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de Menezes AB, Gashchak S, Wood MD, Beresford NA. Relationships between radiation, wildfire and the soil microbial communities in the Chornobyl Exclusion Zone. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175381. [PMID: 39122033 DOI: 10.1016/j.scitotenv.2024.175381] [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: 03/05/2024] [Revised: 08/01/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024]
Abstract
There is considerable uncertainty regarding radiation's effects on biodiversity in natural complex ecosystems typically subjected to multiple environmental disturbances and stresses. In this study we characterised the relationships between soil microbial communities and estimated total absorbed dose rates to bacteria, grassy vegetation and trees in the Red Forest region of the Chornobyl Exclusion Zone. Samples were taken from sites of contrasting ecological histories and along burn and no burn areas following a wildfire. Estimated total absorbed dose rates to bacteria reached levels one order of magnitude higher than those known to affect bacteria in laboratory studies. Sites with harsher ecological conditions, notably acidic pH and low soil moisture, tended to have higher radiation contamination levels. No relationship between the effects of fire and radiation were observed. Microbial groups that correlated with high radiation sites were mostly classified to taxa associated with high environmental stress habitats or stress resistance traits. Distance-based linear models and co-occurrence analysis revealed that the effects of radiation on the soil microbiome were minimal. Hence, the association between high radiation sites and specific microbial groups is more likely a result of the harsher ecological conditions in these sites, rather than due to radiation itself. In this study, we provide a starting point for understanding the relationship between soil microbial communities and estimated total absorbed radiation dose rates to different components of an ecosystem highly contaminated with radiation. Our results suggest that soil microbiomes adapted to natural soil conditions are more likely to be resistant to ionising radiation than expected from laboratory studies, which demonstrates the importance of assessing the impact of ionising radiation on soil microbial communities under field conditions.
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Affiliation(s)
- Alexandre Barretto de Menezes
- University of Galway, School of Biological and Chemical Sciences, Ryan Institute, University Road, H91 TK33, Galway, Ireland.
| | - Sergii Gashchak
- Chornobyl Center for Nuclear Safety, Radioactive Waste & Radioecology, International Radioecology Laboratory, Slavutych, Kyiv Region, Ukraine.
| | - Michael D Wood
- School of Science, Engineering & Environment, University of Salford, Manchester M5 4WT, United Kingdom.
| | - Nicholas A Beresford
- School of Science, Engineering & Environment, University of Salford, Manchester M5 4WT, United Kingdom; Centre for Ecology & Hydrology, CEH Lancaster, Lancaster Environment Centre, Library Av., Bailrigg, Lancaster LA1 4AP, United Kingdom
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2
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Niu G, He C, Mao S, Chen Z, Ma Y, Zhu Y. Enhanced Soil Fertility and Carbon Sequestration in Urban Green Spaces through the Application of Fe-Modified Biochar Combined with Plant Growth-Promoting Bacteria. BIOLOGY 2024; 13:611. [PMID: 39194549 DOI: 10.3390/biology13080611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 08/07/2024] [Accepted: 08/10/2024] [Indexed: 08/29/2024]
Abstract
The soil of urban green spaces is severely degraded due to human activities during urbanization, and it is crucial to investigate effective measures that can restore the ecological functions of the soil. This study investigated the effects of plant growth promoting bacteria (Bacillus clausii) and Fe-modified biochar on soil fertility increases and mechanisms of carbon sequestration. Additionally, the effects on C-cycling-related enzyme activity and the bacterial community were also explored. Six treatments included no biochar or Bacillus clausii suspension added (CK), only Bacillus clausii suspension (BC), only biochar (B), only Fe-modified biochar (FeB), biochar combined with Bacillus clausii (BBC), and Fe-modified biochar combined with Bacillus clausii (FeBBC). Compared with other treatments, the FeBBC treatment significantly decreased soil pH, alleviated soil alkalization, and increased the alkali-hydro nitrogen content in the soil. Compared to the individual application of FeB and BC, the FeBBC treatment significantly improved aggregates' stability and positively improved soil fertility and ecological function. Additionally, compared to the individual application of FeB and BC, the soil organic carbon (SOC), particulate organic carbon (POC), and soil inorganic carbon (SIC) contents for the FeBBC-treated soil increased by 28.46~113.52%, 66.99~434.72%, and 7.34~10.04%, respectively. In the FeBBC treatment, FeB can improve soil physicochemical properties and provide bacterial attachment sites, increase the abundance and diversity of bacterial communities, and promote the uniform distribution of carbon-related bacteria in the soil. Compared to a single ecological restoration method, FeBBC treatment can improve soil fertility and carbon sequestration, providing important reference values for urban green space soil ecological restoration.
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Affiliation(s)
- Guoyao Niu
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Chiquan He
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Shaohua Mao
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Zongze Chen
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Yangyang Ma
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, China
| | - Yi Zhu
- Key Laboratory of National Forestry and Grassland Administration on Ecological Landscaping of Challenging Urban Sites, Shanghai Engineering Research Center of Landscaping on Challenging Urban Sites, Shanghai Academy of Landscape Architecture Science and Planning, Shanghai 200232, China
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Spatola Rossi T, Gallia M, Erijman L, Figuerola E. Biotic and abiotic factors acting on community assembly in parallel anaerobic digestion systems from a brewery wastewater treatment plant. ENVIRONMENTAL TECHNOLOGY 2024:1-16. [PMID: 38686914 DOI: 10.1080/09593330.2024.2343797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 04/09/2024] [Indexed: 05/02/2024]
Abstract
Anaerobic digestion is a complex microbial process that mediates the transformation of organic waste into biogas. The performance and stability of anaerobic digesters relies on the structure and function of the microbial community. In this study, we asked whether the deterministic effect of wastewater composition outweighs the effect of reactor configuration on the structure and dynamics of anaerobic digester archaeal and bacterial communities. Biotic and abiotic factors acting on microbial community assembly in two parallel anaerobic digestion systems, an upflow anaerobic sludge blanket digestor (UASB) and a closed digester tank with a solid recycling system (CDSR), from a brewery WWTP were analysed utilizing 16S rDNA and mcrA amplicon sequencing and genome-centric metagenomics. This study confirmed the deterministic effect of the wastewater composition on bacterial community structure, while the archaeal community composition resulted better explained by organic loading rate (ORL) and volatile free acids (VFA). According to the functions assigned to the differentially abundant metagenome-assembled genomes (MAGs) between reactors, CDSR was enriched in genes related to methanol and methylamines methanogenesis, protein degradation, and sulphate and alcohol utilization. Conversely, the UASB reactor was enriched in genes associated with carbohydrate and lipid degradation, as well as amino acid, fatty acid, and propionate fermentation. By comparing interactions derived from the co-occurrence network with predicted metabolic interactions of the prokaryotic communities in both anaerobic digesters, we conclude that the overall community structure is mainly determined by habitat filtering.
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Affiliation(s)
| | - Mateo Gallia
- IB3- Institute of Biosciences, Biotechnology and Translational Biology- University of Buenos Aires Buenos Aires, Argentina
| | - Leonardo Erijman
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular 'Dr Héctor N. Torres' (INGEBI-CONICET), Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Eva Figuerola
- IB3- Institute of Biosciences, Biotechnology and Translational Biology- University of Buenos Aires Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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Zheng R, Wang C, Sun C. Deep-sea in situ and laboratory multi-omics provide insights into the sulfur assimilation of a deep-sea Chloroflexota bacterium. mBio 2024; 15:e0000424. [PMID: 38417116 PMCID: PMC11005417 DOI: 10.1128/mbio.00004-24] [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: 01/09/2024] [Accepted: 02/13/2024] [Indexed: 03/01/2024] Open
Abstract
Chloroflexota bacteria are abundant and globally distributed in various deep-sea ecosystems. It has been reported based on metagenomics data that two deep-sea Chloroflexota lineages (the SAR202 group and Dehalococcoidia class) have the potential to drive sulfur cycling. However, the absence of cultured Chloroflexota representatives is a significant bottleneck toward understanding their contribution to the deep-sea sulfur cycling. In this study, we find that Phototrophicus methaneseepsis ZRK33 isolated from deep-sea sediment has a heterotrophic lifestyle and can assimilate sulfate and thiosulfate. Using combined physiological, genomic, proteomic, and in situ transcriptomic methods, we find that strain ZRK33 can perform assimilatory sulfate reduction in both laboratory and deep-sea conditions. Metabolism of sulfate or thiosulfate by strain ZRK33 significantly promotes the transport and degradation of various macromolecules and thereby stimulates the energy production. In addition, metagenomic results show that genes associated with assimilatory and dissimilatory sulfate reduction are ubiquitously distributed in the metagenome-assembled genomes of Chloroflexota members derived from deep-sea sediments. Metatranscriptomic results also show that the expression levels of related genes are upregulated, strongly suggesting that Chloroflexota bacteria may play undocumented roles in deep-sea sulfur cycling. IMPORTANCE The cycling of sulfur is one of Earth's major biogeochemical processes and is closely related to the energy metabolism of microorganisms living in the deep-sea cold seep and hydrothermal vents. To date, some of the members of Chloroflexota are proposed to play a previously unrecognized role in sulfur cycling. However, the sulfur metabolic characteristics of deep-sea Chloroflexota bacteria have never been reported, and remain to be verified in cultured deep-sea representatives. Here, we show that the deep-sea Chloroflexota bacterium ZRK33 can perform sulfate assimilation in both laboratory and deep-sea conditions, which expands our knowledge of the sulfur metabolic potential of deep-sea Chloroflexota bacteria. We also show that the genes associated with assimilatory and dissimilatory sulfate reduction ubiquitously distribute in the deep-sea Chloroflexota members, providing hints to the roles of Chloroflexota bacteria in deep-sea sulfur biogeochemical cycling.
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Affiliation(s)
- Rikuan Zheng
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Chong Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Chaomin Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing, China
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Pei L, Ye S, Xie L, Zhou P, He L, Yang S, Ding X, Yuan H, Dai T, Laws EA. Differential effects of warming on the complexity and stability of the microbial network in Phragmites australis and Spartina alterniflora wetlands in Yancheng, Jiangsu Province, China. Front Microbiol 2024; 15:1347821. [PMID: 38601935 PMCID: PMC11004437 DOI: 10.3389/fmicb.2024.1347821] [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: 12/01/2023] [Accepted: 03/11/2024] [Indexed: 04/12/2024] Open
Abstract
The impact of climate warming on soil microbial communities can significantly influence the global carbon cycle. Coastal wetlands, in particular, are susceptible to changes in soil microbial community structure due to climate warming and the presence of invasive plant species. However, there is limited knowledge about how native and invasive plant wetland soil microbes differ in their response to warming. In this study, we investigated the temporal dynamics of soil microbes (prokaryotes and fungi) under experimental warming in two coastal wetlands dominated by native Phragmites australis (P. australis) and invasive Spartina alterniflora (S. alterniflora). Our research indicated that short-term warming had minimal effects on microbial abundance, diversity, and composition. However, it did accelerate the succession of soil microbial communities, with potentially greater impacts on fungi than prokaryotes. Furthermore, in the S. alterniflora wetland, experimental warming notably increased the complexity and connectivity of the microbial networks. While in the P. australis wetland, it decreased these factors. Analysis of robustness showed that experimental warming stabilized the co-occurrence network of the microbial community in the P. australis wetland, but destabilized it in the S. alterniflora wetland. Additionally, the functional prediction analysis using the Faprotax and FunGuild databases revealed that the S. alterniflora wetland had a higher proportion of saprotrophic fungi and prokaryotic OTUs involved in carbon degradation (p < 0.05). With warming treatments, there was an increasing trend in the proportion of prokaryotic OTUs involved in carbon degradation, particularly in the S. alterniflora wetland. Therefore, it is crucial to protect native P. australis wetlands from S. alterniflora invasion to mitigate carbon emissions and preserve the health of coastal wetland ecosystems under future climate warming in China.
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Affiliation(s)
- Lixin Pei
- Qingdao Institute of Marine Geology, China Geologic Survey, Qingdao, China
- Laboratory for Marine Geology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Siyuan Ye
- Qingdao Institute of Marine Geology, China Geologic Survey, Qingdao, China
- Laboratory for Marine Geology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Liujuan Xie
- Qingdao Institute of Marine Geology, China Geologic Survey, Qingdao, China
- Laboratory for Marine Geology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Pan Zhou
- Qingdao Institute of Marine Geology, China Geologic Survey, Qingdao, China
- Laboratory for Marine Geology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Lei He
- Qingdao Institute of Marine Geology, China Geologic Survey, Qingdao, China
- Laboratory for Marine Geology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Shixiong Yang
- Qingdao Institute of Marine Geology, China Geologic Survey, Qingdao, China
- Laboratory for Marine Geology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Xigui Ding
- Qingdao Institute of Marine Geology, China Geologic Survey, Qingdao, China
- Laboratory for Marine Geology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Hongming Yuan
- Qingdao Institute of Marine Geology, China Geologic Survey, Qingdao, China
- Laboratory for Marine Geology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Tianjiao Dai
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, China
| | - Edward A. Laws
- Department of Environmental Sciences, College of the Coast and Environment, Louisiana State University, Baton Rouge, LA, United States
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Huang X, Zhang T, Yu Y, Ding P, Zhao Z, Wang H, Ding J, Zhao C. Dietary tryptophan decreases the impacts of seawater temperature changes on behavior and gut health of the sea cucumber Apostichopus japonicus. MARINE ENVIRONMENTAL RESEARCH 2024; 195:106369. [PMID: 38262135 DOI: 10.1016/j.marenvres.2024.106369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/25/2024]
Abstract
Seawater temperature change is an important concern for seed production and pond culture of sea cucumbers. The present study found that tentacle activity frequency was significantly lower in sea cucumbers exposed to continuous and rapid temperature increases than that of those at ambient temperature. Feeding behavior directly determines food intake, and further affects physiology and growth efficiency of sea cucumbers. This means that the decline in feeding caused by continuous and rapid temperature increases needs to be addressed in sea cucumber aquaculture. However, a sudden temperature change of 5 °C had no significant effect on behaviors of sea cucumbers. This indicates that continuous temperature increases, rather than a sudden increase, result in behavioral impacts on sea cucumbers. Therefore, we recommend aqua-farmers reduce the feeding amount for sea cucumbers during continuous and rapid temperature increases. In the present study, feeding behavior was significantly higher in sea cucumbers fed with 3% dietary tryptophan than that of those fed with 0% and 5% dietary tryptophan. This indicates that 3% dietary tryptophan increases the food intake of sea cucumbers, and mitigates the feeding decline caused by continuous and rapid temperature increase. This indicates that tryptophan has the potential to promote the feeding of sea cucumbers in seed production and pond culture. Adhesion capacity of sea cucumbers fed with 5% dietary tryptophan was significantly higher than that of individuals fed with 0% and 3% dietary tryptophan. This suggests that dietary tryptophan increases the feeding of sea cucumbers exposed to continuous and rapid temperature increases in pond culture and seed production. In addition, this study found that sea cucumbers fed with 3% dietary tryptophan had higher intestinal colony richness under the continuously rapid temperature change. The present study provides an effective method to improve adhesion behavior and to alleviate the impacts on feeding behavior for seed production and pond culture of sea cucumbers exposed to continuous and rapid temperature increases.
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Affiliation(s)
- Xiyuan Huang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Tongdan Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Yushi Yu
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Peng Ding
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Zihe Zhao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Huiyan Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Jun Ding
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Chong Zhao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China.
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Kamagata Y. Cultivating the unseen: Lessons from James Tiedje. MLIFE 2023; 2:217-223. [PMID: 38817816 PMCID: PMC10989887 DOI: 10.1002/mlf2.12083] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/12/2023] [Accepted: 07/22/2023] [Indexed: 06/01/2024]
Affiliation(s)
- Yoichi Kamagata
- National Institute of Advanced and Industrial Science and Technology (AIST)TsukubaJapan
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Zhang SH, Wang Y, Hu JJ, Chen WJ, Wu JL, Seah RWX, Zhu YC, Guo ZP, Chen J. Bamboo charcoal affects soil properties and bacterial community in tea plantations. Open Life Sci 2023; 18:20220681. [PMID: 37589012 PMCID: PMC10426720 DOI: 10.1515/biol-2022-0681] [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: 03/29/2023] [Revised: 05/16/2023] [Accepted: 07/18/2023] [Indexed: 08/18/2023] Open
Abstract
Bamboo charcoal, a type of manufactured biochar, is produced by pyrolyzing bamboo residue under anoxic conditions. Its beneficial properties in absorption, catalyst support, and agricultural function have attracted significant attention; however, relatively few studies have examined its effects on the soil microbiota. In this study, we analyzed the effects of bamboo charcoal on soil physicochemical properties, enzymes, and microbial community structure in tea plantations and investigated the optimal amount of bamboo charcoal to be added to organic fertilizer. The results show that bamboo charcoal can further increase soil available nitrogen, total and available phosphorus and potassium, organic carbon content, pH, and urease activity. However, only the combined use of bamboo charcoal and organic fertilizer significantly increased total nitrogen, sucrase, and β-glucosidase activities in the soil. Bamboo charcoal also significantly increased the Chao1 and Shannon indices of microbiota diversity in a concentration-dependent manner. The structure of the bacterial community changed significantly after the bamboo charcoal addition, with Proteobacteria, Actinobacteria, and Firmicutes increasing and Acidobacteria decreasing. This study provides fundamental insights into the suitability of bamboo charcoal application for the ecological remediation of diseased soils.
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Affiliation(s)
- Si-Hai Zhang
- College of Liangshan, Lishui University, Lishui323000, China
| | - Yue Wang
- College of Horticulture Science, Zhejiang A&F University, Hangzhou311300, China
| | - Jin-Jie Hu
- College of Ecology, Lishui University, No. 1 Xueyuan Road, Lishui323000, China
| | - Wei-Jia Chen
- College of Ecology, Lishui University, No. 1 Xueyuan Road, Lishui323000, China
| | - Jia-Le Wu
- College of Ecology, Lishui University, No. 1 Xueyuan Road, Lishui323000, China
| | - Rachel Wan Xin Seah
- Department of Biological Science, National University of Singapore, Singapore117558, Singapore
| | - Yang-Chun Zhu
- College of Ecology, Lishui University, No. 1 Xueyuan Road, Lishui323000, China
| | - Zhi-Ping Guo
- College of Ecology, Lishui University, No. 1 Xueyuan Road, Lishui323000, China
| | - Jie Chen
- College of Ecology, Lishui University, No. 1 Xueyuan Road, Lishui323000, China
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Zhang X, Geng K, Wu N, Hu G, Fan B, He J, Qiao W. Sustained anaerobic degradation of 4-chloro-2-methylphenoxyacetic acid by acclimated sludge in a continuous-flow reactor. CHEMOSPHERE 2023; 330:138749. [PMID: 37086982 DOI: 10.1016/j.chemosphere.2023.138749] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/03/2023]
Abstract
4-Chloro-2-methylphenoxyacetic acid (MCPA) is a widely used herbicide across the world. MCPA is persistent and easily transports into anoxic environment, such as groundwater, sediments and deep soils. However, little research on anaerobic microbial degradation of MCPA was carried out. The functional microorganisms as well as the catabolic pathway are still unknown. In this research, an anaerobic MCPA-degrading bacterial consortium was enriched from the river sediment near a pesticide-manufacturing plant. After about 6 months' acclimation, the MCPA transformation rate of the consortium reached 4.32 μmol g-1 day-1, 25 times faster than that of the original sludge. 96% of added MCPA (2.5 mM) was degraded within 9 d of incubation. Three metabolites including 4-chloro-2-methylphenol (MCP), 2-methylphenol (2-MP) and phenol were identified during the anaerobic degradation of MCPA. An anaerobic catabolic pathway was firstly proposed: firstly, MCPA was transformed to MCP via the cleavage of the aryl ether, then MCP was reductively dechlorinated to 2-MP which was further demethylated to phenol. The 16S rRNA gene amplicon sequencing revealed a substantial shift in the bacterial community composition after the acclimation. SBR1031, Acidaminococcaceae, Aminicenantales, Syntrophorhabdus, Acidaminobacter, Bacteroidetes_vadinHA17, Methanosaeta, Bathyarchaeia, KD4-96, Anaeromyxobacter, and Dehalobacter were significantly increased in the enriched consortium after acclimation, and positively correlated with the anaerobic degradation of MCPA as suggested by heat map correlation analysis. This study provides a basis for further elucidation of the anaerobic catabolism of MCPA, and contributes to developing efficient and low-cost anaerobic treatment technologies for MCPA pollution.
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Affiliation(s)
- Xuan Zhang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Keke Geng
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Ningning Wu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Gang Hu
- Laboratory Centre of Life Science, College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, PR China
| | - Ben Fan
- College of Forest Resources and Environment, Nanjing Forestry University, Nanjing, Jiangsu, 210037, PR China
| | - Jian He
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Wenjing Qiao
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China.
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10
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Palmer M, Covington JK, Zhou EM, Thomas SC, Habib N, Seymour CO, Lai D, Johnston J, Hashimi A, Jiao JY, Muok AR, Liu L, Xian WD, Zhi XY, Li MM, Silva LP, Bowen BP, Louie K, Briegel A, Pett-Ridge J, Weber PK, Tocheva EI, Woyke T, Northen TR, Mayali X, Li WJ, Hedlund BP. Thermophilic Dehalococcoidia with unusual traits shed light on an unexpected past. THE ISME JOURNAL 2023:10.1038/s41396-023-01405-0. [PMID: 37041326 DOI: 10.1038/s41396-023-01405-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/13/2023]
Abstract
Although the phylum Chloroflexota is ubiquitous, its biology and evolution are poorly understood due to limited cultivability. Here, we isolated two motile, thermophilic bacteria from hot spring sediments belonging to the genus Tepidiforma and class Dehalococcoidia within the phylum Chloroflexota. A combination of cryo-electron tomography, exometabolomics, and cultivation experiments using stable isotopes of carbon revealed three unusual traits: flagellar motility, a peptidoglycan-containing cell envelope, and heterotrophic activity on aromatics and plant-associated compounds. Outside of this genus, flagellar motility has not been observed in Chloroflexota, and peptidoglycan-containing cell envelopes have not been described in Dehalococcoidia. Although these traits are unusual among cultivated Chloroflexota and Dehalococcoidia, ancestral character state reconstructions showed flagellar motility and peptidoglycan-containing cell envelopes were ancestral within the Dehalococcoidia, and subsequently lost prior to a major adaptive radiation of Dehalococcoidia into marine environments. However, despite the predominantly vertical evolutionary histories of flagellar motility and peptidoglycan biosynthesis, the evolution of enzymes for degradation of aromatics and plant-associated compounds was predominantly horizontal and complex. Together, the presence of these unusual traits in Dehalococcoidia and their evolutionary histories raise new questions about the timing and selective forces driving their successful niche expansion into global oceans.
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Affiliation(s)
- Marike Palmer
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
| | - Jonathan K Covington
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - En-Min Zhou
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, 650091, Kunming, People's Republic of China
| | - Scott C Thomas
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Neeli Habib
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, 650091, Kunming, People's Republic of China
- Department of Microbiology, Shaheed Benazir Bhutto Women University, Peshawar, Khyber Pakhtunkhwa (KPK), Pakistan
| | - Cale O Seymour
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Dengxun Lai
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Juliet Johnston
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Ameena Hashimi
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Alise R Muok
- Institute of Biology, Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Xiao-Yang Zhi
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, 650091, Kunming, People's Republic of China
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Leslie P Silva
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Benjamin P Bowen
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Katherine Louie
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ariane Briegel
- Institute of Biology, Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life and Environmental Sciences, University of California Merced, Merced, CA, 95343, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Elitza I Tocheva
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Tanja Woyke
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Life and Environmental Sciences, University of California Merced, Merced, CA, 95343, USA
| | - Trent R Northen
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
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11
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Kambara H, Dinh HTT, Matsushita S, Aoi Y, Kindaichi T, Ozaki N, Ohashi A. New microbial electrosynthesis system for methane production from carbon dioxide coupled with oxidation of sulfide to sulfate. J Environ Sci (China) 2023; 125:786-797. [PMID: 36375960 DOI: 10.1016/j.jes.2022.02.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/16/2022] [Accepted: 02/18/2022] [Indexed: 06/16/2023]
Abstract
Microbial electrosynthesis system (MES) is a promising method that can use carbon dioxide, which is a greenhouse gas, to produce methane which acts as an energy source, without using organic substances. However, this bioelectrical reduction reaction can proceed at a certain high applied voltage when coupled with water oxidation in the anode coated with metallic catalyst. When coupled with the oxidation of HS- to SO42-, methane production is thermodynamically more feasible, thus implying its production at a considerably lower applied voltage. In this study, we demonstrated the possibility of electrotrophic methane production coupled with HS- oxidation in a cost-effective bioanode chamber in the MES without organic substrates at a low applied voltage of 0.2 V. In addition, microbial community analyses of biomass enriched in the bioanode and biocathode were used to reveal the most probable pathway for methane production from HS- oxidation. In the bioanode, electroautotrophic SO42- production accompanied with electron donation to the electrode is performed mainly by the following two steps: first, incomplete sulfide oxidation to sulfur cycle intermediates (SCI) is performed; then the produced SCI are disproportionated to HS- and SO42-. In the biocathode, methane is produced mainly via H2 and acetate by electron-accepting syntrophic bacteria, homoacetogens, and acetoclastic archaea. Here, a new eco-friendly MES with biological H2S removal is established.
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Affiliation(s)
- Hiromi Kambara
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Hiroshima University, 1-4-1, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan
| | - Ha T T Dinh
- Faculty of Environment, Ho Chi Minh City University of Natural Resources and Environment, 236 Le Van Sy, 1 Ward, Tan Binh District, Ho Chi Minh City, Vietnam
| | - Shuji Matsushita
- Agricultural Technology Research Center, Hiroshima Prefectural Technology Research Institute, 6869, Hara, Hachihonmatsu, Higashihiroshima, Hiroshima 739-0151, Japan
| | - Yoshiteru Aoi
- Program of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Tomonori Kindaichi
- Department of Civil and Environmental Engineering, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan
| | - Noriatsu Ozaki
- Department of Civil and Environmental Engineering, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan
| | - Akiyoshi Ohashi
- Department of Civil and Environmental Engineering, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan.
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12
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Bovio-Winkler P, Guerrero LD, Erijman L, Oyarzúa P, Suárez-Ojeda ME, Cabezas A, Etchebehere C. Genome-centric metagenomic insights into the role of Chloroflexi in anammox, activated sludge and methanogenic reactors. BMC Microbiol 2023; 23:45. [PMID: 36809975 PMCID: PMC9942424 DOI: 10.1186/s12866-023-02765-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 01/10/2023] [Indexed: 02/23/2023] Open
Abstract
BACKGROUND The phylum Chloroflexi is highly abundant in a wide variety of wastewater treatment bioreactors. It has been suggested that they play relevant roles in these ecosystems, particularly in degrading carbon compounds and on structuring flocs or granules. Nevertheless, their function is not yet well understood as most species have not been isolated in axenic cultures. Here we used a metagenomic approach to investigate Chloroflexi diversity and their metabolic potential in three environmentally different bioreactors: a methanogenic full-scale reactor, a full-scale activated sludge reactor and a lab scale anammox reactor. RESULTS Differential coverage binning approach was used to assemble the genomes of 17 new Chloroflexi species, two of which are proposed as new Candidatus genus. In addition, we recovered the first representative genome belonging to the genus 'Ca. Villigracilis'. Even though samples analyzed were collected from bioreactors operating under different environmental conditions, the assembled genomes share several metabolic features: anaerobic metabolism, fermentative pathways and several genes coding for hydrolytic enzymes. Interestingly, genome analysis from the anammox reactor indicated a putative role of Chloroflexi in nitrogen conversion. Genes related to adhesiveness and exopolysaccharides production were also detected. Complementing sequencing analysis, filamentous morphology was detected by Fluorescent in situ hybridization. CONCLUSION Our results suggest that Chloroflexi participate in organic matter degradation, nitrogen removal and biofilm aggregation, playing different roles according to the environmental conditions.
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Affiliation(s)
- Patricia Bovio-Winkler
- Microbial Ecology Laboratory, Department of Microbial Biochemistry and Genomic, Biological Research Institute "Clemente Estable", Avenida Italia 3318, CP: 11600, Montevideo, Uruguay
| | - Leandro D Guerrero
- Instituto de Investigaciones en Ingeniería Genética Y Biología Molecular "Dr Héctor N. Torres" (INGEBI-CONICET), Buenos Aires, Argentina
| | - Leonardo Erijman
- Instituto de Investigaciones en Ingeniería Genética Y Biología Molecular "Dr Héctor N. Torres" (INGEBI-CONICET), Buenos Aires, Argentina
| | - Pía Oyarzúa
- GENOCOV Research Group, Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - María Eugenia Suárez-Ojeda
- GENOCOV Research Group, Department of Chemical, Biological and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Angela Cabezas
- Instituto Tecnológico Regional Centro Sur, Universidad Tecnológica, Francisco Antonio Maciel S/N, CP: 97000, Durazno, Uruguay
| | - Claudia Etchebehere
- Microbial Ecology Laboratory, Department of Microbial Biochemistry and Genomic, Biological Research Institute "Clemente Estable", Avenida Italia 3318, CP: 11600, Montevideo, Uruguay.
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13
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Wang H, Liu X, Wang Y, Zhang S, Zhang G, Han Y, Li M, Liu L. Spatial and temporal dynamics of microbial community composition and factors influencing the surface water and sediments of urban rivers. J Environ Sci (China) 2023; 124:187-197. [PMID: 36182129 DOI: 10.1016/j.jes.2021.10.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 09/15/2021] [Accepted: 10/11/2021] [Indexed: 06/16/2023]
Abstract
The temporal and spatial characteristics of urban river bacterial communities help us understand the feedback mechanism of bacteria to changes in the aquatic environment. The Fuhe River plays an important role in determining the water ecological environment of Baiyangdian Lake. 16S rRNA gene sequencing was used to study the microbial distribution characteristics in the Fuhe River in different seasons. The results showed that some environmental factors of the surface water (ammonia nitrogen (NH3-N), total nitrogen (TN), and total phosphorus (TP)) were different on the spatial and temporal scales. Moreover, there were no seasonal differences in the contents of TN, TP, total organic carbon (TOC), or heavy metals in the sediments. The distributions of Cyanobacteria, Actinomycetes and Firmicutes in the water and Actinomycetes and Planctomycetes in the sediments differed significantly among seasons (P < 0.05). There were significant spatial differences in bacteria in the surface water, with the highest abundance of Proteobacteria recorded in the river along with the highest nutrient concentration, while the abundance of Bacteroidetes was higher in the upstream than the downstream. Microbial communities in the water were most sensitive to temperature (T) and the TP concentration (P < 0.01). Moreover, differences in the bacterial community were better explained by the content of heavy metals in the sediments than by the chemical characteristics. A PICRUSt metabolic inference analysis showed that the effect of high summer temperatures on the enzyme action led to an increase in the abundances of the metabolic-related genes of the river microorganisms.
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Affiliation(s)
- Hongjie Wang
- College of Ecology and Environment, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, Baoding 071002, China
| | - Xingchun Liu
- College of Ecology and Environment, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, Baoding 071002, China
| | - Yali Wang
- College of Ecology and Environment, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, Baoding 071002, China
| | - Shengqi Zhang
- College of Ecology and Environment, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, Baoding 071002, China
| | - Guangming Zhang
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300130, China
| | - Yangyang Han
- College of Ecology and Environment, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, Baoding 071002, China
| | - Mengxiang Li
- College of Ecology and Environment, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, Baoding 071002, China
| | - Ling Liu
- College of Ecology and Environment, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, Baoding 071002, China.
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14
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Villena‐Alemany C, Mujakić I, Porcal P, Koblížek M, Piwosz K. Diversity dynamics of aerobic anoxygenic phototrophic bacteria in a freshwater lake. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:60-71. [PMID: 36507772 PMCID: PMC10103773 DOI: 10.1111/1758-2229.13131] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 09/19/2022] [Indexed: 05/20/2023]
Abstract
Aerobic anoxygenic photoheterotrophic (AAP) bacteria represent a functional group of prokaryotic organisms that harvests light energy using bacteriochlorophyll-containing photosynthetic reaction centers. They represent an active and rapidly growing component of freshwater bacterioplankton, with the highest numbers observed usually in summer. Species diversity of freshwater AAP bacteria has been studied before in lakes, but its seasonal dynamics remain unknown. In this report, we analysed temporal changes in the composition of the phototrophic community in an oligo-mesotrophic freshwater lake using amplicon sequencing of the pufM marker gene. The AAP community was dominated by phototrophic Gammaproteobacteria and Alphaproteobacteria, with smaller contribution of phototrophic Chloroflexota and Gemmatimonadota. Phototrophic Eremiobacteriota or members of Myxococcota were not detected. Interestingly, some AAP taxa, such as Limnohabitans, Rhodoferax, Rhodobacterales or Rhizobiales, were permanently present over the sampling period, while others, such as Sphingomonadales, Rhodospirillales or Caulobacterales appeared only transiently. The environmental factors that best explain the seasonal changes in AAP community were temperature, concentrations of oxygen and dissolved organic matter.
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Affiliation(s)
- Cristian Villena‐Alemany
- Laboratory of Anoxygenic PhototrophsInstitute of Microbiology of the Czech Academy of SciencesTřeboňCzechia
- Department of Ecosystem Biology, Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzechia
| | - Izabela Mujakić
- Laboratory of Anoxygenic PhototrophsInstitute of Microbiology of the Czech Academy of SciencesTřeboňCzechia
- Department of Ecosystem Biology, Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzechia
| | - Petr Porcal
- Department of Ecosystem Biology, Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzechia
- Department of Hydrochemistry and Ecosystem Modelling, Biology Centre of the Czech Academy of SciencesInstitute of HydrobiologyČeské BudějoviceCzechia
| | - Michal Koblížek
- Laboratory of Anoxygenic PhototrophsInstitute of Microbiology of the Czech Academy of SciencesTřeboňCzechia
- Department of Ecosystem Biology, Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzechia
| | - Kasia Piwosz
- Department of Fisheries Oceanography and Marine EcologyNational Marine Fisheries Research InstituteGdyniaPoland
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15
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Raiyani NM, Singh SP. Microbial community and predictive functionalities associated with the marine sediment of Coastal Gujarat. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:43245-43266. [PMID: 36650368 DOI: 10.1007/s11356-023-25196-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 01/04/2023] [Indexed: 01/19/2023]
Abstract
Marine sediments are complex ecosystems where structures and functions constantly change due to natural and anthropogenic influences. In this investigation, a comprehensive and comparative analysis of the bacterial communities and their functional potential of the pristine and polluted marine sediments were carried out using MiSeq. The phylum Proteobacteria was dominant in all study sites. Other phyla were Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Chloroflexi, Nitrospirae, Cyanobacteria, Verrucomicrobia, Tenericutes, and Chlorobi. Interestingly, about 50% of genera belong to the unclassified categories. The key genera were identified as Acinetobacter, Bacillus, Pseudomona, Idiomarina, Thalassospira, and Marinobacter, Halomonas, Planctomyces, Psychrobacter, and Vogesella. PICRUSt analysis revealed that major functions are associated with the metabolism category. Additionally, metabolism related to amino acids, carbohydrates, energy generation, xenobiotics degradation, nitrogen, sulfate, and methane were prominent. Similarly, the predicted metabolisms by COG and KEGG were observed in the microbial communities of the marine sediments. To date, a comprehensive description of the microbial life with metabolic potential in these study sites has not been investigated. This study therefore significantly adds to our understanding of the microbiome and its functional attributes of marine sediments.
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Affiliation(s)
- Nirali M Raiyani
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot, 360 005, Gujarat, India
| | - Satya P Singh
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot, 360 005, Gujarat, India.
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16
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Gaio J, Lora NL, Iltchenco J, Magrini FE, Paesi S. Seasonal characterization of the prokaryotic microbiota of full-scale anaerobic UASB reactors treating domestic sewage in southern Brazil. Bioprocess Biosyst Eng 2023; 46:69-87. [PMID: 36401655 DOI: 10.1007/s00449-022-02814-9] [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: 08/26/2022] [Accepted: 11/12/2022] [Indexed: 11/21/2022]
Abstract
Upflow Anaerobic Sludge Blanket (UASB) reactors are alternatives in the anaerobic treatment of sanitary sewage in different parts of the world; however, in temperate environments, they are subject to strong seasonal influence. Understanding the dynamics of the microbial community in these systems is essential to propose operational alternatives, improve projects and increase the quality of treated effluents. In this study, for one year, high-performance sequencing, associated with bioinformatics tools for taxonomic annotation and functional prediction was used to characterize the microbial community present in the sludge of biodigesters on full-scale, treating domestic sewage at ambient temperature. Among the most representative phyla stood out Desulfobacterota (20.21-28.64%), Proteobacteria (7.48-24.90%), Bacteroidota (10.05-18.37%), Caldisericota (9.49-17.20%), and Halobacterota (3.23-6.55%). By performing a Canonical Correspondence Analysis (CCA), Methanolinea was correlated to the efficiency in removing Chemical Oxygen Demand (COD), Bacteroidetes_VadinHA17 to the production of volatile fatty acids (VFAs), and CI75cm.2.12 at temperature. On the other hand, Desulfovibrio, Spirochaetaceae_uncultured, Methanosaeta, Lentimicrobiaceae_unclassified, and ADurb.Bin063-1 were relevant in shaping the microbial community in a co-occurrence network. Diversity analyses showed greater richness and evenness for the colder seasons, possibly, due to the lesser influence of dominant taxa. Among the principal metabolic functions associated with the community, the metabolism of proteins and amino acids stood out (7.74-8.00%), and the genes related to the synthesis of VFAs presented higher relative abundance for the autumn and winter. Despite the differences in diversity and taxonomic composition, no significant changes were observed in the efficiency of the biodigesters.
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Affiliation(s)
- Juliano Gaio
- Molecular Diagnostic Laboratory (LDM), Biotechnology Institute (IB), University of Caxias Do Sul (UCS), Caxias Do Sul, RS, 95070-560, Brazil.
| | - Naline Laura Lora
- Molecular Diagnostic Laboratory (LDM), Biotechnology Institute (IB), University of Caxias Do Sul (UCS), Caxias Do Sul, RS, 95070-560, Brazil
| | - Janaína Iltchenco
- Molecular Diagnostic Laboratory (LDM), Biotechnology Institute (IB), University of Caxias Do Sul (UCS), Caxias Do Sul, RS, 95070-560, Brazil
| | - Flaviane Eva Magrini
- Molecular Diagnostic Laboratory (LDM), Biotechnology Institute (IB), University of Caxias Do Sul (UCS), Caxias Do Sul, RS, 95070-560, Brazil
| | - Suelen Paesi
- Molecular Diagnostic Laboratory (LDM), Biotechnology Institute (IB), University of Caxias Do Sul (UCS), Caxias Do Sul, RS, 95070-560, Brazil
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17
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Rogers TJ, Buongiorno J, Jessen GL, Schrenk MO, Fordyce JA, de Moor JM, Ramírez CJ, Barry PH, Yücel M, Selci M, Cordone A, Giovannelli D, Lloyd KG. Chemolithoautotroph distributions across the subsurface of a convergent margin. THE ISME JOURNAL 2023; 17:140-150. [PMID: 36257972 PMCID: PMC9751116 DOI: 10.1038/s41396-022-01331-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 12/15/2022]
Abstract
Subducting oceanic crusts release fluids rich in biologically relevant compounds into the overriding plate, fueling subsurface chemolithoautotrophic ecosystems. To understand the impact of subsurface geochemistry on microbial communities, we collected fluid and sediments from 14 natural springs across a ~200 km transect across the Costa Rican convergent margin and performed shotgun metagenomics. The resulting 404 metagenome-assembled genomes (MAGs) cluster into geologically distinct regions based on MAG abundance patterns: outer forearc-only (25% of total relative abundance), forearc/arc-only (38% of total relative abundance), and delocalized (37% of total relative abundance) clusters. In the outer forearc, Thermodesulfovibrionia, Candidatus Bipolaricaulia, and Firmicutes have hydrogenotrophic sulfate reduction and Wood-Ljungdahl (WL) carbon fixation pathways. In the forearc/arc, Anaerolineae, Ca. Bipolaricaulia, and Thermodesulfovibrionia have sulfur oxidation, nitrogen cycling, microaerophilic respiration, and WL, while Aquificae have aerobic sulfur oxidation and reverse tricarboxylic acid carbon fixation pathway. Transformation-based canonical correspondence analysis shows that MAG distribution corresponds to concentrations of aluminum, iron, nickel, dissolved inorganic carbon, and phosphate. While delocalized MAGs appear surface-derived, the subsurface chemolithoautotrophic, metabolic, and taxonomic landscape varies by the availability of minerals/metals and volcanically derived inorganic carbon. However, the WL pathway persists across all samples, suggesting that this versatile, energy-efficient carbon fixation pathway helps shape convergent margin subsurface ecosystems.
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Affiliation(s)
| | - Joy Buongiorno
- Division of Natural Sciences, Maryville College, Maryville, TN, USA
| | - Gerdhard L Jessen
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
- Center for Oceanographic Research COPAS COASTAL, Universidad de Concepción, Valdivia, Chile
| | | | | | - J Maarten de Moor
- National University of Costa Rica, Heredia, Costa Rica
- University of New Mexico, Albuquerque, NM, USA
| | | | - Peter H Barry
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Mustafa Yücel
- Institute of Marine Sciences, Middle East Technical University, Erdemli, Turkey
| | - Matteo Selci
- Department of Biology, University of Naples -Federico II, Naples, Italy
| | - Angela Cordone
- Department of Biology, University of Naples -Federico II, Naples, Italy
| | - Donato Giovannelli
- Department of Biology, University of Naples -Federico II, Naples, Italy
- Department of Marine and Coastal Science, Rutgers University, Rutgers, NJ, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- National Research Council - Institute of Marine Biological Resources and Biotechnologies - CNR-IRBIM, Ancona, Italy
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18
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Xin Y, Wu N, Sun Z, Wang H, Chen Y, Xu C, Geng W, Cao H, Zhang X, Zhai B, Yan D. Methane seepage intensity distinguish microbial communities in sediments at the Mid-Okinawa Trough. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158213. [PMID: 36028040 DOI: 10.1016/j.scitotenv.2022.158213] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/14/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
Shallow methane/sulfate transition zones in cold seeps are hotspots to study microbially mediated geochemical cycles due to high methane fluxes. However, our knowledge about the microbial communities in remote seafloor cold seep ecosystems with different methane seepage intensity is still sparse due to the challenge for sampling and visual observations. In this work, three remotely operated vehicle (ROV) video-guided push sediment cores were sampled from cold seep fields with different methane seepage intensity (low-intensity seepage, R5-C1; moderate-intensity seepage, R6-C2; high-intensity seepage, R6-C3) at the western slope of Mid-Okinawa Trough (Mid-OT) and subjected to high throughput sequencing of 16S rRNA genes for bacteria and archaea. Vesicomyid clams and white microbial mats are visible by video at R6-C3 with methane bubbles. The high relative abundances of anaerobic methanotrophic archaea (ANME-1, -2, and -3), δ-Proteobacteriacea and Campylobacteria in R6-C3 indicated that the processes of anaerobic methane oxidation (AOM), sulfate reduction and sulfur oxidation might occur in this active seeping site. In contrast, Bathyarchaeia, Nitrosopumilales, Sphingomonadales, and Burkholderiales were enriched in bubble-free sites, which commonly involved in the degradation of organic compounds. Principal coordinate analysis showed that both bacterial and archaeal communities were clustered according to sampling sites, also indicating the impact of methane seepage intensity on microbial communities. The co-occurrence network analysis revealed that microbes at the site with high methane fluxes mainly cooperated with each other to sustain the ecosystems, whereas competition enhanced at sites with low methane fluxes. Detection of thermophiles Thermoanaerobaculia and Hydrothermarchaeota may indicate microbial transmission from nearby hydrothermal vents, suggesting potential interactions between cold seepage and hydrothermal vent ecosystems. These results expand our knowledge about the composition and distribution of bacteria and archaea with different methane seepage intensity in cold seep field at the Mid-OT, contributing to the ongoing efforts in understanding carbon cycling in the cold seep ecosystems.
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Affiliation(s)
- Youzhi Xin
- School of Earth Sciences, China University of Geosciences, Wuhan 430074, China; Laboratory of Marine Mineral Resources, Pilot National Laboratory of Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Qingdao Institute of Marine Geology, Qingdao 266237, China
| | - Nengyou Wu
- Laboratory of Marine Mineral Resources, Pilot National Laboratory of Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Qingdao Institute of Marine Geology, Qingdao 266237, China
| | - Zhilei Sun
- Laboratory of Marine Mineral Resources, Pilot National Laboratory of Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Qingdao Institute of Marine Geology, Qingdao 266237, China
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China.
| | - Ye Chen
- Laboratory of Marine Mineral Resources, Pilot National Laboratory of Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Qingdao Institute of Marine Geology, Qingdao 266237, China
| | - Cuiling Xu
- Laboratory of Marine Mineral Resources, Pilot National Laboratory of Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Qingdao Institute of Marine Geology, Qingdao 266237, China
| | - Wei Geng
- Laboratory of Marine Mineral Resources, Pilot National Laboratory of Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Qingdao Institute of Marine Geology, Qingdao 266237, China
| | - Hong Cao
- Laboratory of Marine Mineral Resources, Pilot National Laboratory of Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Qingdao Institute of Marine Geology, Qingdao 266237, China
| | - Xilin Zhang
- Laboratory of Marine Mineral Resources, Pilot National Laboratory of Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Qingdao Institute of Marine Geology, Qingdao 266237, China
| | - Bin Zhai
- Laboratory of Marine Mineral Resources, Pilot National Laboratory of Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Qingdao Institute of Marine Geology, Qingdao 266237, China
| | - Dawei Yan
- Laboratory of Marine Mineral Resources, Pilot National Laboratory of Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Qingdao Institute of Marine Geology, Qingdao 266237, China
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Yang C, Zeng Z, Zhang H, Gao D, Wang Y, He G, Liu Y, Wang Y, Du X. Distribution of sediment microbial communities and their relationship with surrounding environmental factors in a typical rural river, Southwest China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:84206-84225. [PMID: 35778666 DOI: 10.1007/s11356-022-21627-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
With rapid urbanization and industrialization, rural rivers in China are facing deterioration in water quality and ecosystem health. Microorganisms living in river sediments are involved in biogeochemical processes, mineralization, and degradation of pollutants. Understanding bacterial community distribution in rural rivers could help evaluate the response of river ecosystems to environmental pollution and understand the river self-purification mechanism. In this study, the relationship between characteristics of sediment microbial communities and the surrounding environmental factors in a typical rural river was analyzed using 16S rRNA gene sequencing technology. The results showed that the dominant bacterial groups in the river sediment were Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, and Firmicutes, accounting for 83.61% of the total microbial load. Different areas have different sources of pollution which give rise to specific dominant bacteria. The upstream part of the river flows through an agricultural cultivation area where the dominant bacteria were norank_f_Gemmatimonadaceae, Haliangium, and Pseudolabrys, possessing obvious nitrogen- and phosphorus-metabolizing activities. The midstream section flows through an urban area where the dominant bacteria were Marmoricola, Nocardioides, Gaiella, Sphingomonas, norank_f_67-14, Subgroup_10, Agromyces, and Lysobacter, with strong metabolizing activity for toxic pollutants. The dominant bacteria in the downstream part were Clostridium_sensu_stricto_1, norank_f__Bacteroidetes_vadinHA17, Candidatus_Competibacter, and Methylocystis. Redundancy analysis and correlation heatmap analysis showed that environmental factors: ammonia nitrogen (NH4+-N) and total nitrogen (TN) in the sediment, and pH, temperature, TN, electrical conductivity (EC), and total dissolved solids (TDS) in the water, significantly affected the bacterial community in the sediment. The PICRUSt2 functional prediction analysis identified that the main function of bacteria in the sediment was metabolism (77.3%), specifically carbohydrate, amino acid, and energy metabolism. These activities are important for degrading organic matter and removing pollutants from the sediments. The study revealed the influence of organic pollutants derived from human activities on the bacterial community composition in the river sediments. It gave a new insight into the relationship between environmental factors and bacterial community distribution in rural watershed ecosystems, providing a theoretical basis for self-purification and bioremediation of rural rivers.
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Affiliation(s)
- Cheng Yang
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, Chengdu, China
| | - Zhuo Zeng
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, Chengdu, China
| | - Han Zhang
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, Chengdu, China.
| | - Dongdong Gao
- Sichuan Academy of Environmental Science, Chengdu, China
| | - Yuanyuan Wang
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, Chengdu, China
| | - Guangyi He
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, Chengdu, China
| | - Ying Liu
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, Chengdu, China
| | - Yan Wang
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xinyu Du
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, Chengdu, China
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20
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Zhao B, Jiao C, Wang S, Zhao D, Jiang C, Zeng J, Wu QL. Contrasting assembly mechanisms explain the biogeographic patterns of benthic bacterial and fungal communities on the Tibetan Plateau. ENVIRONMENTAL RESEARCH 2022; 214:113836. [PMID: 35810809 DOI: 10.1016/j.envres.2022.113836] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 06/22/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
The Tibetan Plateau characterized by high altitude and low temperature, where a great number of lakes are located, is a hotspot of global biodiversity research. Both bacterial and fungal communities are vital participants of biogeochemical cycling in lake ecosystems. However, we know very little about the large-scale biogeographic patterns and the underlying assembly mechanisms of lake benthic microbial communities on the Tibetan Plateau. To investigate the biogeographic patterns and their underlying assembly mechanisms of benthic bacterial and fungal communities, we collected sediment samples from 11 lakes on the Tibetan Plateau (maximum geographic distance between lakes over 1100 km). Benthic community diversity and composition were determined using the high-throughput sequencing technique. Our results indicated that there were contrasting distance-decay relationships between benthic bacterial and fungal communities on a regional scale. Benthic bacterial communities showed a significant distance-decay relationship, whereas no significant relationship was observed for benthic fungal communities. Deterministic processes dominated the bacterial community assembly, whereas fungal community assembly was more stochastic. pH was a dominant factor in influencing the geographic distribution of benthic microbial communities. Co-occurrence network analysis revealed that bacterial communities showed higher complexity and greater stability than those of the fungal communities. Taken together, this study contributes to a novel understanding of the assembly mechanisms underlying the biogeographic distribution of plateau benthic bacterial and fungal communities at a large scale.
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Affiliation(s)
- Baohui Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
| | - Congcong Jiao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Shuren Wang
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
| | - Cuiling Jiang
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Qinglong L Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, 100049, China
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21
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Response of Carbon Emissions and the Bacterial Community to Freeze-Thaw Cycles in a Permafrost-Affected Forest-Wetland Ecotone in Northeast China. Microorganisms 2022; 10:microorganisms10101950. [PMID: 36296226 PMCID: PMC9609725 DOI: 10.3390/microorganisms10101950] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/21/2022] [Accepted: 09/27/2022] [Indexed: 11/07/2022] Open
Abstract
Climate warming can affect freeze–thaw cycle (FTCs) patterns in northern high-latitude regions and may affect permafrost carbon emissions. The response of carbon release and microbial communities to FTCs has not been well characterized. Here, we conducted laboratory incubation experiments to investigate the relationships among carbon emissions, bacterial community, and soil variables in a permafrost-affected forest–wetland ecotone in Northeast China. The emission rates of CO2 and CH4 increased during the FTCs. FTC amplitude, FTC frequency, and patch type had significant effects on carbon emissions. FTCs increased the contents of soil DOC, NH4+-N, and NO3−-N but reduced bacterial alpha diversity. CO2 emissions were mainly affected by bacterial alpha diversity and composition, and the inorganic nitrogen content was the important factor affecting CH4 emissions. Our findings indicated that FTCs could significantly regulate CO2 and CH4 emissions by reducing bacterial community diversity and increasing the concentration of available soil substrates. Our findings shed new light on the microorganism-substrate mechanisms regulating the response patterns of the soil carbon cycle to FTCs in permafrost regions.
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22
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Xu B, Yang X, Li Y, Yang K, Xiong Y, Yuan N. Pyrite-Based Autotrophic Denitrifying Microorganisms Derived from Paddy Soils: Effects of Organic Co-Substrate Addition. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:11763. [PMID: 36142037 PMCID: PMC9517464 DOI: 10.3390/ijerph191811763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
The presence of organic co-substrate in groundwater and soils is inevitable, and much remains to be learned about the roles of organic co-substrates during pyrite-based denitrification. Herein, an organic co-substrate (acetate) was added to a pyrite-based denitrification system, and the impact of the organic co-substrate on the performance and bacterial community of pyrite-based denitrification processes was evaluated. The addition of organic co-substrate at concentrations higher than 48 mg L-1 inhibited pyrite-based autotrophic denitrification, as no sulfate was produced in treatments with high organic co-substrate addition. In contrast, both competition and promotion effects on pyrite-based autotrophic denitrification occurred with organic co-substrate addition at concentrations of 24 and 48 mg L-1. The subsequent validation experiments suggested that competition had a greater influence than promotion when organic co-substrate was added, even at a low concentration. Thiobacillus, a common chemolithoautotrophic sulfur-oxidizing denitrifier, dominated the system with a relative abundance of 13.04% when pyrite served as the sole electron donor. With the addition of organic co-substrate, Pseudomonas became the dominant genus, with 60.82%, 61.34%, 70.37%, 73.44%, and 35.46% abundance at organic matter concentrations of 24, 48, 120, 240, and 480 mg L-1, respectively. These findings provide an important theoretical basis for the cultivation of pyrite-based autotrophic denitrifying microorganisms for nitrate removal in soils and groundwater.
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Affiliation(s)
- Baokun Xu
- Agricultural Water Conservancy Department, Changjiang River Scientific Research Institute, Wuhan 430010, China
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan 430072, China
- Key Laboratory of River Regulation and Flood Control of Ministry of Water Resources, Changjiang River Scientific Research Institute, Wuhan 430010, China
| | - Xiaoxia Yang
- Chongqing Water Resources Bureau, Chongqing 401147, China
| | - Yalong Li
- Agricultural Water Conservancy Department, Changjiang River Scientific Research Institute, Wuhan 430010, China
| | - Kejun Yang
- School of Law, Zhongnan University of Economics and Law, Wuhan 430073, China
- Agricultural and Rural Department of Hubei Province, Wuhan 430070, China
| | - Yujiang Xiong
- Agricultural Water Conservancy Department, Changjiang River Scientific Research Institute, Wuhan 430010, China
| | - Niannian Yuan
- Agricultural Water Conservancy Department, Changjiang River Scientific Research Institute, Wuhan 430010, China
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Zhang Y, Zhang Y, Wei L, Li M, Zhu W, Zhu L. Spatiotemporal correlations between water quality and microbial community of typical inflow river into Taihu Lake, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:63722-63734. [PMID: 35460482 DOI: 10.1007/s11356-022-19023-2] [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: 10/12/2021] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
Changxing River, which is a typical inflow river into Taihu Lake and occurs severe algae invasion, is selected to study the effect of different pollution sources on the water quality and ecological system. Four types of pollution sources, including the estuary of Taihu Lake, discharge outlets of urban wastewater treatment plants, stormwater outlets, and nonpoint source agricultural drainage areas, were chosen, and next-generation sequencing and multivariate statistical analyses were used to characterize the microbial communities and reveal their relationship with water physicochemical properties. The results showed that ammonia nitrogen (NH4+-N), total nitrogen (TN), and total phosphorus (TP) were the main pollutants in Changxing River, especially at stormwater outlets. At the same time, the diversity of microbial communities was the highest in the summer, and dominant microbes included Proteobacteria (40.9%), Bacteroidetes (21.0%), and Euryarchaeota (6.1%). The results of BIOENV analysis showed that the major seasonal differences in the diversity of microbial community of Changxing river were explained by the combination of water temperature (T), air pressure (P), TP, and CODMn. From the perspective of different pollution types, relative abundances of Microcystis and Nostocaceae at the estuary of Taihu Lake were correlated positively with dissolved oxygen (DO) and pH, and relative abundances of Pseudomonas and Arcobacter were correlated positively with concentrations of TN and nitrate nitrogen (NO3--N) at stormwater outlets. This study provided a reference for the impact of pollution types on river microbial ecosystem under complex hydrological conditions and guidance for the selection of restoration techniques for polluted rivers entering the important lake.
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Affiliation(s)
- Yajie Zhang
- Institute of Environmental Pollution Control and Treatment, Zhejiang University, Hangzhou, 310058, China
| | - Ye Zhang
- Institute of Environmental Pollution Control and Treatment, Zhejiang University, Hangzhou, 310058, China
| | - Lecheng Wei
- Institute of Environmental Pollution Control and Treatment, Zhejiang University, Hangzhou, 310058, China
| | - Mengyan Li
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, 07102, USA
| | - Weitang Zhu
- Environmental Protection Bureau of Changxing County, Huzhou, 313100, China
| | - Liang Zhu
- Institute of Environmental Pollution Control and Treatment, Zhejiang University, Hangzhou, 310058, China.
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, 310058, China.
- Zhejiang Provincial Engineering Laboratory of Water Pollution Control, Hangzhou, 310058, China.
- Department of Environmental Engineering, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, People's Republic of China.
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24
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Lopez S, Morel JL, Benizri E. The parameters determining hyperaccumulator rhizobacteria diversity depend on the study scale. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 834:155274. [PMID: 35452722 DOI: 10.1016/j.scitotenv.2022.155274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/23/2022] [Accepted: 04/10/2022] [Indexed: 06/14/2023]
Abstract
Soils harbor some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. Numerous parameters, intrinsic to plant physiology, life history and the soil itself, can influence the structure of rhizomicrobial communities. While our knowledge of rhizosphere microbial diversity is increasing, opinion is divided as to whether the factors that most impact this diversity are abiotic, climatic or plant selection. Here we focused on the rhizosphere bacterial diversity of nickel hyperaccumulator plants (28 species from Mediterranean or tropical climates). We showed, by leveraging 16S Illumina sequencing of 153 ultramafic rhizosphere soils, that bacterial genetic diversity was highest in Mediterranean habitats where plant diversity was the lowest. Concerning those parameters driving this diversity, we demonstrated that climate drives bacterial diversity, in particular with the annual temperature variation. Focusing on each region, we underlined the substantial role of soil physicochemical parameters. Our results highlight the importance of considering spatial scale when explaining bacterial community diversity.
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Affiliation(s)
- Séverine Lopez
- INRAE, Bordeaux Sciences Agro, ISVV, SAVE, F-33140 Villenave d'Ornon, France; Université de Lorraine, INRAE, Laboratoire Sols et Environnement, 54000 Nancy, France
| | - Jean Louis Morel
- Université de Lorraine, INRAE, Laboratoire Sols et Environnement, 54000 Nancy, France
| | - Emile Benizri
- Université de Lorraine, INRAE, Laboratoire Sols et Environnement, 54000 Nancy, France.
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25
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Cardenas Gomez K, Rose A, Gibb KS, Christian KA. Microbial communities associated with mounds of the Orange-footed scrubfowl Megapodius reinwardt. PeerJ 2022; 10:e13600. [PMID: 35910771 PMCID: PMC9332330 DOI: 10.7717/peerj.13600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 05/26/2022] [Indexed: 01/17/2023] Open
Abstract
Megapodius reinwardt, the orange-footed scrubfowl, belongs to a small family of birds that inhabits the Indo-Australian region. Megapodes are unique in incubating their eggs in mounds using heat from microbial decomposition of organic materials and solar radiation. Little is known about the microorganisms involved in the decomposition of organic matter in mounds. To determine the source of microbes in the mounds, we used 16S and 18S rRNA gene sequencing to characterize the microbial communities of mound soil, adjacent soil and scrubfowl faeces. We found that the microbial communities of scrubfowl faeces were substantially different from those of the mounds and surrounding soils, suggesting that scrubfowls probably do not use their faeces to inoculate their mounds although a few microbial sequence variants were present in both faeces and mound samples. Further, the mound microbial community structure was significantly different to the adjacent soils. For example, mounds had a high relative abundance of sequence variants belonging to Thermomonosporaceae, a thermophilic soil bacteria family able to degrade cellulose from plant residues. It is not clear whether members of Thermomonosporaceae disproportionately contribute to the generation of heat in the mound, or whether they simply thrive in the warm mound environment created by the metabolic activity of the mound microbial community. The lack of clarity in the literature between designations of heat-producing (thermogenic) and heat-thriving (thermophilic) microbes poses a challenge to understanding the role of specific bacteria and fungi in incubation.
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26
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Oshiki M, Takaki Y, Hirai M, Nunoura T, Kamigaito A, Okabe S. Metagenomic Analysis of Five Phylogenetically Distant Anammox Bacterial Enrichment Cultures. Microbes Environ 2022; 37. [PMID: 35811137 PMCID: PMC9530715 DOI: 10.1264/jsme2.me22017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria are slow-growing and fastidious bacteria, and limited numbers of enrichment cultures have been established. A metagenomic analysis of our 5 established anammox bacterial enrichment cultures was performed in the present study. Fourteen high-quality metagenome-assembled genomes (MAGs) were obtained, including those of 5 anammox Planctomycetota (Candidatus Brocadia, Ca. Kuenenia, Ca. Jettenia, and Ca. Scalindua), 4 Bacteroidota, and 3 Chloroflexota. Based on the gene sets of metabolic pathways involved in the degradation of polymeric substances found in Chloroflexota and Bacteroidota MAGs, they are expected to be scavengers of extracellular polymeric substances and cell debris.
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Affiliation(s)
- Mamoru Oshiki
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Miho Hirai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), JAMSTEC
| | - Atsushi Kamigaito
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University
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27
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Hellman M, Valhondo C, Martínez-Landa L, Carrera J, Juhanson J, Hallin S. Nitrogen Removal Capacity of Microbial Communities Developing in Compost- and Woodchip-Based Multipurpose Reactive Barriers for Aquifer Recharge With Wastewater. Front Microbiol 2022; 13:877990. [PMID: 35685927 PMCID: PMC9171435 DOI: 10.3389/fmicb.2022.877990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/21/2022] [Indexed: 12/04/2022] Open
Abstract
Global water supplies are threatened by climate changes and the expansion of urban areas, which have led to an increasing interest in nature-based solutions for water reuse and reclamation. Reclaimed water is a possible resource for recharging aquifers, and the addition of an organic reactive barrier has been proposed to improve the removal of pollutants. There has been a large focus on organic pollutants, but less is known about multifunctional barriers, that is, how barriers also remove nutrients that threaten groundwater ecosystems. Herein, we investigated how compost- and woodchip-based barriers affect nitrogen (N) removal in a pilot soil aquifer treatment facility designed for removing nutrients and recalcitrant compounds by investigating the composition of microbial communities and their capacity for N transformations. Secondary-treated, ammonium-rich wastewater was infiltrated through the barriers, and the changes in the concentration of ammonium, nitrate, and dissolved organic carbon (DOC) were measured after passage through the barrier during 1 year of operation. The development and composition of the microbial community in the barriers were examined, and potential N-transforming processes in the barriers were quantified by determining the abundance of key functional genes using quantitative PCR. Only one barrier, based on compost, significantly decreased the ammonium concentration in the infiltrated water. However, the reduction of reactive N in the barriers was moderate (between 21 and 37%), and there were no differences between the barrier types. All the barriers were after 1 year dominated by members of Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria, although the community composition differed between the barriers. Bacterial classes belonging to the phylum Chloroflexi showed an increased relative abundance in the compost-based barriers. In contrast to the increased genetic potential for nitrification in the compost-based barriers, the woodchip-based barrier demonstrated higher genetic potentials for denitrification, nitrous oxide reduction, and dissimilatory reduction of nitrate to ammonium. The barriers have previously been shown to display a high capacity to degrade recalcitrant pollutants, but in this study, we show that most barriers performed poorly in terms of N removal and those based on compost also leaked DOC, highlighting the difficulties in designing barriers that satisfactorily meet several purposes.
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Affiliation(s)
- Maria Hellman
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- *Correspondence: Maria Hellman,
| | - Cristina Valhondo
- Institute of Environmental Assessment and Water Research (IDAEA), CSIC, Barcelona, Spain
- Associate Unit, Hydrogeology Group (UPC-CSIC), Barcelona, Spain
| | - Lurdes Martínez-Landa
- Associate Unit, Hydrogeology Group (UPC-CSIC), Barcelona, Spain
- Department of Civil and Environmental Engineering, Universitat Politècnica de Catalunya (UPC), Barcelona, Spain
| | - Jesús Carrera
- Institute of Environmental Assessment and Water Research (IDAEA), CSIC, Barcelona, Spain
- Associate Unit, Hydrogeology Group (UPC-CSIC), Barcelona, Spain
| | - Jaanis Juhanson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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28
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Characterization of the First Cultured Representative of " Candidatus Thermofonsia" Clade 2 within Chloroflexi Reveals Its Phototrophic Lifestyle. mBio 2022; 13:e0028722. [PMID: 35229635 PMCID: PMC8941918 DOI: 10.1128/mbio.00287-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
“Candidatus Thermofonsia” represents a novel class within the phylum Chloroflexi. Metagenomic analysis reveals “Ca. Thermofonsia” harbors phototrophs outside the classically phototrophic Chloroflexia class. Unfortunately, the paucity of pure cultures limits further insights into their potential phototrophy. Here, we report the successful isolation of a “Ca. Thermofonsia” representative (Phototrophicus methaneseepsis ZRK33) from a deep-sea cold seep. Using combined physiological, genomic, and transcriptomic methods, we further show the long-wavelength light (e.g., red and infrared light) could promote the growth of strain ZRK33 and upregulate the expression of genes associated with phototrophy. In particular, strain ZRK33 has a typical phototrophic lifestyle under both laboratory and deep-sea conditions. Strain ZRK33 also possesses the ability to fix inorganic carbon through the 3-hydroxypropionate bicycle in both laboratory and deep-sea in situ environments, and the combined autotrophic, phototrophic, and heterotrophic capabilities endow strain ZRK33 with a photomixotrophic lifestyle. Notably, the predicted genes associated with phototrophy broadly exist in the metagenomes of 27 deep-sea Chloroflexi members, strongly suggesting diverse phototrophic Chloroflexi members are distributed in various unexplored deep biospheres.
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29
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Zhang H, Yang L, Li Y, Wang C, Zhang W, Wang L, Niu L. Pollution gradients shape the co-occurrence networks and interactions of sedimentary bacterial communities in Taihu Lake, a shallow eutrophic lake. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 305:114380. [PMID: 34995945 DOI: 10.1016/j.jenvman.2021.114380] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/30/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
The co-occurrence networks and interactions of bacterial communities in sediments are highly variable with environmental factors, which are vital to the nutrient biogeochemical cycle, pollutants biodegradation, and microbial community stability in lake ecosystems. Although pollution gradients reflect environmental variation comprehensively, few studies have characterized the changes in co-occurrence networks and interactions of bacterial communities along sediment pollution gradients. In order to investigate the impact of pollution gradients on compositions, co-occurrence networks, and interactions of sedimentary microbial communities, we studied the bacterial communities in the sediments of a typical shallow eutrophic lake, Taihu Lake, along pollution gradients using 16S rRNA gene high-throughput sequencing technology. All the sediment sampling sites were classified into mild, moderate, and severe pollution groups according to the sediments' physicochemical properties. Our results showed that the taxon richness was lowest in the severe pollution group, and the diversity of species decreased with the level of pollution. The complexity of the co-occurrence network decreased as the level of pollution increased, and the severe pollution group was characterized by a small-world network. The relative abundance of Proteobacteria, Bacteroidetes, and Chlorobi increased significantly as the level of pollution increased (P < 0.05). Strong inter-phyla co-occurrence or co-exclusion patterns demonstrated that the strength of interactions was enhanced in the severe pollution group, indicating stronger cooperative or competitive relationships. Chloroflexales and Chlorobiales were unique keystone taxa in the severe pollution group. The results of this study indicate that severe pollution reduces microbial diversity and network complexity, which may lead to community instability. The competition for nutrients of some copiotrophic bacteria may be enhanced as the level of pollution increased. The unique keystone taxa may contribute to photosynthesis and pollutant degradation in the severe pollution group. These findings expand our understanding of variation in bacterial co-occurrence networks and interactions along sediment pollution gradients.
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Affiliation(s)
- Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Liu Yang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China.
| | - Chao Wang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, PR China.
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
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Rakitin AL, Begmatov S, Beletsky AV, Philippov DA, Kadnikov VV, Mardanov AV, Dedysh SN, Ravin NV. Highly Distinct Microbial Communities in Elevated Strings and Submerged Flarks in the Boreal Aapa-Type Mire. Microorganisms 2022; 10:microorganisms10010170. [PMID: 35056619 PMCID: PMC8778904 DOI: 10.3390/microorganisms10010170] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 02/04/2023] Open
Abstract
Large areas in the northern hemisphere are covered by extensive wetlands, which represent a complex mosaic of raised bogs, eutrophic fens, and aapa mires all in proximity to each other. Aapa mires differ from other types of wetlands by their concave surface, heavily watered by the central part, as well as by the presence of large-patterned string-flark complexes. In this paper, we characterized microbial diversity patterns in the surface peat layers of the neighboring string and flark structures located within the mire site in the Vologda region of European North Russia, using 16S rRNA gene sequencing. The microbial communities in raised strings were clearly distinct from those in submerged flarks. Strings were dominated by the Alpha- and Gammaproteobacteria. Other abundant groups were the Acidobacteriota, Bacteroidota, Verrucomicrobiota, Actinobacteriota, and Planctomycetota. Archaea accounted for only 0.4% of 16S rRNA gene sequences retrieved from strings. By contrast, they comprised about 22% of all sequences in submerged flarks and mostly belonged to methanogenic lineages. Methanotrophs were nearly absent. Other flark-specific microorganisms included the phyla Chloroflexi, Spirochaetota, Desulfobacterota, Beijerinckiaceae- and Rhodomicrobiaceae-affiliated Alphaproteobacteria, and uncultivated groups env.OPS_17 and vadinHA17 of the Bacteroidota. Such pattern probably reflects local anaerobic conditions in the submerged peat layers in flarks.
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Affiliation(s)
- Andrey L. Rakitin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.L.R.); (S.B.); (A.V.B.); (V.V.K.); (A.V.M.)
| | - Shahjahon Begmatov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.L.R.); (S.B.); (A.V.B.); (V.V.K.); (A.V.M.)
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.L.R.); (S.B.); (A.V.B.); (V.V.K.); (A.V.M.)
| | - Dmitriy A. Philippov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, 152742 Borok, Russia;
| | - Vitaly V. Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.L.R.); (S.B.); (A.V.B.); (V.V.K.); (A.V.M.)
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.L.R.); (S.B.); (A.V.B.); (V.V.K.); (A.V.M.)
| | - Svetlana N. Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia;
| | - Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.L.R.); (S.B.); (A.V.B.); (V.V.K.); (A.V.M.)
- Correspondence: or
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Vipindas PV, Jabir T, Rahiman KMM, Rehitha TV, Sudheesh V, Jesmi Y, Hatha AAM. Impact of anthropogenic organic matter on bacterial community distribution in the continental shelf sediments of southeastern Arabian Sea. MARINE POLLUTION BULLETIN 2022; 174:113227. [PMID: 34883441 DOI: 10.1016/j.marpolbul.2021.113227] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/24/2021] [Accepted: 11/27/2021] [Indexed: 06/13/2023]
Abstract
The objective of this study was to understand the influence of anthropogenic organic matter on the spatial distribution microbial community in the continental shelf sediments of the Southeastern Arabian Sea (SEAS). The sediment samples were taken from the inner shelf (30 m depths) and outer shelf (100-200 m). The C:Nmolar ratio of the sediment displayed a significant variation between the inner and outer shelf and a higher terrestrial organic input in the inner shelf. Microbial community composition also showed a significant variation between the inner and outer shelf (p ≤ 0.05). Proteobacteria was the dominant phylum in the outer shelf sediments (42.5%), whereas Desulfobacterota (21.9%) was the dominant phylum in the inner shelf. Complex terrestrial organic matter degrading bacteria dominated the inner shelf, whereas oligophilic microbial community and autochthonous organic matter utilizing bacteria dominated the outer shelf. Thus the source of organic matter controlled the microbial distribution in the SEAS.
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Affiliation(s)
- P V Vipindas
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala 682016, India.
| | - T Jabir
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala 682016, India
| | - K M Mujeeb Rahiman
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala 682016, India
| | - T V Rehitha
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala 682016, India
| | - V Sudheesh
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala 682016, India
| | - Y Jesmi
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala 682016, India
| | - A A Mohamed Hatha
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi, Kerala 682016, India.
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Basili M, Campanelli A, Frapiccini E, Luna GM, Quero GM. Occurrence and distribution of microbial pollutants in coastal areas of the Adriatic Sea influenced by river discharge. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 285:117672. [PMID: 34380232 DOI: 10.1016/j.envpol.2021.117672] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 06/21/2021] [Accepted: 06/27/2021] [Indexed: 06/13/2023]
Abstract
The transport of a variety of pollutants from agricultural, industrial and urbanised areas makes rivers major contributors to the contamination of coastal marine environments. Too little is known of their role in carrying pathogens to the coast. We used DNA-based metabarcoding data to describe the microbial community composition in seawater and sediment collected in front of the estuary of the Tronto, the Chienti and the Esino, three Italian rivers with different pollution levels that empty into the north-central Adriatic Sea, and to detect and measure within these communities the relative abundance of microbial pollutants, including traditional faecal indicators and alternative faecal and sewage-associated pollutants. We then applied the FORENSIC algorithm to distinguish human from non-human sources of microbial pollution and FAPROTAX to map prokaryotic clades to established metabolic or other ecologically relevant functions. Finally, we searched the dataset for other common pathogenic taxa. Seawater and sediment contained numerous potentially pathogenic bacteria, mainly faecal and sewage-associated. The samples collected in front of the Tronto estuary showed the highest level of contamination, likely sewage-associated. The pathogenic signature showed a weak but positive correlation with some nutrients and strong correlations with some polycyclic aromatic hydrocarbons. This study confirms that rivers transport pathogenic bacteria to the coastal sea and highlights the value of expanding the use of HTS data, source tracking and functional identification tools to detect microbial pollutants and identify their sources with a view to gaining a better understanding of the pathways of sewage-associated discharges to the sea.
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Affiliation(s)
- Marco Basili
- Institute of Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy
| | - Alessandra Campanelli
- Institute of Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy
| | - Emanuela Frapiccini
- Institute of Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy
| | - Gian Marco Luna
- Institute of Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy
| | - Grazia Marina Quero
- Institute of Marine Biological Resources and Biotechnologies, National Research Council (CNR-IRBIM), Ancona, Italy.
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Ex and In Situ Reactivity and Sorption of Selenium in Opalinus Clay in the Presence of a Selenium Reducing Microbial Community. MINERALS 2021. [DOI: 10.3390/min11070757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
79Se is a critical radionuclide concerning the safety of deep geological disposal of certain radioactive wastes in clay-rich formations. To study the fate of selenium oxyanions in clayey rocks in the presence of a selenium reducing microbial community, in situ tests were performed in the Opalinus Clay at the Mont Terri Rock Laboratory (Switzerland). Furthermore, biotic and abiotic batch tests were performed to assess Se(VI) and Se(IV) reactivity in the presence of Opalinus Clay and/or stainless steel, in order to support the interpretation of the in situ tests. Geochemical modeling was applied to simulate Se(VI) reduction, Se(IV) sorption and solubility, and diffusion processes. This study shows that microbial activity is required to transform Se(VI) into more reduced and sorbing Se species in the Opalinus Clay, while in abiotic conditions, Se(VI) remains unreactive. On the other hand, Se(IV) can be reduced by microorganisms but can also sorb in the presence of clay without microorganisms. In situ microbial reduction of Se oxyanions can occur with electron donors provided by the clay itself. If microorganisms would be active in the clay surrounding a disposal facility, microbial reduction of leached Se could thus contribute to the overall retention of Se in clayey host rocks.
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Khatami K, Atasoy M, Ludtke M, Baresel C, Eyice Ö, Cetecioglu Z. Bioconversion of food waste to volatile fatty acids: Impact of microbial community, pH and retention time. CHEMOSPHERE 2021; 275:129981. [PMID: 33662716 DOI: 10.1016/j.chemosphere.2021.129981] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/23/2020] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Bio-based production of materials from waste streams is a pivotal aspect in a circular economy. This study aimed to investigate the influence of inoculum (three different sludge taken from anaerobic digestors), pH (5 & 10) and retention time on production of total volatile fatty acids (VFAs), VFA composition as well as the microbial community during anaerobic digestion of food waste. The highest VFA production was ∼22000 ± 1036 mg COD/L and 12927 ± 1029 mg COD/L on day 15 using the inoculum acclimated to food waste at pH 10 and pH 5, respectively. Acetic acid was the dominant VFA in the batch reactors with initial alkaline conditions, whereas both propionic and acetic acids were the dominant products in the acidic condition. Firmicutes, Chloroflexi and Bacteroidetes had the highest relative abundance in the reactors. VFA generation was positively correlated to the relative abundance of Firmicutes.
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Affiliation(s)
- Kasra Khatami
- Department of Chemical Engineering, KTH Royal Institute of Technology, Stockholm, SE100 44, Sweden.
| | - Merve Atasoy
- Department of Chemical Engineering, KTH Royal Institute of Technology, Stockholm, SE100 44, Sweden.
| | - Maximilian Ludtke
- Department of Chemical Engineering, KTH Royal Institute of Technology, Stockholm, SE100 44, Sweden; IVL Swedish Environmental Research Institute, Stockholm, Sweden.
| | | | - Özge Eyice
- School of Biological and Chemical Sciences, Queen Mary University of London, E1 4NS, UK.
| | - Zeynep Cetecioglu
- Department of Chemical Engineering, KTH Royal Institute of Technology, Stockholm, SE100 44, Sweden.
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Yin Z, Yang X, Wang X, Wang S. Effects of operating conditions on microbial consortium of the heterotrophic ammonia oxidation process. BIORESOURCE TECHNOLOGY 2021; 328:124823. [PMID: 33592544 DOI: 10.1016/j.biortech.2021.124823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 06/12/2023]
Abstract
This study aimed to investigate the ammonia removal by the consortium mainly comprising of ammonia-oxidizing bacteria under different initial pH, temperatures and stress of heavy metals. The results showed that the consortium exhibited a strong adaptation for broad pH ranging from 5 to 9. When the temperature dropped to 15℃, its ammonium removal and nitrate accumulation rates decreased by 72.23% and 95.12%, respectively. Meanwhile, the temperature correction coefficients of the ammonium removal and nitrate accumulation rates reached the maximum. In addition, the consortium could survive in the solutions containing 0-1.0 mg·L-1 Cu2+ and 0-5.0 mg·L-1 Fe3+. Moreover, the inhibition of free nitrous acid (FNA) against nitrite oxidation activity was found to be much more significant than that low-temperature treatment. Microbial diversity analysis showed that the bacterial community structure was shift significantly by the temperature drop, especially change the abundance of Nitrosomonas, Paracoccus, Pseudomonas and Nitrospirae.
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Affiliation(s)
- Zhikai Yin
- Department of Environmental Science and Engineering, Fudan University, 2005 Songhu Road, Shanghai 200433, PR China
| | - Xiaolong Yang
- Department of Environmental Science and Engineering, Fudan University, 2005 Songhu Road, Shanghai 200433, PR China
| | - Xingyu Wang
- Department of Environmental Science and Engineering, Fudan University, 2005 Songhu Road, Shanghai 200433, PR China
| | - Shoubing Wang
- Department of Environmental Science and Engineering, Fudan University, 2005 Songhu Road, Shanghai 200433, PR China.
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36
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Quach NT, Dam HT, Tran DM, Vu THN, Nguyen QV, Nguyen KT, Nguyen QH, Phi CB, Le TH, Chu HH, Thuoc Doan V, Shyu DJH, Kang H, Li WJ, Phi QT. Diversity of microbial community and its metabolic potential for nitrogen and sulfur cycling in sediments of Phu Quoc island, Gulf of Thailand. Braz J Microbiol 2021; 52:1385-1395. [PMID: 33856662 DOI: 10.1007/s42770-021-00481-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 03/29/2021] [Indexed: 11/29/2022] Open
Abstract
Although Phu Quoc island, Gulf of Thailand possesses diverse marine and coastal ecosystems, biodiversity and metabolic capability of microbial communities remain poorly investigated. The aim of our study was to evaluate the biodiversity and metabolic potential of sediment microbial communities in Phu Quoc island. The marine sediments were collected from three different areas and analyzed by using 16S rRNA gene-based amplicon approach. A total of 1,143,939 reads were clustered at a 97% sequence similarity into 8,331 unique operational taxonomic units, representing 52 phyla. Bacteria and archaea occupied averagely around 86% and 14%, respectively, of the total prokaryotic community. Proteobacteria, Planctomycetes, Chloroflexi, and Thaumarchaeota were the dominant phyla in all sediments, which were involved in nitrogen and sulfur metabolism. Sediments harboring of higher nitrogen sources were found to coincide with increased abundance of archaeal phylum Thaumarchaeota. Predictive functional analysis showed high abundance prokaryotic genes associated with nitrogen cycling including nifA-Z, amoABC, nirA, narBIJ, napA, nxrAB, nrfA-K, nirBD, nirS, nirK, norB-Z, nlnA, ald, and ureA-J, based on taxonomic groups detected by 16S rRNA sequencing. Although the key genes involved in sulfur cycling were found to be at low to undetectable levels, the other genes encoding for sulfur-related biological processes were present, suggesting that alternative pathways may be involved in sulfur cycling at our study site. In conclusion, our study for the first time shed light on diversity of microbial communities in Phu Quoc island.
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Affiliation(s)
- Ngoc Tung Quach
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam
| | - Hang Thuy Dam
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Hanoi, 10000, Vietnam
| | - Dinh Man Tran
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam.
| | - Thi Hanh Nguyen Vu
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam
| | - Quoc Viet Nguyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam
| | - Kim Thoa Nguyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam
| | - Quang Huy Nguyen
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam
| | | | - Thanh Ha Le
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Hanoi, 10000, Vietnam
| | - Hoang Ha Chu
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam
| | - Van Thuoc Doan
- Hanoi National University of Education, Hanoi, 10000, Vietnam
| | - Douglas J H Shyu
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan
| | - Heonjoong Kang
- School of Earth and Environmental Sciences, College of Natural Sciences, Seoul National University NS80, Seoul, 08826, Korea
| | - Wen-Jun Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Quyet Tien Phi
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam. .,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, 10000, Vietnam.
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Jin Y, Zhang B, Chen J, Mao W, Lou L, Shen C, Lin Q. Biofertilizer-induced response to cadmium accumulation in Oryza sativa L. grains involving exogenous organic matter and soil bacterial community structure. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 211:111952. [PMID: 33513523 DOI: 10.1016/j.ecoenv.2021.111952] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 11/25/2020] [Accepted: 01/14/2021] [Indexed: 06/12/2023]
Abstract
The accumulation of cadmium (Cd) in Oryza sativa L., the world's most significant staple crop, is a health threat to millions of people. The objective of this study was to evaluate the effectiveness of commercially available biofertilizers (with high (BF2) and low organic matter (OM) content (BF1)) on Cd accumulation in two types of soils and to determine the bacterial community responses by high-throughput sequencing. The study was conducted in the form of pot experiment in greenhouse in 2018. Four treatments were set: BF1, BF2, organic fertilizer (OF), and control (CK) and the amendments were applied before the rice cultivation. The results showed that the addition of biofertilizers immobilized or mobilized Cd in soils, depending on the soil type and the OM content in biofertilizers. The exogenous OM in biofertilizers was the driving factor for the difference in pH and Cd accumulation in rice grains. The application of biofertilizers with high OM content was effective in reducing Cd accumulation in the rice grains (19.7% lower than CK) by significantly increasing soil pH (from 6.02 to 6.67) in acid silt loam soil (TZ). The consumption of acid fermentation products by soil chemoorganotrophs and the complexation of organic anions in the biofertilizer treatment tended to buffer the pH drop in the drainage and decrease the Cd availability. However, in the weak acid silty clay loam soil (SX), the addition of biofertilizer with high OM significantly increased Cd accumulation in rice grains (21.9% higher than CK), probably owing to the release of acid substances, resulting from the significant increase of the predominant bacteria Chloroflexi. The addition of biofertilizer with low OM content did not significantly change Cd accumulation in rice grains or affect the soil microbial structures in both soils. In conclusion, the effects of biofertilizer on rice Cd accumulation were related to the OM content and soil bacterial community. Biofertilizers with high organic matter may not be suitable for amendments in the paddy soils with high clay content to reduce Cd accumulation in rice grains.
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Affiliation(s)
- Yu Jin
- Department of Environmental Engineering, Zhejiang University, 310058 Hangzhou, China
| | - Baofeng Zhang
- Hangzhou Environmental Monitoring Central Station, 310007 Hangzhou, China
| | - Junqiao Chen
- Department of Environmental Engineering, Zhejiang University, 310058 Hangzhou, China
| | - Weihua Mao
- The Center of Analysis and Measurement, Zhejiang University, Hangzhou 310058, China
| | - Liping Lou
- Department of Environmental Engineering, Zhejiang University, 310058 Hangzhou, China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, 310058 Hangzhou, China
| | - Chaofeng Shen
- Department of Environmental Engineering, Zhejiang University, 310058 Hangzhou, China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, 310058 Hangzhou, China
| | - Qi Lin
- Department of Environmental Engineering, Zhejiang University, 310058 Hangzhou, China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, 310058 Hangzhou, China.
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Song J, Min L, Wu J, He Q, Chen F, Wang Y. Response of the microbial community to phosphate-solubilizing bacterial inoculants on Ulmus chenmoui Cheng in Eastern China. PLoS One 2021; 16:e0247309. [PMID: 33630914 PMCID: PMC7906385 DOI: 10.1371/journal.pone.0247309] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 02/04/2021] [Indexed: 11/24/2022] Open
Abstract
Phosphate-solubilizing bacteria (PSB) have beneficial effects on plant health and soil composition. To date, studies of PSB in soil have largely been performed under field or greenhouse conditions. However, less is known about the impact of introducing indigenous PSB in the field, including their effects on the local microbial community. In this study, we conducted greenhouse and field experiments to explore the effects of the addition of indigenous PSB on the growth of Chenmou elm (Ulmus chenmoui) and on the diversity and composition of the bacterial community in the soil. We obtained four bacterial isolates with the highest phosphate-solubilizing activity: UC_1 (Pseudomonas sp.), UC_M (Klebsiella sp.), UC_J (Burkholderia sp.), and UC_3 (Chryseobacterium sp.). Sequencing on the Illumina MiSeq platform showed that the inoculated PSB did not become the dominant strains in the U. chenmoui rhizosphere. However, the soil bacterial community structure was altered by the addition of these PSB. The relative abundance of Chloroflexi decreased significantly in response to PSB application in all treatment groups, whereas the populations of several bacteria, including Proteobacteria and Bacteroidetes, increased. Network analysis indicated that Chloroflexi was the most strongly negatively correlated with Proteobacteria, whereas Proteobacteria was strongly positively correlated with Bacteroidetes. Our findings indicate that inoculation with PSB (UC_1, UC_M, UC_J, and UC_3) can improve the growth of U. chenmoui and regulate its rhizosphere microbial community. Therefore, inoculation with these bacterial strains could promote the efficient cultivation and production of high-quality plant materials.
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Affiliation(s)
- Juan Song
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
- Institute of Forest Protection, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - LiJing Min
- College of Life Science, Huzhou University, Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, Huzhou, Zhejiang, China
| | - JunRong Wu
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
- Institute of Forest Protection, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Qingfang He
- Department of Biology, University of Arkansas at Little Rock, Little Rock, Arkansas, United States of America
| | - FengMao Chen
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
- Institute of Forest Protection, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Yang Wang
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
- Institute of Forest Protection, College of Forestry, Nanjing Forestry University, Nanjing, China
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Chen L, Hao Z, Li K, Sha Y, Wang E, Sui X, Mi G, Tian C, Chen W. Effectsof growth-promoting rhizobacteria on maize growth and rhizosphere microbial community under conservation tillage in Northeast China. Microb Biotechnol 2020; 14:535-550. [PMID: 33166080 PMCID: PMC7936301 DOI: 10.1111/1751-7915.13693] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/09/2020] [Accepted: 10/11/2020] [Indexed: 12/04/2022] Open
Abstract
Conservation tillage in conjunction with straw mulching is a sustainable agricultural approach. However, straw mulching reduces the soil temperature, inhibits early maize growth and reduces grain yield in cold regions. To address this problem, we investigated the effects of inoculation of plant growth‐promoting rhizobacteria (PGPR) on maize growth and rhizosphere microbial communities under conservation tillage in Northeast China. The PGPR strains Sinorhizobium sp. A15, Bacillus sp. A28, Sphingomonas sp. A55 and Enterobacter sp. P24 were isolated from the maize rhizosphere in the same area and inoculated separately. Inoculation of these strains significantly enhanced maize growth, and the strains A15, A28 and A55 significantly increased grain yield by as much as 22%–29%. Real‐time quantitative PCR and high‐throughput sequencing showed that separate inoculation with the four strains increased the abundance and species richness of bacteria in the maize rhizosphere. Notably, the relative abundance of Acidobacteria_Subgroup_6, Chloroflexi_KD4‐96, and Verrucomicrobiae at the class level and Mucilaginibacter at the genus level were positively correlated with maize biomass and yield. Inoculation with PGPR shows potential for improvement of maize production under conservation tillage in cold regions by regulating the rhizosphere bacterial community structure and by direct stimulation of plant growth.
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Affiliation(s)
- La Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhanhong Hao
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Keke Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Ye Sha
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Entao Wang
- Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional, Mexico D.F., 11340, Mexico
| | - Xinhua Sui
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Guohua Mi
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Changfu Tian
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Wenxin Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
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Jiao C, Zhao D, Zeng J, Guo L, Yu Z. Disentangling the seasonal co-occurrence patterns and ecological stochasticity of planktonic and benthic bacterial communities within multiple lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 740:140010. [PMID: 32563874 DOI: 10.1016/j.scitotenv.2020.140010] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 06/04/2020] [Accepted: 06/04/2020] [Indexed: 06/11/2023]
Abstract
Both the planktonic bacterial community (PBC) and benthic bacterial community (BBC) are important for biogeochemical processes in freshwater lakes. Despite their ecological significance, little is known about their seasonal co-occurrence patterns and the ecological processes that drive them. In this study, we aimed to investigate the ecological associations among bacterial taxa and assembly processes of PBC and BBC in different seasons. We used 16S rRNA gene high-throughput sequencing of a total of 150 water and sediment samples collected from multiple lakes distributed in an urban region of China during winter and summer. Our results revealed that PBC showed stronger seasonal variations in co-occurrence patterns than BBC, suggesting that BBC had greater temporal stability than PBC. Winter PBC network was characterized by higher connectivity and complexity, and thereby the formation of a highly stable community structure; whereas lower connectivity arising from the presence of fewer predicted keystone taxa (hubs and connectors in a network) was destabilizing to summer PBC network. In addition, the phylum Firmicutes identified as a putative keystone taxon of PBC in both seasons played a non-negligible role in maintaining network structure which may result from strong functional associations with other bacterioplankton. Temperature and pH were the best explanatory factors predicting the seasonal co-occurrence patterns of PBC and BBC, respectively. Normalized stochasticity ratio based on null-model analysis indicated that deterministic processes overwhelmed stochastic processes in governing the assembly of PBC and BBC in both seasons. However, we observed a greater influence of ecological stochasticity on BBC assembly than PBC assembly in both seasons. Taken together, these findings provide insights into understanding the impacts of habitat heterogeneity and seasonal variability on microbial assemblage patterns in lake ecosystems.
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Affiliation(s)
- Congcong Jiao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Lin Guo
- Department of Biological and Environmental Sciences, Texas A&M University, Commerce, TX 76129, USA
| | - Zhongbo Yu
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, China
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Kadnikov VV, Mardanov AV, Beletsky AV, Karnachuk OV, Ravin NV. Microbial Life in the Deep Subsurface Aquifer Illuminated by Metagenomics. Front Microbiol 2020; 11:572252. [PMID: 33013807 PMCID: PMC7509429 DOI: 10.3389/fmicb.2020.572252] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 08/13/2020] [Indexed: 01/08/2023] Open
Abstract
To get insights into microbial diversity and biogeochemical processes in the terrestrial deep subsurface aquifer, we sequenced the metagenome of artesian water collected at a 2.8 km deep oil exploration borehole 5P in Western Siberia, Russia. We obtained 71 metagenome-assembled genomes (MAGs), altogether comprising 93% of the metagenome. Methanogenic archaea accounted for about 20% of the community and mostly belonged to hydrogenotrophic Methanobacteriaceae; acetoclastic and methylotrophic lineages were less abundant. ANME archaea were not found. The most numerous bacteria were the Firmicutes, Ignavibacteriae, Deltaproteobacteria, Chloroflexi, and Armatimonadetes. Most of the community was composed of anaerobic heterotrophs. Only six MAGs belonged to sulfate reducers. These MAGs accounted for 5% of the metagenome and were assigned to the Firmicutes, Deltaproteobacteria, Candidatus Kapabacteria, and Nitrospirae. Organotrophic bacteria carrying cytochrome c oxidase genes and presumably capable of aerobic respiration mostly belonged to the Chloroflexi, Ignavibacteriae, and Armatimonadetes. They accounted for 13% of the community. The first complete closed genomes were obtained for members of the Ignavibacteriae SJA-28 lineage and the candidate phylum Kapabacteria. Metabolic reconstruction of the SJA-28 bacterium, designated Candidatus Tepidiaquacella proteinivora, predicted that it is an anaerobe growing on proteinaceous substrates by fermentation or anaerobic respiration. The Ca. Kapabacteria genome contained both the sulfate reduction pathway and cytochrome c oxidase. Presumably, the availability of buried organic matter of Mesozoic marine sediments, long-term recharge of the aquifer with meteoric waters and its spatial heterogeneity provided the conditions for the development of microbial communities, taxonomically and functionally more diverse than those found in oligotrophic underground ecosystems.
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Affiliation(s)
- Vitaly V Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Olga V Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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42
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Banda DM, Pereira JH, Liu AK, Orr DJ, Hammel M, He C, Parry MAJ, Carmo-Silva E, Adams PD, Banfield JF, Shih PM. Novel bacterial clade reveals origin of form I Rubisco. NATURE PLANTS 2020; 6:1158-1166. [PMID: 32868887 DOI: 10.1038/s41477-020-00762-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 07/28/2020] [Indexed: 05/12/2023]
Abstract
Rubisco sustains the biosphere through the fixation of CO2 into biomass. In plants and cyanobacteria, form I Rubisco is structurally comprised of large and small subunits, whereas all other Rubisco forms lack small subunits. The rise of the form I complex through the innovation of small subunits represents a key, yet poorly understood, transition in Rubisco's evolution. Through metagenomic analyses, we discovered a previously uncharacterized clade sister to form I Rubisco that evolved without small subunits. This clade diverged before the evolution of cyanobacteria and the origin of the small subunit; thus, it provides a unique reference point to advance our understanding of form I Rubisco evolution. Structural and kinetic data presented here reveal how a proto-form I Rubisco assembled and functioned without the structural stability imparted from small subunits. Our findings provide insight into a key evolutionary transition of the most abundant enzyme on Earth and the predominant entry point for nearly all global organic carbon.
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Affiliation(s)
- Douglas M Banda
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jose H Pereira
- Technology Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Albert K Liu
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Douglas J Orr
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christine He
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
| | - Martin A J Parry
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | | | - Paul D Adams
- Technology Division, Joint BioEnergy Institute, Emeryville, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA.
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Patrick M Shih
- Department of Plant Biology, University of California, Davis, Davis, CA, USA.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA.
- Genome Center, University of California, Davis, Davis, CA, USA.
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43
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Ouyang L, Chen H, Liu X, Wong MH, Xu F, Yang X, Xu W, Zeng Q, Wang W, Li S. Characteristics of spatial and seasonal bacterial community structures in a river under anthropogenic disturbances. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 264:114818. [PMID: 32559870 DOI: 10.1016/j.envpol.2020.114818] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/16/2020] [Accepted: 05/13/2020] [Indexed: 06/11/2023]
Abstract
In this study, the seasonal characteristics of microbial community compositions at different sites in a river under anthropogenic disturbances (Maozhou River) were analyzed using Illumina HiSeq sequencing. Taxonomic analysis revealed that Proteobacteria was the most abundant phylum in all sites, followed by Actinobacteria, Bacteroidetes, Chloroflexi, Acidobacteria and Firmicutes. The variations of the community diversities and compositions between the seasons were not significant. However, significant differences between sites as well as water and sediment samples were observed. These results indicated that sites under different levels of anthropogenic disturbances have selected distinct bacterial communities. pH, dissolved oxygen (DO), concentrations of total nitrogen (TN) and heavy metals were the main factors that influence the diversity and the composition of bacterial community. Specifically, the relative abundance of Proteobacteria was negatively correlated with pH and DO and positively correlated with TN, while Actinobacteria and Verrucomicrobia showed the opposite pattern. Moreover, positive correlations between the relative abundances of Firmicutes and Bacteroidetes and the concentration of heavy metals were also found. Results of functional prediction analysis showed no significant differences of the carbon, nitrogen and phosphorus metabolism across the sites and seasons. Potential pathogens such as Vibrio, Arcobacter, Acinetobacter and Pseudomonas were found in these samples, which may pose potential risks for environment and human health. This study reveals the effect of anthropogenic activities on the riverine bacterial community compositions and provides new insights into the relationships between the environmental factors and the bacterial community distributions in a freshwater ecosystem under anthropogenic disturbances.
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Affiliation(s)
- Liao Ouyang
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China; College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Huirong Chen
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Xinyue Liu
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Ming Hung Wong
- Consortium on Health, Environment, Education and Research (CHEER), The Education University of HongKong, Taipo, Hong Kong, China
| | - Fangfang Xu
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Xuewei Yang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Wang Xu
- Shenzhen Environmental Monitoring Center, Shenzhen, 518049, Guangdong, China
| | - Qinghuai Zeng
- Shenzhen Environmental Monitoring Center, Shenzhen, 518049, Guangdong, China
| | - Weimin Wang
- Shenzhen Environmental Monitoring Center, Shenzhen, 518049, Guangdong, China
| | - Shuangfei Li
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
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Ozuolmez D, Moore EK, Hopmans EC, Sinninghe Damsté JS, Stams AJM, Plugge CM. Butyrate Conversion by Sulfate-Reducing and Methanogenic Communities from Anoxic Sediments of Aarhus Bay, Denmark. Microorganisms 2020; 8:microorganisms8040606. [PMID: 32331369 PMCID: PMC7232339 DOI: 10.3390/microorganisms8040606] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/17/2020] [Accepted: 04/19/2020] [Indexed: 11/29/2022] Open
Abstract
The conventional perception that the zone of sulfate reduction and methanogenesis are separated in high- and low-sulfate-containing marine sediments has recently been changed by studies demonstrating their co-occurrence in sediments. The presence of methanogens was linked to the presence of substrates that are not used by sulfate reducers. In the current study, we hypothesized that both groups can co-exist, consuming common substrates (H2 and/or acetate) in sediments. We enriched butyrate-degrading communities in sediment slurries originating from the sulfate, sulfate–methane transition, and methane zone of Aarhus Bay, Denmark. Sulfate was added at different concentrations (0, 3, 20 mM), and the slurries were incubated at 10 °C and 25 °C. During butyrate conversion, sulfate reduction and methanogenesis occurred simultaneously. The syntrophic butyrate degrader Syntrophomonas was enriched both in sulfate-amended and in sulfate-free slurries, indicating the occurrence of syntrophic conversions at both conditions. Archaeal community analysis revealed a dominance of Methanomicrobiaceae. The acetoclastic Methanosaetaceae reached high relative abundance in the absence of sulfate, while presence of acetoclastic Methanosarcinaceae was independent of the sulfate concentration, temperature, and the initial zone of the sediment. This study shows that there is no vertical separation of sulfate reducers, syntrophs, and methanogens in the sediment and that they all participate in the conversion of butyrate.
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Affiliation(s)
- Derya Ozuolmez
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (D.O.); (A.J.M.S.)
| | - Elisha K. Moore
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, P.O. Box 59, 1790 AB Den Burg, The Netherlands; (E.K.M.); (E.C.H.); (J.S.S.D.)
- Department of Environmental Science, Rowan University, 201 Mullica Hill Rd, Glassboro, NJ 08028, USA
| | - Ellen C. Hopmans
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, P.O. Box 59, 1790 AB Den Burg, The Netherlands; (E.K.M.); (E.C.H.); (J.S.S.D.)
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, P.O. Box 59, 1790 AB Den Burg, The Netherlands; (E.K.M.); (E.C.H.); (J.S.S.D.)
- Faculty of Geosciences, Utrecht University, P.O. Box 80.021, 3508 TA Utrecht, The Netherlands
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (D.O.); (A.J.M.S.)
| | - Caroline M. Plugge
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (D.O.); (A.J.M.S.)
- Correspondence: ; Tel.: +31-317-483116
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Ji M, Sang W, Tsang DCW, Usman M, Zhang S, Luo G. Molecular and microbial insights towards understanding the effects of hydrochar on methane emission from paddy soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 714:136769. [PMID: 31982762 DOI: 10.1016/j.scitotenv.2020.136769] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/15/2020] [Accepted: 01/16/2020] [Indexed: 06/10/2023]
Abstract
Directly returning rice straw to the paddy soil would significantly stimulate methane emission, and hydrochar has potential to be used as soil conditioner. However, the effects of hydrochar on the methane emission from paddy soil and the related mechanisms are still unclear. In the present study, straw-based hydrochar obtained at 200 °C (HC200), 250 °C (HC250) and 300 °C (HC300) and hydrochar after removal of bio-oil at these temperatures (CHC200, CHC250, and CHC300) were prepared and added to the paddy soil. The application of HC200, HC250 and HC300 resulted in the enhanced methane production compared to the control, showing 4.3, 1.6 and 1.5-fold higher methane production, respectively. It was related to the large amount of dissolved organic matter (DOM) released from hydrochar. Excitation-emission matrix fluorescence spectroscopy with parallel factor analysis (EEM-PARAFAC) showed that the hydrochar-derived DOM mainly included humic-like, phenolic and less aromatic structures, and with the increase of hydrothermal temperature, the content of humic-like substances and phenols increased, while biodegradable organics decreased. This was consistent with the maximum methane production by HC200. After incubation, there was no low-aromatic structures observed in the soil leachate, and the residual organics were mainly humus. The EEM-PARAFAC results were supported by compositional characterization of soil leachate by high-resolution mass spectrometry, and the refractory organics released from hydrochar was mainly lignins or (CRAM)-like structures in the range of H/C = 0.8-1.6 and O/C = 0.1-0.5. The organics dissolved from the washed hydrochar was significantly reduced, and some washed hydrochar (CHC250 and CHC300) even inhibited methane emission possibly due to their ability to adsorb organics. Microbial analysis further showed that the increased methane production resulted from hydrochar was associated with the enrichment of Janibacter, Anaeromyxobacter, Anaerolinea and Sporacetigenium. This present study provided a better understanding to the effect of hydrochar on methanogenesis in paddy soil.
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Affiliation(s)
- Mengyuan Ji
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China; Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Wenjing Sang
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China.
| | - Daniel C W Tsang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Muhammad Usman
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Shicheng Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China.
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46
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Mei R, Nobu MK, Liu WT. Identifying anaerobic amino acids degraders through the comparison of short-term and long-term enrichments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:173-184. [PMID: 31965729 DOI: 10.1111/1758-2229.12821] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/24/2019] [Accepted: 01/14/2020] [Indexed: 06/10/2023]
Abstract
Degradation of amino acids is an important process in methanogenic environments. Early studies in the 1980s focused on isolated clostridia species to study the degradation behaviours. However, it is now well-recognized that isolated species may not represent those with important roles in situ. This study conducted a continuous enrichment experiment with focus on the comparison of the microbial communities after short-term enrichment (SE) and long-term enrichment (LE). Individual amino acids were used as the substrate, and two different anaerobic digester sludge were used as the inoculum. Based on 16S rRNA and 16S rRNA gene, a clear community shift was observed during a time course of 18 months. The SE communities were dominated by microbial populations such as an uncultured Bacteroidales that was different from known fermenters. In the LE communities, known amino acids fermenters were consistently observed with high abundance, including Peptoclostridium acidaminophilum, Acidaminobacter hydrogenoformans and Propionivibrio pelophilus. The community structures could be classified into four types depending on the diversity of fermenters and syntrophs. A culturability index was developed to compare the SE and LE community and revealed that long-term enrichment tended to select microbial populations closely related to species that has been cultivated whereas larger fractions of the inoculum and SE communities remained uncultured.
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Affiliation(s)
- Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Masaru K Nobu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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47
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Cao J, Feng Y, Lin X, Wang J. A beneficial role of arbuscular mycorrhizal fungi in influencing the effects of silver nanoparticles on plant-microbe systems in a soil matrix. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:11782-11796. [PMID: 31975001 DOI: 10.1007/s11356-020-07781-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
Silver nanoparticles (AgNPs) are considered to be emerging contaminant for plant-soil systems. AM arbuscular mycorrhizal (AM) fungi can alleviate the negative effects of a variety of pollutants on their hosts, but its potential roles in influencing the toxicity of AgNPs and the underlying mechanisms are still an open question. This study investigated the responses of maize (Zea mays L.) inoculated with or without AM fungi and soil microorganisms to different concentrations of AgNPs (0, 0.025, 0.25, and 2.5 mg kg-1). The inoculation of AM fungi helps to alleviate the AgNP-induced phytotoxicity. Compared to the non-AM fungal inoculated treatments, AM fungal inoculation significantly increased the mycorrhizal colonization, biomass and phosphorus (P) acquisitions of maize, with an upregulation of P transporter gene expression under AgNP treatments. AM fungal inoculation decreased Ag content in plant shoots and roots, downregulated expression levels of genes involved in Ag transport and gene encoding a metallothionein involved in metal homeostasis. The beneficial role of AM fungi extended to soil microbes. Compared to the non-AM fungal inoculated treatments, AM fungal inoculation decreased the toxicity of AgNPs to soil microbial activities and bacterial abundance. AM fungal inoculation increased the bacterial diversity and induced changes in the soil bacterial community composition. Altogether, the present study revealed that AM fungal symbiosis can play beneficial roles in mediating the negative effects exposed by AgNPs on plants probably through changing the expressions of potential Ag transporters and cooperating with soil bacterial community.
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Affiliation(s)
- Jiling Cao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu, People's Republic of China
| | - Youzhi Feng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu, People's Republic of China
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu, People's Republic of China.
| | - Junhua Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu, People's Republic of China
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48
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Spieck E, Spohn M, Wendt K, Bock E, Shively J, Frank J, Indenbirken D, Alawi M, Lücker S, Hüpeden J. Extremophilic nitrite-oxidizing Chloroflexi from Yellowstone hot springs. THE ISME JOURNAL 2020; 14:364-379. [PMID: 31624340 PMCID: PMC6976673 DOI: 10.1038/s41396-019-0530-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 08/03/2019] [Accepted: 09/06/2019] [Indexed: 12/21/2022]
Abstract
Nitrifying microorganisms occur across a wide temperature range from 4 to 84 °C and previous studies in geothermal systems revealed their activity under extreme conditions. Archaea were detected to be responsible for the first step of nitrification, but it is still a challenging issue to clarify the identity of heat-tolerant nitrite oxidizers. In a long-term cultivation approach, we inoculated mineral media containing ammonium and nitrite as substrates with biofilms and sediments of two hot springs in Yellowstone National Park (USA). The nitrifying consortia obtained at 70 °C consisted mostly of novel Chloroflexi as revealed by metagenomic sequencing. Among these, two deep-branching novel Chloroflexi were identified as putative nitrite-oxidizing bacteria (NOB) by the presence of nitrite oxidoreductase encoding genes in their genomes. Stoichiometric oxidation of nitrite to nitrate occurred under lithoautotrophic conditions, but was stimulated by organic matter. Both NOB candidates survived long periods of starvation and the more abundant one formed miniaturized cells and was heat resistant. This detection of novel thermophilic NOB exemplifies our still incomplete knowledge of nitrification, and indicates that nitrite oxidation might be an ancient and wide-spread form of energy conservation.
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Affiliation(s)
- Eva Spieck
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany.
| | - Michael Spohn
- Technology Platform Next Generation Sequencing, Heinrich Pette Institut, Hamburg, Germany
| | - Katja Wendt
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| | - Eberhard Bock
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| | - Jessup Shively
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
| | - Jeroen Frank
- Department of Microbiology, IWWR, Radboud University, Nijmegen, The Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Daniela Indenbirken
- Technology Platform Next Generation Sequencing, Heinrich Pette Institut, Hamburg, Germany
| | - Malik Alawi
- Bioinformatics Core, University Medical-Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sebastian Lücker
- Department of Microbiology, IWWR, Radboud University, Nijmegen, The Netherlands
| | - Jennifer Hüpeden
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
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49
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Changes in the microbial community during the acclimation process of anaerobic digestion for treatment of synthetic lipid-rich wastewater. J Biotechnol 2019; 306:32-37. [DOI: 10.1016/j.jbiotec.2019.09.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/28/2019] [Accepted: 09/09/2019] [Indexed: 11/23/2022]
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50
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Feng C, Jia J, Wang C, Han M, Dong C, Huo B, Li D, Liu X. Phytoplankton and Bacterial Community Structure in Two Chinese Lakes of Different Trophic Status. Microorganisms 2019; 7:E621. [PMID: 31783682 PMCID: PMC6956004 DOI: 10.3390/microorganisms7120621] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/20/2019] [Accepted: 11/25/2019] [Indexed: 01/18/2023] Open
Abstract
Phytoplankton are the primary producers at the basis of aquatic food webs, and bacteria play an important role in energy flow and biochemical cycling in aquatic ecosystems. In this study, both the bacterial and phytoplankton communities were examined in the oligotrophic Lake Basomtso and the eutrophic Lake South (China). The results of this study showed that the phytoplankton density and diversity in the eutrophic lake were higher than those in the oligotrophic lake. Furthermore, Chlorophyta (68%) and Cryptophyta (24%) were the dominant groups in the eutrophic lake, while Bacillariophyta (95%) dominated in the oligotrophic lake. The bacterial communities in the waters and sediments of the two lakes were mainly composed of Proteobacteria (mean of 32%), Actinobacteria (mean of 25%), Bacteroidetes (mean of 12%), and Chloroflexi (mean of 6%). Comparative analysis showed that the abundance of bacteria in the eutrophic lake was higher than that in the oligotrophic lake (p < 0.05), but the bacterial diversity in the oligotrophic lake was higher than that in the eutrophic lake (p < 0.05). Finally, the bacterial abundance and diversity in the sediments of the two lakes were higher than those in the water samples (p < 0.05), and the Latescibacteria and Nitrospinae groups were identified only in the sediments. These results suggest that both the phytoplankton and bacterial communities differed considerably between the oligotrophic lake and the eutrophic lake.
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Affiliation(s)
| | | | | | | | | | | | | | - Xiangjiang Liu
- College of Fisheries, Hubei Province Engineering Laboratory for Pond Aquaculture, Huazhong Agricultural University, Wuhan 430070, China; (C.F.); (J.J.); (C.W.); (M.H.); (C.D.); (B.H.); (D.L.)
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