Jie Bai
- Department of Psychiatry, Gaoxin Hospital, Xi'an 710077, China
| | - Jia-Bin Yang
- Department of Psychiatry, Chang'an Hospital, Xi'an 710000, China
| | - Qing-Rong Tan
- Department of Psychiatry, Chang'an Hospital, Xi'an 710000, China.
| | - Zheng-Wu Peng
- Department of Psychiatry, Chang'an Hospital, Xi'an 710000, China; Department of Psychiatry, Xijing Hospital, Air Force Medical University, Xi'an 710032, China.
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48
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Ma B, Lu C, Wang Y, Yu J, Zhao K, Xue R, Ren H, Lv X, Pan R, Zhang J, Zhu Y, Xu J. A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources. Nat Commun 2023; 14:7318. [PMID: 37951952 PMCID: PMC10640626 DOI: 10.1038/s41467-023-43000-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 10/27/2023] [Indexed: 11/14/2023] Open
Abstract
Soil harbors a vast expanse of unidentified microbes, termed as microbial dark matter, presenting an untapped reservo)ir of microbial biodiversity and genetic resources, but has yet to be fully explored. In this study, we conduct a large-scale excavation of soil microbial dark matter by reconstructing 40,039 metagenome-assembled genome bins (the SMAG catalogue) from 3304 soil metagenomes. We identify 16,530 of 21,077 species-level genome bins (SGBs) as unknown SGBs (uSGBs), which expand archaeal and bacterial diversity across the tree of life. We also illustrate the pivotal role of uSGBs in augmenting soil microbiome's functional landscape and intra-species genome diversity, providing large proportions of the 43,169 biosynthetic gene clusters and 8545 CRISPR-Cas genes. Additionally, we determine that uSGBs contributed 84.6% of previously unexplored viral-host associations from the SMAG catalogue. The SMAG catalogue provides an useful genomic resource for further studies investigating soil microbial biodiversity and genetic resources.
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Affiliation(s)
- Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Caiyu Lu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Yiling Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Jingwen Yu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Kankan Zhao
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Ran Xue
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Hao Ren
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Xiaofei Lv
- Department of Environmental Engineering, China Jiliang University, Hangzhou, 310018, China
| | - Ronghui Pan
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Jiabao Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yongguan Zhu
- Research Center for Eco-environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China.
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49
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Singh P, Al Mohannadi N, Murugesan S, Almarzooqi F, Kabeer BSA, Marr AK, Kino T, Brummaier T, Terranegra A, McGready R, Nosten F, Chaussabel D, Al Khodor S. Unveiling the dynamics of the breast milk microbiome: impact of lactation stage and gestational age. J Transl Med 2023; 21:784. [PMID: 37932773 PMCID: PMC10629158 DOI: 10.1186/s12967-023-04656-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 10/24/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND Breast milk (BM) provides complete nutrition for infants for the first six months of life and is essential for the development of the newborn's immature immune and digestive systems. While BM was conventionally believed to be sterile, recent advanced high throughput technologies have unveiled the presence of diverse microbial communities in BM. These insights into the BM microbiota have mainly originated from uncomplicated pregnancies, possibly not reflecting the circumstances of mothers with pregnancy complications like preterm birth (PTB). METHODS In this article, we investigated the BM microbial communities in mothers with preterm deliveries (before 37 weeks of gestation). We compared these samples with BM samples from healthy term pregnancies across different lactation stages (colostrum, transitional and mature milk) using 16S rRNA gene sequencing. RESULTS Our analysis revealed that the microbial communities became increasingly diverse and compositionally distinct as the BM matured. Specifically, mature BM samples were significantly enriched in Veillonella and lactobacillus (Kruskal Wallis; p < 0.001) compared to colostrum. The comparison of term and preterm BM samples showed that the community structure was significantly different between the two groups (Bray Curtis and unweighted unifrac dissimilarity; p < 0.001). Preterm BM samples exhibited increased species richness with significantly higher abundance of Staphylococcus haemolyticus, Propionibacterium acnes, unclassified Corynebacterium species. Whereas term samples were enriched in Staphylococcus epidermidis, unclassified OD1, and unclassified Veillonella among others. CONCLUSION Our study underscores the significant influence of pregnancy-related complications, such as preterm birth (before 37 weeks of gestation), on the composition and diversity of BM microbiota. Given the established significance of the maternal microbiome in shaping child health outcomes, this investigation paves the way for identifying modifiable factors that could optimize the composition of BM microbiota, thereby promoting maternal and infant health.
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Affiliation(s)
- Parul Singh
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Research Department, Sidra Medicine, Doha, Qatar
| | | | | | | | | | | | | | - Tobias Brummaier
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | | | - Rose McGready
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Damien Chaussabel
- Research Department, Sidra Medicine, Doha, Qatar
- The Jackson Laboratories, Farmington, CT, USA
| | - Souhaila Al Khodor
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
- Research Department, Sidra Medicine, Doha, Qatar.
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50
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Barak H, Fuchs N, Liddor-Naim M, Nir I, Sivan A, Kushmaro A. Microbial dark matter sequences verification in amplicon sequencing and environmental metagenomics data. Front Microbiol 2023; 14:1247119. [PMID: 38029171 PMCID: PMC10656735 DOI: 10.3389/fmicb.2023.1247119] [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: 06/25/2023] [Accepted: 10/04/2023] [Indexed: 12/01/2023] Open
Abstract
Although microorganisms constitute the most diverse and abundant life form on Earth, in many environments, the vast majority of them remain uncultured. As it is based on information gleaned mainly from cultivated microorganisms, our current body of knowledge regarding microbial life is partial and does not reflect actual microbial diversity. That diversity is hidden in the uncultured microbial majority, termed by microbiologists as "microbial dark matter" (MDM), a term borrowed from astrophysics. Metagenomic sequencing analysis techniques (both 16S rRNA gene and shotgun sequencing) compare gene sequences to reference databases, each of which represents only a small fraction of the existing microorganisms. Unaligned sequences lead to groups of "unknown microorganisms" that are usually ignored and rarefied from diversity analysis. To address this knowledge gap, we analyzed the 16S rRNA gene sequences of microbial communities from four different environments-a living organism, a desert environment, a natural aquatic environment, and a membrane bioreactor for wastewater treatment. From those datasets, we chose representative sequences of potentially unknown bacteria for additional examination as "microbial dark matter sequences" (MDMS). Sequence existence was validated by specific amplification and re-sequencing. These sequences were screened against databases and aligned to the Genome Taxonomy Database to build a comprehensive phylogenetic tree for additional sequence classification, revealing potentially new candidate phyla and other lineages. These putative MDMS were also screened against metagenome-assembled genomes from the explored environments for additional validation and for taxonomic and metabolic characterizations. This study shows the immense importance of MDMS in environmental metataxonomic analyses of 16S rRNA gene sequences and provides a simple and readily available methodology for the examination of MDM hidden behind amplicon sequencing results.
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Affiliation(s)
- Hana Barak
- Department of Civil and Environmental Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Naomi Fuchs
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Michal Liddor-Naim
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Irit Nir
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Alex Sivan
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ariel Kushmaro
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- The Ilse Katz Center for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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