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Zhu W, Zhao H, Ke J, Zhang J, Liu X, Zhou Y, Chen R, Wang A, Li X. Deciphering the environmental adaptation and functional trait of core and noncore bacterial communities in impacted coral reef seawater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172897. [PMID: 38697527 DOI: 10.1016/j.scitotenv.2024.172897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 11/01/2023] [Accepted: 04/28/2024] [Indexed: 05/05/2024]
Abstract
Microorganisms play pivotal roles in different biogeochemical cycles within coral reef waters. Nevertheless, our comprehension of the microbially mediated processes following environmental perturbation is still limited. To gain a deeper insight into the environmental adaptation and nutrient cycling, particularly within core and noncore bacterial communities, it is crucial to understand reef ecosystem functioning. In this study, we delved into the microbial community structure and function of seawater in a coral reef under different degrees of anthropogenic disturbance. To achieve this, we harnessed the power of 16S rRNA gene high-throughput sequencing and metagenomics techniques. The results showed that a continuous temporal succession but little spatial heterogeneity in the bacterial communities of core and noncore taxa and functional profiles involved in nitrogen (N) and phosphorus (P) cycling. Eutrophication state (i.e., nutrient concentration and turbidity) and temperature played pivotal roles in shaping both the microbial community composition and functional traits of coral reef seawater. Within this context, the core subcommunity exhibited a remarkably broader habitat niche breadth, stronger phylogenetic signal and lower environmental sensitivity when compared to the noncore taxa. Null model analysis further revealed that the core subcommunity was governed primarily by stochastic processes, while deterministic processes played a more significant role in shaping the noncore subcommunity. Furthermore, our observations indicated that changes in function related to N cycling were correlated to the variations in noncore taxa, while core taxa played a more substantial role in critical processes such as P cycling. Collectively, these findings facilitated our knowledge about environmental adaptability of core and noncore bacterial taxa and shed light on their respective roles in maintaining diverse nutrient cycling within coral reef ecosystems.
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Affiliation(s)
- Wentao Zhu
- College of Ecology and Environment, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - He Zhao
- College of Ecology and Environment, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Jingzhao Ke
- College of Marine Biology and Fisheries, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Junling Zhang
- College of Marine Biology and Fisheries, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Xiangbo Liu
- College of Marine Biology and Fisheries, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Yinyin Zhou
- College of Marine Biology and Fisheries, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Rouwen Chen
- College of Marine Biology and Fisheries, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Aimin Wang
- College of Marine Biology and Fisheries, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Xiubao Li
- College of Marine Biology and Fisheries, Hainan University, Haikou, China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China.
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2
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Ferreira CR, Lima Gomes PCFD, Robison KM, Cooper BR, Shannahan JH. Implementation of multiomic mass spectrometry approaches for the evaluation of human health following environmental exposure. Mol Omics 2024; 20:296-321. [PMID: 38623720 PMCID: PMC11163948 DOI: 10.1039/d3mo00214d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/22/2024] [Indexed: 04/17/2024]
Abstract
Omics analyses collectively refer to the possibility of profiling genetic variants, RNA, epigenetic markers, proteins, lipids, and metabolites. The most common analytical approaches used for detecting molecules present within biofluids related to metabolism are vibrational spectroscopy techniques, represented by infrared, Raman, and nuclear magnetic resonance (NMR) spectroscopies and mass spectrometry (MS). Omics-based assessments utilizing MS are rapidly expanding and being applied to various scientific disciplines and clinical settings. Most of the omics instruments are operated by specialists in dedicated laboratories; however, the development of miniature portable omics has made the technology more available to users for field applications. Variations in molecular information gained from omics approaches are useful for evaluating human health following environmental exposure and the development and progression of numerous diseases. As MS technology develops so do statistical and machine learning methods for the detection of molecular deviations from personalized metabolism, which are correlated to altered health conditions, and they are intended to provide a multi-disciplinary overview for researchers interested in adding multiomic analysis to their current efforts. This includes an introduction to mass spectrometry-based omics technologies, current state-of-the-art capabilities and their respective strengths and limitations for surveying molecular information. Furthermore, we describe how knowledge gained from these assessments can be applied to personalized medicine and diagnostic strategies.
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Affiliation(s)
- Christina R Ferreira
- Purdue Metabolite Profiling Facility, Purdue University, West Lafayette, IN 47907, USA.
| | | | - Kiley Marie Robison
- School of Health Sciences, College of Health and Human Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Bruce R Cooper
- Purdue Metabolite Profiling Facility, Purdue University, West Lafayette, IN 47907, USA.
| | - Jonathan H Shannahan
- School of Health Sciences, College of Health and Human Sciences, Purdue University, West Lafayette, IN 47907, USA
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3
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Shi J, Qian W, Zhou Z, Jin Z, Gao X, Fan J, Wang X. Effects of acid mine drainage and sediment contamination on soil bacterial communities, interaction patterns, and functions in alkaline desert grassland. JOURNAL OF HAZARDOUS MATERIALS 2024; 474:134832. [PMID: 38852245 DOI: 10.1016/j.jhazmat.2024.134832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 05/22/2024] [Accepted: 06/04/2024] [Indexed: 06/11/2024]
Abstract
Acid mine drainage and sediments (AMD-Sed) contamination pose serious ecological and environmental problems. This study investigated the geochemical parameters and bacterial communities in the sediment layer (A) and buried soil layer (B) of desert grassland contaminated with AMD-Sed and compared them to an uncontaminated control soil layer (CK). The results showed that soil pH was significantly lower and iron, sulfur, and electroconductivity levels were significantly higher in the B layer compared to CK. A and B were dominated by Proteobacteria and Actinobacteriota, while CK was dominated by Firmicutes and Bacteroidota. The pH, Fe, S, and potentially toxic elements (PTEs) gradients were key influences on bacterial community variability, with AMD contamination characterization factors (pH, Fe, and S) explaining 48.6 % of bacterial community variation. A bacterial co-occurrence network analysis showed that AMD-Sed contamination significantly affected topological properties, reduced network complexity and stability, and increased the vulnerability of desert grassland soil ecosystems. In addition, AMD-Sed contamination reduced C/N-cycle functioning in B, but increased S-cycle functioning. The results highlight the effects of AMD-Sed contamination on soil bacterial communities and ecological functions in desert grassland and provide a reference basis for the management and restoration of desert grassland ecosystems in their later stages.
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Affiliation(s)
- Jianfei Shi
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, Xinjiang, China; University of Chinese Academy of Sciences, Beijing 100049, China; National Engineering Technology Research Center for Desert-Oasis Ecological Construction, Urumqi, Xinjiang 830011, China
| | - Wenting Qian
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, Xinjiang, China; Public Technology Service Center, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, Xinjiang, China
| | - Zhibin Zhou
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, Xinjiang, China; National Engineering Technology Research Center for Desert-Oasis Ecological Construction, Urumqi, Xinjiang 830011, China; Taklimakan Station for Desert Research, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Zhengzhong Jin
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, Xinjiang, China; National Engineering Technology Research Center for Desert-Oasis Ecological Construction, Urumqi, Xinjiang 830011, China; Taklimakan Station for Desert Research, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China.
| | - Xin Gao
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, Xinjiang, China; National Engineering Technology Research Center for Desert-Oasis Ecological Construction, Urumqi, Xinjiang 830011, China; Taklimakan Station for Desert Research, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Jinglong Fan
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, Xinjiang, China; National Engineering Technology Research Center for Desert-Oasis Ecological Construction, Urumqi, Xinjiang 830011, China; Taklimakan Station for Desert Research, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Xin Wang
- Shaanxi Forestry Survey and Planning Institute, Xi'an, Shaanxi 710082, China
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Wu H, Nie WB, Tan X, Xie GJ, Qu H, Zhang X, Xian Z, Dai J, Yang C, Chen Y. Different oxygen affinities of methanotrophs and Comammox Nitrospira inform an electrically induced symbiosis for nitrogen loss. WATER RESEARCH 2024; 256:121606. [PMID: 38631236 DOI: 10.1016/j.watres.2024.121606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 04/01/2024] [Accepted: 04/10/2024] [Indexed: 04/19/2024]
Abstract
Aerobic methanotrophs establish a symbiotic association with denitrifiers to facilitate the process of aerobic methane oxidation coupled with denitrification (AME-D). However, the symbiosis has been frequently observed in hypoxic conditions continuing to pose an enigma. The present study has firstly characterized an electrically induced symbiosis primarily governed by Methylosarcina and Hyphomicrobium for the AME-D process in a hypoxic niche caused by Comammox Nitrospira. The kinetic analysis revealed that Comammox Nitrospira exhibited a higher apparent oxygen affinity compared to Methylosarcina. While the coexistence of comammox and AME-D resulted in an increase in methane oxidation and nitrogen loss rates, from 0.82 ± 0.10 to 1.72 ± 0.09 mmol CH4 d-1 and from 0.59 ± 0.04 to 1.30 ± 0.15 mmol N2 d-1, respectively. Furthermore, the constructed microbial fuel cells demonstrated a pronounced dependence of the biocurrents on AME-D due to oxygen competition, suggesting the involvement of direct interspecies electron transfer in the AME-D process under hypoxic conditions. Metagenomic and metatranscriptomic analysis revealed that Methylosarcina efficiently oxidized methane to formaldehyde, subsequently generating abundant NAD(P)H for nitrate reduction by Hyphomicrobium through the dissimilatory RuMP pathway, leading to CO2 production. This study challenges the conventional understanding of survival mechanism employed by AME-D symbionts, thereby contributing to the characterization responsible for limiting methane emissions and promoting nitrogen removal in hypoxic regions.
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Affiliation(s)
- Hao Wu
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Wen-Bo Nie
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China.
| | - Xin Tan
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland 4072, Australia; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Han Qu
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Xin Zhang
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Zhihao Xian
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Jingyi Dai
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Chun Yang
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Yi Chen
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China.
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5
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Qi YL, Chen YT, Xie YG, Li YX, Rao YZ, Li MM, Xie QJ, Cao XR, Chen L, Qu YN, Yuan ZX, Xiao ZC, Lu L, Jiao JY, Shu WS, Li WJ, Hedlund BP, Hua ZS. Analysis of nearly 3000 archaeal genomes from terrestrial geothermal springs sheds light on interconnected biogeochemical processes. Nat Commun 2024; 15:4066. [PMID: 38744885 PMCID: PMC11094006 DOI: 10.1038/s41467-024-48498-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 05/02/2024] [Indexed: 05/16/2024] Open
Abstract
Terrestrial geothermal springs are physicochemically diverse and host abundant populations of Archaea. However, the diversity, functionality, and geological influences of these Archaea are not well understood. Here we explore the genomic diversity of Archaea in 152 metagenomes from 48 geothermal springs in Tengchong, China, collected from 2016 to 2021. Our dataset is comprised of 2949 archaeal metagenome-assembled genomes spanning 12 phyla and 392 newly identified species, which increases the known species diversity of Archaea by ~48.6%. The structures and potential functions of the archaeal communities are strongly influenced by temperature and pH, with high-temperature acidic and alkaline springs favoring archaeal abundance over Bacteria. Genome-resolved metagenomics and metatranscriptomics provide insights into the potential ecological niches of these Archaea and their potential roles in carbon, sulfur, nitrogen, and hydrogen metabolism. Furthermore, our findings illustrate the interplay of competition and cooperation among Archaea in biogeochemical cycles, possibly arising from overlapping functional niches and metabolic handoffs. Taken together, our study expands the genomic diversity of Archaea inhabiting geothermal springs and provides a foundation for more incisive study of biogeochemical processes mediated by Archaea in geothermal ecosystems.
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Affiliation(s)
- Yan-Ling Qi
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Ya-Ting Chen
- Institute for Disaster Management and Reconstruction, Sichuan University-Hong Kong Polytechnic University, Chengdu, 610207, China
| | - Yuan-Guo Xie
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yu-Xian Li
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yang-Zhi Rao
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Qi-Jun Xie
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Xing-Ru Cao
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Lei Chen
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yan-Ni Qu
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Zhen-Xuan Yuan
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Zhi-Chao Xiao
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Lu Lu
- College of Environmental Science and Engineering, China West Normal University, Nanchong, 637009, China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR 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.
| | - Zheng-Shuang Hua
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, 230026, China.
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6
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Dong X, Chen M, Chen Q, Liu K, Long J, Li Y, Ren Y, Yang T, Zhou J, Herath S, Peng X. Rare microbial taxa as the major drivers of nutrient acquisition under moss biocrusts in karst area. Front Microbiol 2024; 15:1384367. [PMID: 38751717 PMCID: PMC11094542 DOI: 10.3389/fmicb.2024.1384367] [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: 02/09/2024] [Accepted: 04/08/2024] [Indexed: 05/18/2024] Open
Abstract
Karst rocky desertification refers to the process of land degradation caused by various factors such as climate change and human activities including deforestation and agriculture on a fragile karst substrate. Nutrient limitation is common in karst areas. Moss crust grows widely in karst areas. The microorganisms associated with bryophytes are vital to maintaining ecological functions, including climate regulation and nutrient circulation. The synergistic effect of moss crusts and microorganisms may hold great potential for restoring degraded karst ecosystems. However, our understanding of the responses of microbial communities, especially abundant and rare taxa, to nutrient limitations and acquisition in the presence of moss crusts is limited. Different moss habitats exhibit varying patterns of nutrient availability, which also affect microbial diversity and composition. Therefore, in this study, we investigated three habitats of mosses: autochthonal bryophytes under forest, lithophytic bryophytes under forest and on cliff rock. We measured soil physicochemical properties and enzymatic activities. We conducted high-throughput sequencing and analysis of soil microorganisms. Our finding revealed that autochthonal moss crusts under forest had higher nutrient availability and a higher proportion of copiotrophic microbial communities compared to lithophytic moss crusts under forest or on cliff rock. However, enzyme activities were lower in autochthonal moss crusts under forest. Additionally, rare taxa exhibited distinct structures in all three habitats. Analysis of co-occurrence network showed that rare taxa had a relatively high proportion in the main modules. Furthermore, we found that both abundant and rare taxa were primarily assembled by stochastic processes. Soil properties significantly affected the community assembly of the rare taxa, indirectly affecting microbial diversity and complexity and finally nutrient acquisition. These findings highlight the importance of rare taxa under moss crusts for nutrient acquisition. Addressing this knowledge gap is essential for guiding ongoing ecological restoration projects in karst rocky desertification regions.
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Affiliation(s)
- Xintong Dong
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Man Chen
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Qi Chen
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Kangfei Liu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jie Long
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yunzhou Li
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yinuo Ren
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Tao Yang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jinxing Zhou
- Jianshui Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing, China
| | - Saman Herath
- Department of Export Agriculture, Faculty of Animal Science and Export Agriculture, Uva Wellassa University, Badulla, Sri Lanka
| | - Xiawei Peng
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Beijing Key Laboratory of Food Processing and Safety in Forestry, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing, China
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7
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Ji C, Guo J, Ma Y, Xu X, Zang T, Liu S, An Z, Yang M, He X, Zheng W. Application Progress of Culturomics in the Isolated Culture of Rhizobacteria: A Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:7586-7595. [PMID: 38530921 DOI: 10.1021/acs.jafc.3c08885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Comprehending the structure and function of rhizobacteria components and their regulation are crucial for sustainable agricultural management. However, obtaining comprehensive species information for most bacteria in the natural environment, particularly rhizobacteria, presents a challenge using traditional culture methods. To obtain diverse and pure cultures of rhizobacteria, this study primarily reviews the evolution of rhizobacteria culturomics and associated culture methods. Furthermore, it explores new strategies for enhancing the application of culturomics, providing valuable insights into efficiently enriching and isolate target bacterial strains/groups from the environment. The findings will help improve rhizobacteria's culturability and enrich the functional bacterial library.
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Affiliation(s)
- Chao Ji
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Junli Guo
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Ying Ma
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Xiangfu Xu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Tongyu Zang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Sentao Liu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Zhenzhen An
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Min Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Xiahong He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan 650201, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, Yunnan 650224, China
| | - Wenjie Zheng
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, National Engineering Research Center for Applied Technology of Agricultural Biodiversity, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan 650201, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Landscape Architecture Engineering Research Center of National Forestry and Grassland Administration, Southwest Forestry University, Kunming, Yunnan 650224, China
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8
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Luo ZH, Li Q, Xie YG, Lv AP, Qi YL, Li MM, Qu YN, Liu ZT, Li YX, Rao YZ, Jiao JY, Liu L, Narsing Rao MP, Hedlund BP, Evans PN, Fang Y, Shu WS, Huang LN, Li WJ, Hua ZS. Temperature, pH, and oxygen availability contributed to the functional differentiation of ancient Nitrososphaeria. THE ISME JOURNAL 2024; 18:wrad031. [PMID: 38365241 PMCID: PMC10833072 DOI: 10.1093/ismejo/wrad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/13/2023] [Accepted: 12/13/2023] [Indexed: 02/18/2024]
Abstract
Ammonia-oxidizing Nitrososphaeria are among the most abundant archaea on Earth and have profound impacts on the biogeochemical cycles of carbon and nitrogen. In contrast to these well-studied ammonia-oxidizing archaea (AOA), deep-branching non-AOA within this class remain poorly characterized because of a low number of genome representatives. Here, we reconstructed 128 Nitrososphaeria metagenome-assembled genomes from acid mine drainage and hot spring sediment metagenomes. Comparative genomics revealed that extant non-AOA are functionally diverse, with capacity for carbon fixation, carbon monoxide oxidation, methanogenesis, and respiratory pathways including oxygen, nitrate, sulfur, or sulfate, as potential terminal electron acceptors. Despite their diverse anaerobic pathways, evolutionary history inference suggested that the common ancestor of Nitrososphaeria was likely an aerobic thermophile. We further surmise that the functional differentiation of Nitrososphaeria was primarily shaped by oxygen, pH, and temperature, with the acquisition of pathways for carbon, nitrogen, and sulfur metabolism. Our study provides a more holistic and less biased understanding of the diversity, ecology, and deep evolution of the globally abundant Nitrososphaeria.
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Affiliation(s)
- Zhen-Hao Luo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Qi Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Yuan-Guo Xie
- Chinese Academy of Sciences, Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, PR China
| | - Ai-Ping Lv
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Yan-Ling Qi
- Chinese Academy of Sciences, Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, PR 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), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Yan-Ni Qu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Ze-Tao Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Yu-Xian Li
- Chinese Academy of Sciences, Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, PR China
| | - Yang-Zhi Rao
- Chinese Academy of Sciences, Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, PR China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Manik Prabhu Narsing Rao
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Sede Talca, 3460000 Talca, Chile
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, United States
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, United States
| | - Paul N Evans
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Yuan Fang
- Chinese Academy of Sciences, Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, PR China
| | - Wen-Sheng Shu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
- Guangdong Provincial Key Laboratory of Chemical Pollution, South China Normal University, Guangzhou 510006, PR China
| | - Li-Nan Huang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Zheng-Shuang Hua
- Chinese Academy of Sciences, Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, PR China
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9
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Ullrich SR, Fuchs H, Schlömann M. Shedding light on the electron transfer chain of a moderately acidophilic iron oxidizer: characterization of recombinant HiPIP-41, CytC-18 and CytC-78 derived from Ferrovum sp. PN-J47-F6. Res Microbiol 2024; 175:104088. [PMID: 37348744 DOI: 10.1016/j.resmic.2023.104088] [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: 03/29/2023] [Revised: 06/07/2023] [Accepted: 06/07/2023] [Indexed: 06/24/2023]
Abstract
Efficient electron transfer from the donor to the acceptor couple presents a necessary requirement for acidophilic and neutrophilic iron oxidizers due to the low energy yield of aerobic ferrous iron oxidation. Involved periplasmic electron carriers are very diverse in these bacteria and show adaptations to the respective thermodynamic constraints such as a more positive redox potential reported for extreme acidophilic Acidithiobacillus spp. Respiratory chain candidates of moderately acidophilic members of the genus Ferrovum share similarities with both their neutrophilic iron oxidizing relatives and the more distantly related Acidithiobacillus spp. We examined our previous omics-based conclusions on the potential electron transfer chain in Ferrovum spp. by characterizing the three redox protein candidates CytC-18, CytC-78 and HiPIP-41 of strain PN-J47-F6 which were produced as recombinant proteins in Eschericha coli. UV/Vis-based redox assays suggested that HiPIP-41 has a very positive redox potential while redox potentials of CytC-18 and CytC-78 are more negative than their counterparts in Acidithiobacillus spp. Far Western dot blotting demonstrated interactions between all three recombinant redox proteins while redox assays showed the electron transfer from HiPIP-41 to either of the cytochromes. Altogether, CytC-18, CytC-78 and HiPIP-41 indeed represent very likely candidates of the electron transfer in Ferrovum sp. PN-J4-F6.
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Affiliation(s)
- Sophie R Ullrich
- TU Bergakademie Freiberg, Institute for Biological Sciences, Leipziger Strasse 29, Freiberg, Germany.
| | - Helena Fuchs
- TU Bergakademie Freiberg, Institute for Biological Sciences, Leipziger Strasse 29, Freiberg, Germany
| | - Michael Schlömann
- TU Bergakademie Freiberg, Institute for Biological Sciences, Leipziger Strasse 29, Freiberg, Germany
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10
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Odisi EJ, de Freitas RC, do Amaral DS, da Silva SB, da Silva MAC, de Oliveira Sant Ana W, de Souza Lima AO, Rörig LR. Metataxonomy of acid mine drainage microbiomes from the Santa Catarina Carboniferous Basin (Southern Brazil). Extremophiles 2023; 28:8. [PMID: 38133826 DOI: 10.1007/s00792-023-01324-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023]
Abstract
Mining activities generate large quantities of wastes that significantly alter the biogeochemistry and ecological structure of entire river basins. Microbial communities that develop in these areas present a variety of survival and adaptation mechanisms. Knowing this diversity at the molecular level is strategic both for understanding adaptive processes and for identifying genomes with potential use in bioremediation and bioprospecting. In this work, prokaryotic and eukaryotic communities were evaluated by meta-taxonomics (16S and 18S amplicons) in sediments and water bodies impacted by acid mine drainage in an important coal mining area in southern Brazil. Five sampling stations were defined on a gradient of impacts (pH 2.7-4.25). Taxon diversity was directly proportional to pH, being greater in sediments than in water. The dominant prokaryotic phyla in the samples were Proteobacteria, Actinobacteria, Acidobacteria, OD1, Nitrospirae, and Euryarchaeota, and among the eukaryotes, algae (Ochrophyta, Chlorophyta, Cryptophyceae), fungi (Basidiomycota, Ascomycota, and Cryptomycota), and protists (Ciliophora, Heterolobosea, Cercozoa). The prokaryotic genera Leptospirillum, Acidithiobacillus, Acidiphilium, Thiomonas, Thermogymnomonas, and Acidobacterium, and the eukaryotic genera Pterocystis and Poteriospumella were associated with more acidic conditions and higher metal concentrations, while the prokaryotic genera Sediminibacterium, Gallionella Geothrix, and Geobacter were more abundant in transitional environments.
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Affiliation(s)
- Estácio Jussie Odisi
- Laboratory of Phycology, Department of Botany, Federal University of Santa Catarina (LAFIC - UFSC), Florianópolis, Campus Universitário Trindade, Caixa Postal 476, Florianópolis, SC, 88040-900, Brazil
- Biome4All, São Paulo, SP, 01419-909, Brazil
| | | | - Diego Serrasol do Amaral
- Laboratory of Phycology, Department of Botany, Federal University of Santa Catarina (LAFIC - UFSC), Florianópolis, Campus Universitário Trindade, Caixa Postal 476, Florianópolis, SC, 88040-900, Brazil
| | | | - Marcus Adonai Castro da Silva
- Center for Earth and Sea Technological Sciences, University of Vale Do Itajaí (UNIVALI), Rua Uruguai, 458, Itajaí, SC, 88302-202, Brazil
| | - William de Oliveira Sant Ana
- SATC Technological Center, Beneficent Association of the Santa Catarina Coal Industry (SATC), Pascoal Meller St. 73, Criciúma, SC, Brazil
| | - André Oliveira de Souza Lima
- Center for Earth and Sea Technological Sciences, University of Vale Do Itajaí (UNIVALI), Rua Uruguai, 458, Itajaí, SC, 88302-202, Brazil
| | - Leonardo Rubi Rörig
- Laboratory of Phycology, Department of Botany, Federal University of Santa Catarina (LAFIC - UFSC), Florianópolis, Campus Universitário Trindade, Caixa Postal 476, Florianópolis, SC, 88040-900, Brazil.
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11
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Pan D, Chen P, Yang G, Niu R, Bai Y, Cheng K, Huang G, Liu T, Li X, Li F. Fe(II) Oxidation Shaped Functional Genes and Bacteria Involved in Denitrification and Dissimilatory Nitrate Reduction to Ammonium from Different Paddy Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:21156-21167. [PMID: 38064275 DOI: 10.1021/acs.est.3c06337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Microbial nitrate reduction can drive Fe(II) oxidation in anoxic environments, affecting the nitrous oxide emission and ammonium availability. The nitrate-reducing Fe(II) oxidation usually causes severe cell encrustation via chemodenitrification and potentially inhibits bacterial activity due to the blocking effect of secondary minerals. However, it remains unclear how Fe(II) oxidation and subsequent cell encrustation affect the functional genes and bacteria for denitrification and dissimilatory nitrate reduction to ammonium (DNRA). Here, bacteria were enriched from different paddy soils with and without Fe(II) under nitrate-reducing conditions. Fe(II) addition decelerated nitrate reduction and increased NO2- accumulation, due to the rapid Fe(II) oxidation and cell encrustation in the periplasm and on the cell surface. The N2O accumulation was lower in the treatment with Fe(II) and nitrate than that in the treatment with nitrate only, although the proportions of N2O and NH4+ to the reduced NO3- were low (3.25% ∼ 6.51%) at the end of incubation regardless of Fe(II) addition. The dominant bacteria varied from soils under nitrate-reducing conditions, while Fe(II) addition shaped a similar microbial community, including Dechloromonas, Azospira, and Pseudomonas. Fe(II) addition increased the relative abundance of napAB, nirS, norBC, nosZ, and nirBD genes but decreased that of narG and nrfA, suggesting that Fe(II) oxidation favored denitrification in the periplasm and NO2--to-NH4+ reduction in the cytoplasm. Dechloromonas dominated the NO2--to-N2O reduction, while Thauera mediated the periplasmic nitrate reduction and cytoplasmic NO2--to-NH4+ during Fe(II) oxidation. However, Thauera showed much lower abundance than the dominant genera, resulting in slow nitrate reduction and limited NH4+ production. These findings provide new insights into the response of denitrification and DNRA bacteria to Fe(II) oxidation and cell encrustation in anoxic environments.
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Affiliation(s)
- Dandan Pan
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Provincial Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- School of Environment, South China Normal University, Guangzhou 510006, China
| | - Pengcheng Chen
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Guang Yang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
- School of Environment, South China Normal University, Guangzhou 510006, China
| | - Rumiao Niu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
- School of Environment, South China Normal University, Guangzhou 510006, China
| | - Yan Bai
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Provincial Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- School of Environment, South China Normal University, Guangzhou 510006, China
| | - Kuan Cheng
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Provincial Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Guoyong Huang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Provincial Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- School of Environment, South China Normal University, Guangzhou 510006, China
| | - Tongxu Liu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Provincial Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Xiaomin Li
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
- School of Environment, South China Normal University, Guangzhou 510006, China
| | - Fangbai Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Provincial Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
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12
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Yang J, He J, Jia L, Gu H. Integrating metagenomics and metabolomics to study the response of microbiota in black soil degradation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 899:165486. [PMID: 37442461 DOI: 10.1016/j.scitotenv.2023.165486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/10/2023] [Accepted: 07/10/2023] [Indexed: 07/15/2023]
Abstract
As the largest commercial food production base and ecological security barrier, land degradation in black soil areas seriously threatens the global food supply and natural ecosystems. Therefore, determining the response of soil microbiota is crucial to restoring degraded soils. This study combined metagenomics and metabolomics to investigate the effect of different degrees of soil degradation on microbial community composition and metabolic function in black soils. It was found that alpha diversity in degraded soils (Shannon: 22.3) was higher than in nondegraded soil (ND) (Shannon: 21.8), and the degree of degradation significantly altered the structure and composition of soil microbial communities. The results of LEfSe analysis obtained 9 (ND), 7 (lightly degraded, LD), 10 (moderately degraded, MD), and 1 (severely degraded, SD) biomarkers in four samples. Bradyrhizobium, Sphingomonas, and Ramlibacter were significantly affected by soil degradation and can be considered biomarkers of ND, MD, and SD, respectively. Soil nutrient and enzyme activities decreased significantly with increasing black soil degradation, soil organic matter (SOM) content decreased from 11.12 % to 1.97 %, and Sucrase decreased from 23.53 to 6.59 mg/g/d. In addition, C was the critical driver affecting microbial community structure, contributing 61.2 % to differences in microbial community distribution, and microbial altering relative abundance which participle in the carbon cycle to respond to soil degradation. Metabolomic analyses indicated that soil degradation significantly modified the soil metabolite spectrum, and the metabolic functions of most microorganisms responding to soil degradation were adversely affected. The combined multi-omics analysis further indicated that biomarkers dominate in accumulating metabolites. These findings confirmed that due to their role in the composition and functioning of these degraded soils, these biomarkers could be employed in strategies for managing and restoring degraded black soils.
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Affiliation(s)
- Jia Yang
- School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Jianhu He
- School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Lin Jia
- School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Huiyan Gu
- School of Forestry, Northeast Forestry University, Harbin 150040, China.
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13
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Ibáñez A, Garrido-Chamorro S, Coque JJR, Barreiro C. From Genes to Bioleaching: Unraveling Sulfur Metabolism in Acidithiobacillus Genus. Genes (Basel) 2023; 14:1772. [PMID: 37761912 PMCID: PMC10531304 DOI: 10.3390/genes14091772] [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: 08/12/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Sulfur oxidation stands as a pivotal process within the Earth's sulfur cycle, in which Acidithiobacillus species emerge as skillful sulfur-oxidizing bacteria. They are able to efficiently oxidize several reduced inorganic sulfur compounds (RISCs) under extreme conditions for their autotrophic growth. This unique characteristic has made these bacteria a useful tool in bioleaching and biological desulfurization applications. Extensive research has unraveled diverse sulfur metabolism pathways and their corresponding regulatory systems. The metabolic arsenal of the Acidithiobacillus genus includes oxidative enzymes such as: (i) elemental sulfur oxidation enzymes, like sulfur dioxygenase (SDO), sulfur oxygenase reductase (SOR), and heterodisulfide reductase (HDR-like system); (ii) enzymes involved in thiosulfate oxidation pathways, including the sulfur oxidation (Sox) system, tetrathionate hydrolase (TetH), and thiosulfate quinone oxidoreductase (TQO); (iii) sulfide oxidation enzymes, like sulfide:quinone oxidoreductase (SQR); and (iv) sulfite oxidation pathways, such as sulfite oxidase (SOX). This review summarizes the current state of the art of sulfur metabolic processes in Acidithiobacillus species, which are key players of industrial biomining processes. Furthermore, this manuscript highlights the existing challenges and barriers to further exploring the sulfur metabolism of this peculiar extremophilic genus.
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Affiliation(s)
- Ana Ibáñez
- Instituto de Investigación de la Viña y el Vino, Escuela de Ingeniería Agraria, Universidad de León, 24009 León, Spain; (A.I.); (J.J.R.C.)
- Instituto Tecnológico Agrario de Castilla y León (ITACyL), Área de Investigación Agrícola, 47071 Valladolid, Spain
| | - Sonia Garrido-Chamorro
- Área de Bioquímica y Biología Molecular, Departamento de Biología Molecular, Universidad de León, 24007 León, Spain;
| | - Juan J. R. Coque
- Instituto de Investigación de la Viña y el Vino, Escuela de Ingeniería Agraria, Universidad de León, 24009 León, Spain; (A.I.); (J.J.R.C.)
| | - Carlos Barreiro
- Área de Bioquímica y Biología Molecular, Departamento de Biología Molecular, Universidad de León, 24007 León, Spain;
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14
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Wang M, Wang X, Zhou S, Chen Z, Chen M, Feng S, Li J, Shu W, Cao B. Strong succession in prokaryotic association networks and community assembly mechanisms in an acid mine drainage-impacted riverine ecosystem. WATER RESEARCH 2023; 243:120343. [PMID: 37482007 DOI: 10.1016/j.watres.2023.120343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
Acid mine drainage (AMD) serves as an ideal model system for investigating microbial ecology, interaction, and assembly mechanism in natural environments. While previous studies have explored the structure and function of microbial communities in AMD, the succession patterns of microbial association networks and underlying assembly mechanisms during natural attenuation processes remain elusive. Here, we investigated prokaryotic microbial diversity and community assembly along an AMD-impacted river, from the extremely acidic, heavily polluted headwaters to the nearly neutral downstream sites. Microbial diversity was increased along the river, and microbial community composition shifted from acidophile-dominated to freshwater taxa-dominated communities. The complexity and relative modularity of the microbial networks were also increased, indicating greater network stability during succession. Deterministic processes, including abiotic selection of pH and high contents of sulfur and iron, governed community assembly in the headwaters. Although the stochasticity ratio was increased downstream, manganese content, microbial negative cohesion, and relative modularity played important roles in shaping microbial community structure. Overall, this study provides valuable insights into the ecological processes that govern microbial community succession in AMD-impacted riverine ecosystems. These findings have important implications for in-situ remediation of AMD contamination.
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Affiliation(s)
- Mengmeng Wang
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Xiaonan Wang
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Sining Zhou
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Zifeng Chen
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Mengyun Chen
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Shiwei Feng
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Jintian Li
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Wensheng Shu
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Baichuan Cao
- Institute of Ecological Science and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
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15
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Li L, Meng D, Yin H, Zhang T, Liu Y. Genome-resolved metagenomics provides insights into the ecological roles of the keystone taxa in heavy-metal-contaminated soils. Front Microbiol 2023; 14:1203164. [PMID: 37547692 PMCID: PMC10402746 DOI: 10.3389/fmicb.2023.1203164] [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: 04/10/2023] [Accepted: 06/29/2023] [Indexed: 08/08/2023] Open
Abstract
Microorganisms that exhibit resistance to environmental stressors, particularly heavy metals, have the potential to be used in bioremediation strategies. This study aimed to explore and identify microorganisms that are resistant to heavy metals in soil environments as potential candidates for bioremediation. Metagenomic analysis was conducted using microbiome metagenomes obtained from the rhizosphere of soil contaminated with heavy metals and mineral-affected soil. The analysis resulted in the recovery of a total of 175 metagenome-assembled genomes (MAGs), 73 of which were potentially representing novel taxonomic levels beyond the genus level. The constructed ecological network revealed the presence of keystone taxa, including Rhizobiaceae, Xanthobacteraceae, Burkholderiaceae, and Actinomycetia. Among the recovered MAGs, 50 were associated with these keystone taxa. Notably, these MAGs displayed an abundance of genes conferring resistance to heavy metals and other abiotic stresses, particularly those affiliated with the keystone taxa. These genes were found to combat excessive accumulation of zinc/manganese, arsenate/arsenite, chromate, nickel/cobalt, copper, and tellurite. Furthermore, the keystone taxa were found to utilize both organic and inorganic energy sources, such as sulfur, arsenic, and carbon dioxide. Additionally, these keystone taxa exhibited the ability to promote vegetation development in re-vegetated mining areas through phosphorus solubilization and metabolite secretion. In summary, our study highlights the metabolic adaptability and ecological significance of microbial keystone taxa in mineral-affected soils. The MAGs associated with keystone taxa exhibited a markedly higher number of genes related to abiotic stress resistance and plant growth promotion compared to non-keystone taxa MAGs.
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Affiliation(s)
- Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Teng Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
- Hunan Urban and Rural Environmental Construction Co., Ltd, Changsha, China
| | - Yongjun Liu
- Hunan Tobacco Science Institute, Changsha, China
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16
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Wang J, Qu YN, Evans PN, Guo Q, Zhou F, Nie M, Jin Q, Zhang Y, Zhai X, Zhou M, Yu Z, Fu QL, Xie YG, Hedlund BP, Li WJ, Hua ZS, Wang Z, Wang Y. Evidence for nontraditional mcr-containing archaea contributing to biological methanogenesis in geothermal springs. SCIENCE ADVANCES 2023; 9:eadg6004. [PMID: 37379385 DOI: 10.1126/sciadv.adg6004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/24/2023] [Indexed: 06/30/2023]
Abstract
Recent discoveries of methyl-coenzyme M reductase-encoding genes (mcr) in uncultured archaea beyond traditional euryarchaeotal methanogens have reshaped our view of methanogenesis. However, whether any of these nontraditional archaea perform methanogenesis remains elusive. Here, we report field and microcosm experiments based on 13C-tracer labeling and genome-resolved metagenomics and metatranscriptomics, revealing that nontraditional archaea are predominant active methane producers in two geothermal springs. Archaeoglobales performed methanogenesis from methanol and may exhibit adaptability in using methylotrophic and hydrogenotrophic pathways based on temperature/substrate availability. A five-year field survey found Candidatus Nezhaarchaeota to be the predominant mcr-containing archaea inhabiting the springs; genomic inference and mcr expression under methanogenic conditions strongly suggested that this lineage mediated hydrogenotrophic methanogenesis in situ. Methanogenesis was temperature-sensitive , with a preference for methylotrophic over hydrogenotrophic pathways when incubation temperatures increased from 65° to 75°C. This study demonstrates an anoxic ecosystem wherein methanogenesis is primarily driven by archaea beyond known methanogens, highlighting diverse nontraditional mcr-containing archaea as previously unrecognized methane sources.
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Affiliation(s)
- Jiajia Wang
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Yan-Ni Qu
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Paul N Evans
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia 4072, QLD, Australia
| | - Qinghai Guo
- MOE Key Laboratory of Groundwater Quality and Health, State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
| | - Fengwu Zhou
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
- College of Geography Science, Nanjing Normal University, Nanjing 210023, China
| | - Ming Nie
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Fudan University, Shanghai 200433, China
| | - Qusheng Jin
- Department of Earth Sciences, University of Oregon, Eugene, OR 97403, USA
| | - Yan Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiangmei Zhai
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Ming Zhou
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Zhiguo Yu
- School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Qing-Long Fu
- MOE Key Laboratory of Groundwater Quality and Health, State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
| | - Yuan-Guo Xie
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, 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
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zheng-Shuang Hua
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Zimeng Wang
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Fudan University, Shanghai 200433, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Yanxin Wang
- MOE Key Laboratory of Groundwater Quality and Health, State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
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Egas C, Galbán-Malagón C, Castro-Nallar E, Molina-Montenegro MA. Role of Microbes in the degradation of organic semivolatile compounds in polar ecosystems: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 879:163046. [PMID: 36965736 DOI: 10.1016/j.scitotenv.2023.163046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/09/2023] [Accepted: 03/20/2023] [Indexed: 05/17/2023]
Abstract
The Arctic and the Antarctic Continent correspond to two eco-regions with extreme climatic conditions. These regions are exposed to the presence of contaminants resulting from human activity (local and global), which, in turn, represent a challenge for life forms in these environments. Anthropogenic pollution by semi-volatile organic compounds (SVOCs) in polar ecosystems has been documented since the 1960s. Currently, various studies have shown the presence of SVOCs and their bioaccumulation and biomagnification in the polar regions with negative effects on biodiversity and the ecosystem. Although the production and use of these compounds has been regulated, their persistence continues to threaten biodiversity and the ecosystem. Here, we summarize the current literature regarding microbes and SVOCs in polar regions and pose that bioremediation by native microorganisms is a feasible strategy to mitigate the presence of SVOCs. Our systematic review revealed that microbial communities in polar environments represent a wide reservoir of biodiversity adapted to extreme conditions, found both in terrestrial and aquatic environments, freely or in association with vegetation. Microorganisms adapted to these environments have the potential for biodegradation of SVOCs through a variety of genes encoding enzymes with the capacity to metabolize SVOCs. We suggest that a comprehensive approach at the molecular and ecological level is required to mitigate SVOCs presence in these regions. This is especially patent when considering that SVOCs degrade at slow rates and possess the ability to accumulate in polar ecosystems. The implications of SVOC degradation are relevant for the preservation of polar ecosystems with consequences at a global level.
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Affiliation(s)
- Claudia Egas
- Centre for Integrative Ecology (CIE), Universidad de Talca, Campus Lircay, Talca, Chile; Instituto de Ciencias Biológicas (ICB), Universidad de Talca, Campus Lircay, Talca, Chile
| | - Cristóbal Galbán-Malagón
- Centro de Genómica, Ecología y Medio Ambiente (GEMA), Universidad Mayor, Campus Huechuraba, Santiago, Chile; Institute of Environment, Florida International University, University Park, Miami, FL 33199, USA
| | - Eduardo Castro-Nallar
- Centre for Integrative Ecology (CIE), Universidad de Talca, Campus Lircay, Talca, Chile; Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Campus Lircay, Talca, Chile
| | - Marco A Molina-Montenegro
- Centre for Integrative Ecology (CIE), Universidad de Talca, Campus Lircay, Talca, Chile; Instituto de Ciencias Biológicas (ICB), Universidad de Talca, Campus Lircay, Talca, Chile; Centro de Investigación en Estudios Avanzados del Maule (CIEAM), Universidad Católica del Maule, Talca, Chile.
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18
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Shu W, Li F, Zhang Q, Li Z, Qiao Y, Audet J, Chen G. Pollution caused by mining reshaped the structure and function of bacterial communities in China's largest ion-adsorption rare earth mine watershed. JOURNAL OF HAZARDOUS MATERIALS 2023; 451:131221. [PMID: 36934702 DOI: 10.1016/j.jhazmat.2023.131221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/21/2023] [Accepted: 03/14/2023] [Indexed: 06/18/2023]
Abstract
Ion-adsorption rare earth mining results in the production of high levels of nitrogen, multiple metals, and strong acidic mine drainage (AMD), the impacts of which on microbial assembly and ecological functions remain unclear. To address this knowledge gap, we collected river sediments from the watershed of China's largest ion-adsorption rare earth mine and analyzed the bacterial community's structure, function, and assembly mechanisms. Results showed that bacterial community assembly was weakly affected by spatial dispersion, and dispersal limitation and homogeneous selection were the dominant ecological processes, with the latter increasing with pollution gradients. Bacterial alpha diversity decreased with pollution, which was mainly influenced by lead (Pb), pH, rare earth elements (REEs), and electrical conductivity (EC). However, bacteria developed survival strategies (i.e., enhanced acid tolerance and interspecific competition) to adapt to extreme environments, sustaining species diversity and community stability. Community structure and function showed a consistent response to the polluted environment (r = 0.662, P = 0.001). Enhanced environmental selection reshaped key microbial-mediated biogeochemical processes in the mining area, in particular weakening the potential for microbial denitrification. These findings provide new insights into the ecological response of microbes to compound pollution and offer theoretical support for proposing effective remediation and management strategies for polluted areas.
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Affiliation(s)
- Wang Shu
- Shandong Yucheng Agro-Ecosystem National Observation and Research Station, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, 100101 Beijing, China; Sino-Danish College of University of Chinese Academy of Sciences, 101408 Beijing, China; Sino-Danish Centre for Education and Research, 101408 Beijing, China
| | - Fadong Li
- Shandong Yucheng Agro-Ecosystem National Observation and Research Station, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, 100101 Beijing, China; Sino-Danish College of University of Chinese Academy of Sciences, 101408 Beijing, China
| | - Qiuying Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 100012 Beijing, China.
| | - Zhao Li
- Shandong Yucheng Agro-Ecosystem National Observation and Research Station, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, 100101 Beijing, China
| | - Yunfeng Qiao
- Shandong Yucheng Agro-Ecosystem National Observation and Research Station, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, 100101 Beijing, China
| | - Joachim Audet
- Department of Ecoscience, Aarhus University, C.F. Møllers Allé, 8000 Aarhus, Denmark
| | - Gang Chen
- Department of Civil and Environmental Engineering, Florida A&M University (FAMU)-Florida State University (FSU) Joint College of Engineering, 32310, United States
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19
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Wang G, Yin X, Feng Z, Chen C, Chen D, Wu B, Liu C, Morel JL, Jiang Y, Yu H, He H, Chao Y, Tang Y, Qiu R, Wang S. Novel biological aqua crust enhances in situ metal(loid) bioremediation driven by phototrophic/diazotrophic biofilm. MICROBIOME 2023; 11:110. [PMID: 37202810 DOI: 10.1186/s40168-023-01549-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 04/13/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND Understanding the ecological and environmental functions of phototrophic biofilms in the biological crust is crucial for improving metal(loid) (e.g. Cd, As) bioremediation in mining ecosystems. In this study, in combination with metal(loid) monitoring and metagenomic analysis, we systematically evaluated the effect of biofilm in a novel biological aqua crust (biogenic aqua crust-BAC) on in situ metal(loid) bioremediation of a representative Pb/Zn tailing pond. RESULTS We observed strong accumulation of potentially bioavailable metal(loid)s and visible phototrophic biofilms in the BAC. Furthermore, dominating taxa Leptolyngbyaceae (10.2-10.4%, Cyanobacteria) and Cytophagales (12.3-22.1%, Bacteroidota) were enriched in biofilm. Along with predominant heterotrophs (e.g. Cytophagales sp.) as well as diazotrophs (e.g. Hyphomonadaceae sp.), autotrophs/diazotrophs (e.g. Leptolyngbyaceae sp.) in phototrophic biofilm enriched the genes encoding extracellular peptidase (e.g. family S9, S1), CAZymes (e.g. CBM50, GT2) and biofilm formation (e.g. OmpR, CRP and LuxS), thus enhancing the capacity of nutrient accumulation and metal(loid) bioremediation in BAC system. CONCLUSIONS Our study demonstrated that a phototrophic/diazotrophic biofilm constitutes the structured communities containing specific autotrophs (e.g. Leptolyngbyaceae sp.) and heterotrophs (e.g. Cytophagales sp.), which effectively control metal(loid) and nutrient input using solar energy in aquatic environments. Elucidation of the mechanisms of biofilm formation coupled with metal(loid) immobilization in BAC expands the fundamental understanding of the geochemical fate of metal(loid)s, which may be harnessed to enhance in situ metal(loid) bioremediation in the aquatic ecosystem of the mining area. Video Abstract.
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Affiliation(s)
- Guobao Wang
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Xiuran Yin
- Microbial Ecophysiology Group, University of Bremen, Bremen, Germany
| | - Zekai Feng
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Chiyu Chen
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Daijie Chen
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Bo Wu
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Chong Liu
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jean Louis Morel
- Laboratoire Sols Et Environnement, UMR 1120, Université de Lorraine, INRAE, 54518, Vandoeuvre-Lès-Nancy, France
| | - Yuanyuan Jiang
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Hang Yu
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Huan He
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Yuanqing Chao
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yetao Tang
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Rongliang Qiu
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China.
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou, 510275, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China.
| | - Shizhong Wang
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China.
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-Sen University, Guangzhou, 510275, China.
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20
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Zhu M, Qi X, Yuan Y, Zhou H, Rong X, Dang Z, Yin H. Deciphering the distinct successional patterns and potential roles of abundant and rare microbial taxa of urban riverine plastisphere. JOURNAL OF HAZARDOUS MATERIALS 2023; 450:131080. [PMID: 36842200 DOI: 10.1016/j.jhazmat.2023.131080] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/01/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
Microbial colonization on microplastics has provoked global concern; however, many studies have not considered the successional patterns and potential roles of abundant and rare taxa of the plastisphere during colonization. Hence, we investigate the taxonomic composition, assembly, interaction and function of abundant and rare taxa in the riverine plastisphere by conducting microcosm experiments. Results showed that rare taxa occupied significantly high community diversity and niche breadth than the abundant taxa, which implies that rare taxa are essential components in maintaining the community stability of the plastisphere. However, the abundant taxa played a major role in driving the succession of plastisphere communities during colonization. Both stochastic and deterministic processes signally affected the plastisphere community assemblies; while, the deterministic patterns (heterogeneous selection) were especially pronounced for rare biospheres. Plastisphere microbial networks were shaped by the enhancement of network modularity and reinforcement of positive interactions. Rare taxa played critical roles in shaping stable plastisphere by occupying the key status in microbial networks. The strong interaction of rare and non-rare taxa suggested that multi-species collaboration might be conducive to the formation and stability of the plastisphere. Both abundant and rare taxa were enriched with plentiful functional genes related to carbon, nitrogen, phosphorus and sulfur cycling; however, their potential metabolic functions were significantly discrepant, implying that the abundant and rare microbes may play different roles in ecosystems. Overall, this study strengthens our comprehending of the mechanisms regarding the formation and maintenance of the plastisphere.
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Affiliation(s)
- Minghan Zhu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Xin Qi
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Yibo Yuan
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Heyang Zhou
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Xufa Rong
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, China
| | - Hua Yin
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou 510006, China.
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21
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Nie WB, Xie GJ, Tan X, Ding J, Lu Y, Chen Y, Yang C, He Q, Liu BF, Xing D, Ren N. Microbial Niche Differentiation during Nitrite-Dependent Anaerobic Methane Oxidation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:7029-7040. [PMID: 37041123 DOI: 10.1021/acs.est.2c08094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Nitrite-dependent anaerobic methane oxidation (n-DAMO) has been demonstrated to play important roles in the global methane and nitrogen cycle. However, despite diverse n-DAMO bacteria widely detected in environments, little is known about their physiology for microbial niche differentiation. Here, we show the microbial niche differentiation of n-DAMO bacteria through long-term reactor operations combining genome-centered omics and kinetic analysis. With the same inoculum dominated by both species "Candidatus Methylomirabilis oxyfera" and "Candidatus Methylomirabilis sinica", n-DAMO bacterial population was shifted to "Ca. M. oxyfera" in a reactor fed with low-strength nitrite, but shifted to "Ca. M. sinica" with high-strength nitrite. Metatranscriptomic analysis showed that "Ca. M. oxyfera" harbored more complete function in cell chemotaxis, flagellar assembly, and two-component system for better uptake of nitrite, while "Ca. M. sinica" had a more active ion transport and stress response system, and more redundant function in nitrite reduction to mitigate nitrite inhibition. Importantly, the half-saturation constant of nitrite (0.057 mM vs 0.334 mM NO2-) and inhibition thresholds (0.932 mM vs 2.450 mM NO2-) for "Ca. M. oxyfera" vs "Ca. M. sinica", respectively, were highly consistent with genomic results. Integrating these findings demonstrated biochemical characteristics, especially the kinetics of nitrite affinity and inhibition determine niche differentiation of n-DAMO bacteria.
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Affiliation(s)
- Wen-Bo Nie
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Guo-Jun Xie
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang District, Harbin 150090, China
| | - Xin Tan
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang District, Harbin 150090, China
| | - Jie Ding
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang District, Harbin 150090, China
| | - Yang Lu
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Yi Chen
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Chun Yang
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Qiang He
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Bing-Feng Liu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang District, Harbin 150090, China
| | - Defeng Xing
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang District, Harbin 150090, China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, No. 73, Huanghe Road, Nangang District, Harbin 150090, China
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22
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Cui W, Li R, Fan Z, Wu L, Zhao X, Wei G, Shu D. Weak environmental adaptation of rare phylotypes sustaining soil multi-element cycles in response to decades-long fertilization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:162063. [PMID: 36746286 DOI: 10.1016/j.scitotenv.2023.162063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/29/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Deciphering the ecological role of soil communities in the maintenance of multiple ecosystem functions is pivotal for the conservation and sustainability of soil biodiversity. However, few studies have investigated niche differentiation of abundant and rare microbiota, as well as their contributions to multiple soil elemental cycles, particularly in agroecosystems that have received decades of intense fertilization. Here, we characterized the environmental thresholds and phylogenetic signals for the environmental adaptation of both abundant and rare microbial subcommunities via amplicon sequencing and metagenomic sequencing and explored their importance in sustaining soil multiple nutrient cycling in agricultural fields that were fertilized for two decades. The results showed that rare taxa exhibited narrower niche breadths and weaker phylogenetic signals than abundant species. The assembly of abundant subcommunity was shaped predominantly by dispersal limitation (explained 71.1 % of the variation in bacteria) and undominated processes (explained 75 % of the variation in fungi), whereas the assembly of rare subcommunity was dominated by homogeneous selection process (explained 100 % of the variation in bacteria and 60 % of the variation in fungi). Soil ammonia nitrogen was the leading factor mediating the balance between stochastic and deterministic processes in both abundant (R2 = 0.15, P < 0.001) and rare (R2 = 0.08, P < 0.001) bacterial communities. Notably, the rare biosphere largely contributed to key soil processes such as carbon (R2bacteria = 0.03, P < 0.05; R2fungi = 0.05, P < 0.05) and nitrogen (R2bacteria = 0.03, P < 0.05; R2fungi = 0.17, P < 0.001) cycling. Collectively, these findings facilitate our understanding of the maintenance of rhizosphere bacterial and fungal diversity in response to agricultural fertilization and highlight the key role of rare taxa in sustaining agricultural ecosystem functions.
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Affiliation(s)
- Weili Cui
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ruochen Li
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhen Fan
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Likun Wu
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xining Zhao
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, 712100 Yangling, Shaanxi, China; Institute of Soil and Water Conservation, Northwest A&F University, 712100 Yangling, Shaanxi, China
| | - Gehong Wei
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Duntao Shu
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China; State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
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23
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Zhang Y, Liu T, Li MM, Hua ZS, Evans P, Qu Y, Tan S, Zheng M, Lu H, Jiao JY, Lücker S, Daims H, Li WJ, Guo J. Hot spring distribution and survival mechanisms of thermophilic comammox Nitrospira. THE ISME JOURNAL 2023:10.1038/s41396-023-01409-w. [PMID: 37069235 DOI: 10.1038/s41396-023-01409-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/19/2023]
Abstract
The recent discovery of Nitrospira species capable of complete ammonia oxidation (comammox) in non-marine natural and engineered ecosystems under mesothermal conditions has changed our understanding of microbial nitrification. However, little is known about the occurrence of comammox bacteria or their ability to survive in moderately thermal and/or hyperthermal habitats. Here, we report the wide distribution of comammox Nitrospira in five terrestrial hot springs at temperatures ranging from 36 to 80°C and provide metagenome-assembled genomes of 11 new comammox strains. Interestingly, the identification of dissimilatory nitrate reduction to ammonium (DNRA) in thermophilic comammox Nitrospira lineages suggests that they have versatile ecological functions as both sinks and sources of ammonia, in contrast to the described mesophilic comammox lineages, which lack the DNRA pathway. Furthermore, the in situ expression of key genes associated with nitrogen metabolism, thermal adaptation, and oxidative stress confirmed their ability to survive in the studied hot springs and their contribution to nitrification in these environments. Additionally, the smaller genome size and higher GC content, less polar and more charged amino acids in usage profiles, and the expression of a large number of heat shock proteins compared to mesophilic comammox strains presumably confer tolerance to thermal stress. These novel insights into the occurrence, metabolic activity, and adaptation of comammox Nitrospira in thermal habitats further expand our understanding of the global distribution of comammox Nitrospira and have significant implications for how these unique microorganisms have evolved thermal tolerance strategies.
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Affiliation(s)
- Yan Zhang
- School of Environmental and Chemical Engineering, Foshan University, Foshan, China
| | - Tao Liu
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, QLD, Australia
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zheng-Shuang Hua
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China.
| | - Paul Evans
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Yanni Qu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Sha Tan
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Min Zheng
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, QLD, Australia
| | - Hui Lu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Sebastian Lücker
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Holger Daims
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- The Comammox Research Platform, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St Lucia, QLD, Australia.
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24
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Li XT, Huang ZS, Huang Y, Jiang Z, Liang ZL, Yin HQ, Zhang GJ, Jia Y, Deng Y, Liu SJ, Jiang CY. Responses of microbial community to geochemical parameters on vertical depth in bioheap system of low-grade copper sulfide. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 869:161752. [PMID: 36690115 DOI: 10.1016/j.scitotenv.2023.161752] [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: 10/15/2022] [Revised: 01/15/2023] [Accepted: 01/17/2023] [Indexed: 06/17/2023]
Abstract
Monitoring of the microbial community in bioleaching system is essential for control process parameters and enhance the leaching efficiency. Due to the difficulty of sampling, microbial distribution, community succession and bioleaching activity along the vertical depth of bioleaching heaps remain unresolved. This study investigated the geochemical parameters and microbial community structure along a depth profile in a bioleaching heap and leachate. 80 ore samples at different heap depths and 9 leaching solution samples from three bioheaps of Zijin Copper Mine were collected. Microbial composition, mineral types and geochemical parameters of these samples were analyzed by 16S rRNA high-throughput sequencing and a series of chemical measurement technologies. The results revealed that the pH, Cu, Fe and the total sulfur contents were the major factors shaping the composition of the microbial communities in the bioleaching system. The extent of mineral oxidation increased as the sample depth increases, followed by the increasing of sulfur oxidizers. The abundance of sulfur and iron oxidizers including members of Acidithiobacillus, Sulfobacillus and Acidiferrobacter were significantly higher in the leaching heap than in the leaching solution, meanwhile, they showed strong positive interactions with other members within the same genera and iron oxidizer Leptospirillum and Ferroplasma. Besides, Acidithiobacillus negatively interacted with heterotrophs such as Sphingobium, Exiguobacterium, Brevundimonas and so on. On the contrast, members of Leptospirillum and unclassified Archaea were significantly abundant in the leaching solution and revealed strong interactions with members of Thermoplasmatales. The main conclusion of this study, especially the leaching potential of microorganisms prevailing in bioheaps and their relationships with geochemical factors, provides theoretical guidance for future process design such as the control of processing parameters and microbial community in heap leaching.
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Affiliation(s)
- Xiu-Tong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhong-Sheng Huang
- School of Metallurgy and Environment, Central South University, Changsha 410083, Hunan, China; Zijin Mining Group Company Limited, Shanghang 364200, Fujian, China
| | - Ye Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zong-Lin Liang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hua-Qun Yin
- Key Laboratory of Biometallurgy of Ministry of Education, School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Guang-Ji Zhang
- Innovation Academy for Green Manufacture, Chinese Academy of Sciences, Beijing 100190, China; Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Yan Jia
- Innovation Academy for Green Manufacture, Chinese Academy of Sciences, Beijing 100190, China; Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Ye Deng
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Whaley-Martin KJ, Chen LX, Nelson TC, Gordon J, Kantor R, Twible LE, Marshall S, McGarry S, Rossi L, Bessette B, Baron C, Apte S, Banfield JF, Warren LA. O 2 partitioning of sulfur oxidizing bacteria drives acidity and thiosulfate distributions in mining waters. Nat Commun 2023; 14:2006. [PMID: 37037821 PMCID: PMC10086054 DOI: 10.1038/s41467-023-37426-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 03/14/2023] [Indexed: 04/12/2023] Open
Abstract
The acidification of water in mining areas is a global environmental issue primarily catalyzed by sulfur-oxidizing bacteria (SOB). Little is known about microbial sulfur cycling in circumneutral pH mine tailing impoundment waters. Here we investigate biological sulfur oxidation over four years in a mine tailings impoundment water cap, integrating aqueous sulfur geochemistry, genome-resolved metagenomics and metatranscriptomics. The microbial community is consistently dominated by neutrophilic, chemolithoautotrophic SOB (relative abundances of ~76% in 2015, ~55% in 2016/2017 and ~60% in 2018). Results reveal two SOB strategies alternately dominate across the four years, influencing acid generation and sulfur speciation. Under oxic conditions, novel Halothiobacillus drive lower pH conditions (as low as 4.3) and lower [S2O32-] via the complete Sox pathway coupled to O2. Under anoxic conditions, Thiobacillus spp. dominate in activity, via the incomplete Sox and rDSR pathways coupled to NO3-, resulting in higher [S2O32-] and no net significant acidity generation. This study provides genomic evidence explaining acidity generation and thiosulfate accumulation patterns in a circumneutral mine tailing impoundment and has significant environmental applications in preventing the discharge of sulfur compounds that can impact downstream environments. These insights illuminate opportunities for in situ biotreatment of reduced sulfur compounds and prediction of acidification events using gene-based monitoring and in situ RNA detection.
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Affiliation(s)
- Kelly J Whaley-Martin
- University of Toronto, Toronto, ON, Canada
- Environmental Resources management (ERM), Toronto, ON, Canada
| | - Lin-Xing Chen
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | | | | | - Rose Kantor
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | | | - Stephanie Marshall
- Environmental Resources management (ERM), Toronto, ON, Canada
- McMaster University, Hamilton, ON, Canada
| | - Sam McGarry
- Glencore, Sudbury Integrated Nickel Operations, Sudbury, ON, Canada
| | | | | | | | - Simon Apte
- CSIRO Land and Water, Clayton, NSW, Australia
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
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Kumar J, Sharma N, Singh SP. Genome-resolved metagenomics inferred novel insights into the microbial community, metabolic pathways, and biomining potential of Malanjkhand acidic copper mine tailings. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:50864-50882. [PMID: 36807860 DOI: 10.1007/s11356-023-25893-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 02/08/2023] [Indexed: 04/16/2023]
Abstract
Mine tailing sites provide profound opportunities to elucidate the microbial mechanisms involved in ecosystem functioning. In the present study, metagenomic analysis of dumping soil and adjacent pond around India's largest copper mine at Malanjkhand has been done. Taxonomic analysis deciphered the abundance of phyla Proteobacteria, Bacteroidetes, Acidobacteria, and Chloroflexi. Genomic signatures of viruses were predicted in the soil metagenome, whereas Archaea and Eukaryotes were noticed in water samples. Mesophilic chemolithotrophs, such as Acidobacteria bacterium, Chloroflexi bacterium, and Verrucomicrobia bacterium, were predominant in soil, whereas, in the water sample, the abundance of Methylobacterium mesophilicum, Pedobacter sp., and Thaumarchaeota archaeon was determined. The functional potential analysis highlighted the abundance of genes related to sulfur, nitrogen, methane, ferrous oxidation, carbon fixation, and carbohydrate metabolisms. The genes for copper, iron, arsenic, mercury, chromium, tellurium, hydrogen peroxide, and selenium resistance were found to be predominant in the metagenomes. Metagenome-assembled genomes (MAGs) were constructed from the sequencing data, indicating novel microbial species genetically related to the phylum predicted through whole genome metagenomics. Phylogenetic analysis, genome annotations, functional potential, and resistome analysis showed the resemblance of assembled novel MAGs with traditional organisms used in bioremediation and biomining applications. Microorganisms harboring adaptive mechanisms, such as detoxification, hydroxyl radical scavenging, and heavy metal resistance, could be the potent benefactions for their utility as bioleaching agents. The genetic information produced in the present investigation provides a foundation for pursuing and understanding the molecular aspects of bioleaching and bioremediation applications.
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Affiliation(s)
- Jitesh Kumar
- Center of Innovative and Applied Bioprocessing, Department of Biotechnology (DBT), Govt. of India, S.A.S. Nagar, Sector-81, (Knowledge City) Mohali, 140306, India
| | - Nitish Sharma
- Center of Innovative and Applied Bioprocessing, Department of Biotechnology (DBT), Govt. of India, S.A.S. Nagar, Sector-81, (Knowledge City) Mohali, 140306, India
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing, Department of Biotechnology (DBT), Govt. of India, S.A.S. Nagar, Sector-81, (Knowledge City) Mohali, 140306, India.
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Li D, Ren Z, Zhou Y, Jiang L, Zheng M, Liu G. Comammox Nitrospira and Ammonia-Oxidizing Archaea Are Dominant Ammonia Oxidizers in Sediments of an Acid Mine Lake Containing High Ammonium Concentrations. Appl Environ Microbiol 2023; 89:e0004723. [PMID: 36912626 PMCID: PMC10056971 DOI: 10.1128/aem.00047-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 01/31/2023] [Indexed: 03/14/2023] Open
Abstract
Exploring nitrifiers in extreme environments is vital to expanding our understanding of nitrogen cycle and microbial diversity. This study presents that complete ammonia oxidation (comammox) Nitrospira, together with acidophilic ammonia-oxidizing archaea (AOA), dominate in the nitrifying guild in sediments of an acid mine lake (AML). The lake water was characterized by acidic pH below 5 with a high ammonium concentration of 175 mg-N/liter, which is rare on the earth. Nitrification was active in sediments with a maximum nitrate production potential of 70.5 μg-N/(g-dry weight [dw] day) for mixed sediments. Quantitative PCR assays determined that in AML sediments, comammox Nitrospira and AOA amoA genes had relative abundances of 52% and 41%, respectively, among the total amoA genes. Further assays with 16S rRNA and amoA gene amplicon sequencing and metagenomics confirmed their dominance and revealed that the comammox Nitrospira found in sediments belonged to comammox Nitrospira clade A.2. Metagenomic binning retrieved a metagenome-assembled genome (MAG) of the comammox Nitrospira from sediments (completeness = 96.76%), and phylogenomic analysis suggested that it was a novel comammox Nitrospira. Comparative genomic investigation revealed that this comammox Nitrospira contained diverse metal resistance genes and an acidophile-affiliated F-type ATPase. Moreover, it had a more diverse genomic characteristic on nitrogen metabolism than the AOA in sediments and canonical AOB did. The results suggest that comammox Nitrospira is a versatile nitrifier that can adapt to acidic environments even with high ammonium concentrations. IMPORTANCE Ammonia-oxidizing archaea (AOA) was previously considered the sole dominant ammonia oxidizer in acidic environments. This study, however, found that complete ammonia oxidation (comammox) Nitrospira was also a dominant ammonia oxidizer in the sediments of an acidic mine lake, which had an acidic pH < 5 and a high ammonium concentration of 175 mg-N/liter. In combination with average nucleotide identity analysis, phylogenomic analysis suggested it is a novel strain of comammox Nitrospira. Moreover, the adaption of comammox Nitrospira to the acidic lake had been comprehensively investigated based on genome-centric metagenomic approaches. The outcomes of this study significantly expand our understanding of the diversity and adaptability of ammonia oxidizers in the acidic environments.
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Affiliation(s)
- Deyong Li
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Zhichang Ren
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Yangqi Zhou
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Lugao Jiang
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Min Zheng
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), University of Queensland, St. Lucia, Brisbane, Queensland, Australia
| | - Guoqiang Liu
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
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Determinants of Total and Active Microbial Communities Associated with Cyanobacterial Aggregates in a Eutrophic Lake. mSystems 2023; 8:e0099222. [PMID: 36927063 PMCID: PMC10134853 DOI: 10.1128/msystems.00992-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
Cyanobacterial aggregates (CAs) comprised of photosynthetic and phycospheric microorganisms are often the cause of cyanobacterial blooms in eutrophic freshwater lakes. Although phylogenetic diversity in CAs has been extensively studied, much less was understood about the activity status of microorganisms inside CAs and determinants of their activities. In this study, the 16S rRNA gene (rDNA)-based total communities within CAs in Lake Taihu of China were analyzed over a period of 6 months during the bloom season; the 16S rRNA-based active communities during daytime, nighttime, and under anoxic conditions were also profiled. Synchronous turnover of both cyanobacterial and phycospheric communities was observed, suggesting the presence of close interactions. The rRNA/rDNA ratio-based relative activities of individual taxa were predominantly determined by their rDNA-based relative abundances. In particular, high-abundance taxa demonstrated comparatively lower activities, whereas low-abundance taxa were generally more active. In comparison, hydrophysicochemical factors as well as diurnal and redox conditions showed much less impact on relative activities of microbial taxa within CAs. Nonetheless, total and active communities exhibited differences in community assembly processes, the former of which were almost exclusively controlled by homogeneous selection during daytime and under anoxia. Taken together, the results from this study provide novel insights into the relationships among microbial activities, community structure, and environmental conditions and highlight the importance of further exploring the regulatory mechanisms of microbial activities at the community level. IMPORTANCE Cyanobacterial aggregates are important mediators of biogeochemical cycles in eutrophic lakes during cyanobacterial blooms, yet regulators of microbial activities within them are not well understood. This study revealed rDNA-based abundances strongly affected the relative activities of microbial taxa within Microcystis aggregates, as well as trade-off effects between microbial abundances and activities. Environmental conditions further improved the levels of relative activities and affected community assembly mechanisms in phycospheric communities. The relationships among microbial activities, abundances, and environmental conditions improve our understanding of the regulatory mechanisms of microbial activities in cyanobacterial aggregates and also provide a novel clue for studying determinants of microbial activities in other ecosystems.
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Wang W, Cheng X, Song Y, Wang H, Wu M, Ma L, Lu X, Liu X, Tuovinen OH. Elevated antimony concentration stimulates rare taxa of potential autotrophic bacteria in the Xikuangshan groundwater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 864:161105. [PMID: 36566853 DOI: 10.1016/j.scitotenv.2022.161105] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/29/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
Microbial communities composed of few abundant and many rare species are widely involved in the biogeochemical cycles of elements. Yet little is known about the ecological roles of rare taxa in antimony (Sb) contaminated groundwater. Groundwater samples were collected along an Sb concentration gradient in the Xikuangshan antimony mine area and subjected to high through-put sequencing of 16S rRNA genes to investigate the bacterial communities. Results suggested that both abundant and rare sub-communities were dominated by Betaproteobacteria, Gammaproteobacteria, and Alphaproteobacteria, whereas rare sub-communities showed higher alpha-diversities. Multivariate analysis showed that both the abundant and rare taxa were under the stress of Sb, but the impact on rare taxa was greater. Nitrate explained a large part for the variation of the abundant sub-communities, indicating the critical role of nitrate for their activities under anoxic conditions. In contrast, bicarbonate significantly impacted rare sub-communities, suggesting their potential autotrophic characteristics. To further explore the role of rare taxa in the communities and the mechanism of affecting the community composition, a network was constructed to display the co-occurrence pattern of bacterial communities. The rare taxa contributed most of the network nodes and served as keystone species to maintain the stability of community. Abiotic factors (mainly Sb and pH) and bacterial interspecific interactions (interactions between keystone species and other bacterial groups) jointly affect the community dynamics. Functional prediction was performed to further reveal the ecological function of rare taxa in the Sb-disturbed groundwater environment. The results indicated that the rare taxa harbored much more diverse functions than their abundant counterparts. Notably, elevated Sb concentration promoted some potential autotrophic functions in rare taxa such as the oxidation of S-, N-, and Fe(II)-compounds. These results offer new insights into the roles of rare species in elemental cycles in the Sb-impacted groundwater.
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Affiliation(s)
- Weiqi Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Xiaoyu Cheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Yuyang Song
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China.
| | - Mengxiaojun Wu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Liyuan Ma
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Xiaolu Lu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Xiaoyan Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Olli H Tuovinen
- Department of Microbiology, Ohio State University, Columbus 43210, USA
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30
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Dopson M, González-Rosales C, Holmes DS, Mykytczuk N. Eurypsychrophilic acidophiles: From (meta)genomes to low-temperature biotechnologies. Front Microbiol 2023; 14:1149903. [PMID: 37007468 PMCID: PMC10050440 DOI: 10.3389/fmicb.2023.1149903] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/16/2023] [Indexed: 03/17/2023] Open
Abstract
Low temperature and acidic environments encompass natural milieus such as acid rock drainage in Antarctica and anthropogenic sites including drained sulfidic sediments in Scandinavia. The microorganisms inhabiting these environments include polyextremophiles that are both extreme acidophiles (defined as having an optimum growth pH < 3), and eurypsychrophiles that grow at low temperatures down to approximately 4°C but have an optimum temperature for growth above 15°C. Eurypsychrophilic acidophiles have important roles in natural biogeochemical cycling on earth and potentially on other planetary bodies and moons along with biotechnological applications in, for instance, low-temperature metal dissolution from metal sulfides. Five low-temperature acidophiles are characterized, namely, Acidithiobacillus ferriphilus, Acidithiobacillus ferrivorans, Acidithiobacillus ferrooxidans, “Ferrovum myxofaciens,” and Alicyclobacillus disulfidooxidans, and their characteristics are reviewed. Our understanding of characterized and environmental eurypsychrophilic acidophiles has been accelerated by the application of “omics” techniques that have aided in revealing adaptations to low pH and temperature that can be synergistic, while other adaptations are potentially antagonistic. The lack of known acidophiles that exclusively grow below 15°C may be due to the antagonistic nature of adaptations in this polyextremophile. In conclusion, this review summarizes the knowledge of eurypsychrophilic acidophiles and places the information in evolutionary, environmental, biotechnological, and exobiology perspectives.
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Affiliation(s)
- Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
- *Correspondence: Mark Dopson
| | - Carolina González-Rosales
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastian, Santiago, Chile
| | - Nadia Mykytczuk
- Goodman School of Mines, Laurentian University, Sudbury, ON, Canada
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Diverse Methylmercury (MeHg) Producers and Degraders Inhabit Acid Mine Drainage Sediments, but Few Taxa Correlate with MeHg Accumulation. mSystems 2023; 8:e0073622. [PMID: 36507660 PMCID: PMC9948709 DOI: 10.1128/msystems.00736-22] [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] [Indexed: 12/15/2022] Open
Abstract
Methylmercury (MeHg) is a notorious neurotoxin, and its production and degradation in the environment are mainly driven by microorganisms. A variety of microbial MeHg producers carrying the gene pair hgcAB and degraders carrying the merB gene have been separately reported in recent studies. However, surprisingly little attention has been paid to the simultaneous investigation of the diversities of microbial MeHg producers and degraders in a given habitat, and no studies have been performed to explore to what extent these two contrasting microbial groups correlate with MeHg accumulation in the habitat of interest. Here, we collected 86 acid mine drainage (AMD) sediments from an area spanning approximately 500,000 km2 in southern China and profiled the sediment-borne putative MeHg producers and degraders using genome-resolved metagenomics. 46 metagenome-assembled genomes (MAGs) containing hgcAB and 93 MAGs containing merB were obtained, including those from various taxa without previously known MeHg-metabolizing microorganisms. These diverse MeHg-metabolizing MAGs were formed largely via multiple independent horizontal gene transfer (HGT) events. The putative MeHg producers from Deltaproteobacteria and Firmicutes as well as MeHg degraders from Acidithiobacillia were closely correlated with MeHg accumulation in the sediments. Furthermore, these three taxa, in combination with two abiotic factors, explained over 60% of the variance in MeHg accumulation. Most of the members of these taxa were characterized by their metabolic potential for nitrogen fixation and copper tolerance. Overall, these findings improve our understanding of the ecology of MeHg-metabolizing microorganisms and likely have implications for the development of management strategies for the reduction of MeHg accumulation in the AMD sediments. IMPORTANCE Microorganisms are the main drivers of MeHg production and degradation in the environment. However, little attention has been paid to the simultaneous investigation of the diversities of microbial MeHg producers and degraders in a given habitat. We used genome-resolved metagenomics to reveal the vast phylogenetic and metabolic diversities of putative MeHg producers and degraders in AMD sediments. Our results show that the diversity of MeHg-metabolizing microorganisms (particularly MeHg degraders) in AMD sediments is much higher than was previously recognized. Via multiple linear regression analysis, we identified both microbial and abiotic factors affecting MeHg accumulation in AMD sediments. Despite their great diversity, only a few taxa of MeHg-metabolizing microorganisms were closely correlated with MeHg accumulation. This work underscores the importance of using genome-resolved metagenomics to survey MeHg-metabolizing microorganisms and provides a framework for the illumination of the microbial basis of MeHg accumulation via the characterization of physicochemical properties, MeHg-metabolizing microorganisms, and the correlations between them.
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Qu YN, Rao YZ, Qi YL, Li YX, Li A, Palmer M, Hedlund BP, Shu WS, Evans PN, Nie GX, Hua ZS, Li WJ. Panguiarchaeum symbiosum, a potential hyperthermophilic symbiont in the TACK superphylum. Cell Rep 2023; 42:112158. [PMID: 36827180 DOI: 10.1016/j.celrep.2023.112158] [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: 09/08/2022] [Revised: 12/27/2022] [Accepted: 02/09/2023] [Indexed: 02/24/2023] Open
Abstract
The biology of Korarchaeia remains elusive due to the lack of genome representatives. Here, we reconstruct 10 closely related metagenome-assembled genomes from hot spring habitats and place them into a single species, proposed herein as Panguiarchaeum symbiosum. Functional investigation suggests that Panguiarchaeum symbiosum is strictly anaerobic and grows exclusively in thermal habitats by fermenting peptides coupled with sulfide and hydrogen production to dispose of electrons. Due to its inability to biosynthesize archaeal membranes, amino acids, and purines, this species likely exists in a symbiotic lifestyle similar to DPANN archaea. Population metagenomics and metatranscriptomic analyses demonstrated that genes associated with amino acid/peptide uptake and cell attachment exhibited positive selection and were highly expressed, supporting the proposed proteolytic catabolism and symbiotic lifestyle. Our study sheds light on the metabolism, evolution, and potential symbiotic lifestyle of Panguiarchaeum symbiosum, which may be a unique host-dependent archaeon within the TACK superphylum.
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Affiliation(s)
- Yan-Ni Qu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Yang-Zhi Rao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Yan-Ling Qi
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Yu-Xian Li
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Andrew Li
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Marike Palmer
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - 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
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
| | - Paul N Evans
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Guo-Xing Nie
- College of Fisheries, Henan Normal University, Xinxiang, China
| | - Zheng-Shuang Hua
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China.
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Yi X, Wen P, Liang JL, Jia P, Yang TT, Feng SW, Liao B, Shu WS, Li JT. Phytostabilization mitigates antibiotic resistance gene enrichment in a copper mine tailings pond. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130255. [PMID: 36327844 DOI: 10.1016/j.jhazmat.2022.130255] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/06/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
Mining-impacted environments are distributed globally and have become increasingly recognized as hotspots of antibiotic resistance genes (ARGs). However, there are currently no reports on treatment technologies to deal with such an important environmental problem. To narrow this knowledge gap, we implemented a phytostabilization project in an acidic copper mine tailings pond and employed metagenomics to explore ARG characteristics in the soil samples. Our results showed that phytostabilization decreased the total ARG abundance in 0-10 cm soil layer by 75 %, which was companied by a significant decrease in ARG mobility, and a significant increase in ARG diversity and microbial diversity. Phytostabilization was also found to drastically alter the ARG host composition and to significantly reduce the total abundance of virulence factor genes of ARG hosts. Soil nutrient status, heavy metal toxicity and SO42- concentration were important physicochemical factors to affect the total ARG abundance, while causal mediation analysis showed that their effects were largely mediated by the changes in ARG mobility and microbial diversity. The increase in ARG diversity associated with phytostabilization was mainly mediated by a small subgroup of ARG hosts, most of which could not be classified at the genus level and deserve further research in the future.
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Affiliation(s)
- Xinzhu Yi
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
| | - Ping Wen
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
| | - Jie-Liang Liang
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
| | - Pu Jia
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
| | - Tao-Tao Yang
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Shi-Wei Feng
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
| | - Bin Liao
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Wen-Sheng Shu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
| | - Jin-Tian Li
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, PR China.
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Xu Y, You G, Yin J, Zhang M, Peng D, Xu J, Yang S, Hou J. Salt tolerance evolution facilitates antibiotic resistome in soil microbiota: Evidences from dissemination evaluation, hosts identification and co-occurrence exploration. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 317:120830. [PMID: 36481466 DOI: 10.1016/j.envpol.2022.120830] [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: 08/10/2022] [Revised: 11/26/2022] [Accepted: 12/04/2022] [Indexed: 06/17/2023]
Abstract
Salinity is considered as one of the vital factors affecting the profiles of antibiotic resistance genes (ARGs) in soils, whereby its roles in shaping the antibiotic resistome were still poorly understood. Here, metagenomic analysis was conducted to track the ARGs distributions and dissemination in soils during salt accumulation and desalinization processes. Neutral-salt accumulation for 45 and 90 days significantly increased the relative abundances of ARGs and mobile genetic elements (MGEs) carrying antibiotic resistance contigs (ARCs). The ARGs within antibiotic efflux and target protection families primarily carried by Streptomyces, Nocardioides, Rhodanobacter and Monashia were largely enriched by salinity. The ARGs subtypes of the resistance-nodulation-division (RND) family, ATP-binding cassette (ABC) family, rRNA methyltransferase and other efflux were closely associated with MGEs, contributing to the enrichment of ARGs. Moreover, the ARGs subtypes and transposons were genetically linked with the salt-tolerance mechanisms of organic osmolyte transporters and K+ uptake proteins on the same ARC, demonstrating the coselection of ARGs and halotolerant genes. Furthermore, the antibiotic resistome could recover to a normal state after the prolonged incubation by alleviating salt stress. Nevertheless, the acquisition of ARGs by opportunistic pathogens after salt treatment was increased, serving to prioritize further efforts on the health risks correlated with resistance propagation and human exposure in saline soils.
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Affiliation(s)
- Yi Xu
- College of Agricultural Science and Engineering, Hohai University, Nanjing, People's Republic of China, 210098.
| | - Guoxiang You
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, People's Republic of China, 210098
| | - Jinbao Yin
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, People's Republic of China, 210098
| | - Mairan Zhang
- College of Agricultural Science and Engineering, Hohai University, Nanjing, People's Republic of China, 210098
| | - Dengyun Peng
- College of Agricultural Science and Engineering, Hohai University, Nanjing, People's Republic of China, 210098
| | - Junzeng Xu
- College of Agricultural Science and Engineering, Hohai University, Nanjing, People's Republic of China, 210098; State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, PR China
| | - Shihong Yang
- College of Agricultural Science and Engineering, Hohai University, Nanjing, People's Republic of China, 210098; State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, PR China.
| | - Jun Hou
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, People's Republic of China, 210098
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Lian WH, Mohamad OAA, Dong L, Zhang LY, Wang D, Liu L, Han MX, Li S, Wang S, Antunes A, Fang BZ, Jiao JY, Li WJ. Culturomics- and metagenomics-based insights into the microbial community and function of rhizosphere soils in Sinai desert farming systems. ENVIRONMENTAL MICROBIOME 2023; 18:4. [PMID: 36639807 PMCID: PMC9840269 DOI: 10.1186/s40793-023-00463-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 01/08/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND The microbiome of the Sinai Desert farming system plays an important role in the adaptive strategy of growing crops in a harsh, poly-extreme, desert environment. However, the diversity and function of microbial communities under this unfavorable moisture and nutritional conditions have not yet been investigated. Based on culturomic and metagenomic methods, we analyzed the microbial diversity and function of a total of fourteen rhizosphere soil samples (collected from twelve plants in four farms of the Sinai desert), which may provide a valuable and meaningful guidance for the design of microbial inoculants. RESULTS The results revealed a wide range of microbial taxa, including a high proportion of novel undescribed lineages. The composition of the rhizosphere microbial communities differed according to the sampling sites, despite similarities or differences in floristics. Whereas, the functional features of rhizosphere microbiomes were significantly similar in different sampling sites, although the microbial communities and the plant hosts themselves were different. Importantly, microorganisms involved in ecosystem functions are different between the sampling sites, for example nitrogen fixation was prevalent in all sample sites while microorganisms responsible for this process were different. CONCLUSION Here, we provide the first characterization of microbial communities and functions of rhizosphere soil from the Sinai desert farming systems and highlight its unexpectedly high diversity. This study provides evidence that the key microorganisms involved in ecosystem functions are different between sampling sites with different environment conditions, emphasizing the importance of the functional microbiomes of rhizosphere microbial communities. Furthermore, we suggest that microbial inoculants to be used in future agricultural production should select microorganisms that can be involved in plant-microorganism interactions and are already adapted to a similar environmental setting.
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Affiliation(s)
- Wen-Hui Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Osama Abdalla Abdelshafy Mohamad
- Department of Environmental Protection, Faculty of Environmental Agricultural Sciences, Arish University, Arish, 45511, Egypt
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Macau, People's Republic of China
| | - Lei Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ling-Yu Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Dong Wang
- College of Life Science and Technology, Honghe University, Mengzi, 661199, People's Republic of China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ming-Xian Han
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shuang Wang
- Heilongjiang Academy of Black Soil Conservation and Utilization, Harbin, 150086, People's Republic of China
| | - André Antunes
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Macau, People's Republic of China
| | - Bao-Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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Cao H, Li S, He H, Sun Y, Wu Y, Huang Q, Cai P, Gao CH. Stronger linkage of diversity-carbon decomposition for rare rather than abundant bacteria in woodland soils. Front Microbiol 2023; 14:1115300. [PMID: 36937304 PMCID: PMC10017465 DOI: 10.3389/fmicb.2023.1115300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 02/03/2023] [Indexed: 03/06/2023] Open
Abstract
Soil microbial diversity is important for maintaining ecosystem functions. However, the linkage between microbial diversity, especially rare and abundant bacterial diversity, and carbon decomposition remains largely unknown. In this study, we assessed the establishment and maintenance of rare and abundant bacterial α-diversities at the taxonomic and phylogenetic levels and their linkages with soil carbon decomposition separately in four Chinese woodlands. Compared to abundant bacteria, rare bacteria showed higher community diversity, tighter phylogenetic clustering, wider environmental breadth, stronger phylogenetic signals, and higher functional redundancy. The assembly of the abundant bacterial subcommunity was governed by stochastic (59.2%) and deterministic (41.8%) processes, whereas the assembly of the rare bacterial subcommunity was mainly dominated by deterministic processes (85.8%). Furthermore, total phosphorus, soil pH, and ammonium nitrogen balanced stochastic and deterministic processes in both rare and abundant bacterial subcommunities. Our results reveal that rare bacteria displayed stronger environmental adaptability and environmental constraint. Importantly, the α-diversities of rare taxa, rather than abundant taxa, were significantly related to carbon decomposition. This study provides a holistic understanding of biogeographic patterns of abundant and rare bacteria and their α-diversities in relation to carbon decomposition, thus helping us better predict and regulate carbon dynamics under the background of global climate change.
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Ye F, Sun Z, Moore SS, Wu J, Hong Y, Wang Y. Discrepant Effects of Flooding on Assembly Processes of Abundant and Rare Communities in Riparian Soils. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02152-z. [PMID: 36502425 DOI: 10.1007/s00248-022-02152-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Numerous rare species coexist with a few abundant species in microbial communities and together play an essential role in riparian ecosystems. Relatively little is understood, however, about the nature of assembly processes of these communities and how they respond to a fluctuating environment. In this study, drivers controlling the assembly of abundant and rare subcommunities for bacteria and archaea in a riparian zone were determined, and their resulting patterns on these processes were analyzed. Abundant and rare bacteria and archaea showed a consistent variation in the community structure along the riparian elevation gradient, which was closely associated with flooding frequency. The community assembly of abundant bacteria was not affected by any measured environmental variables, while soil moisture and ratio of submerged time to exposed time were the two most decisive factors determining rare bacterial community. Assembly of abundant archaeal community was also determined by these two factors, whereas rare archaea was significantly associated with soil carbon-nitrogen ratio and total carbon content. The assembly process of abundant and rare bacterial subcommunities was driven respectively by dispersal limitation and variable selection. Undominated processes and dispersal limitation dominated the assembly of abundant archaea, whereas homogeneous selection primarily driven rare archaea. Flooding may therefore play a crucial role in determining the community assembly processes by imposing disturbances and shaping soil niches. Overall, this study reveals the assembly patterns of abundant and rare communities in the riparian zone and provides further insight into the importance of their respective roles in maintaining a stable ecosystem during times of environmental perturbations.
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Affiliation(s)
- Fei Ye
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Zhaohong Sun
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Selina Sterup Moore
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Padua, Italy
| | - Jiapeng Wu
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China.
| | - Yu Wang
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China.
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Sun P, Chen Y, Liu J, Xu Y, Zhou L, Wu Y. Periphytic biofilms function as a double-edged sword influencing nitrogen cycling in paddy fields. Environ Microbiol 2022; 24:6279-6289. [PMID: 36335557 DOI: 10.1111/1462-2920.16277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/01/2022] [Indexed: 11/07/2022]
Abstract
It remains unclear whether periphytic biofilms are beneficial to N cycling in paddy fields. Here, based on a national-scale field investigation covering 220 rice fields in China, the N accumulation potential of periphytic biofilms was found to decrease from 8.8 ± 2.4 to 4.5 ± 0.7 g/kg and 3.1 ± 0.6 g/kg with increasing habitat latitude and longitude, respectively. The difference in abundant and rare subcommunities likely accounts for their geo-difference in N accumulation potential. The N cycling pathways involved in periphytic biofilms inferred that soil N and N2 were two potential sources for N accumulation in periphytic biofilms. Meanwhile, some of the accumulated N may be lost via N2 , N2 O, NO, or NH3 outputs. Superficially, periphytic biofilms are double-edged swords to N cycling by increasing soil N through biological N fixation but accelerating greenhouse gas emissions. Essentially, augmented periphytic biofilms increased change of TN (ΔTN) content in paddy soil from -231.9 to 31.9 mg/kg, indicating that periphytic biofilms overall benefit N content enhancement in paddy fields. This study highlights the contribution of periphytic biofilms to N cycling in rice fields, thus, drawing attention to their effect on rice production and environmental security.
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Affiliation(s)
- Pengfei Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resource of the Peoples' Republic of China, Shuitianba, Zigui, Yichang, China
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Junzhuo Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resource of the Peoples' Republic of China, Shuitianba, Zigui, Yichang, China
| | - Ying Xu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resource of the Peoples' Republic of China, Shuitianba, Zigui, Yichang, China
| | - Lei Zhou
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resource of the Peoples' Republic of China, Shuitianba, Zigui, Yichang, China
| | - Yonghong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resource of the Peoples' Republic of China, Shuitianba, Zigui, Yichang, China
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Yin X, Gong W, Zhan Z, Wei W, Li M, Jiao J, Chen B, Liu L, Li W, Gao Z. Mining and engineering of valine dehydrogenases from a hot spring sediment metagenome for the synthesis of chiral non-natural L-amino acids. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Ayala-Muñoz D, Macalady JL, Sánchez-España J, Falagán C, Couradeau E, Burgos WD. Microbial carbon, sulfur, iron, and nitrogen cycling linked to the potential remediation of a meromictic acidic pit lake. THE ISME JOURNAL 2022; 16:2666-2679. [PMID: 36123522 PMCID: PMC9666448 DOI: 10.1038/s41396-022-01320-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 09/02/2022] [Accepted: 09/07/2022] [Indexed: 12/15/2022]
Abstract
Cueva de la Mora is a permanently stratified acidic pit lake and a model system for extreme acid mine drainage (AMD) studies. Using a combination of amplicon sequencing, metagenomics and metatranscriptomics we performed a taxonomically resolved analysis of microbial contributions to carbon, sulfur, iron, and nitrogen cycling. We found that active green alga Coccomyxa onubensis dominated the upper layer and chemocline. The chemocline had activity for iron(II) oxidation carried out by populations of Ca. Acidulodesulfobacterium, Ferrovum, Leptospirillium, and Armatimonadetes. Predicted activity for iron(III) reduction was only detected in the deep layer affiliated with Proteobacteria. Activity for dissimilatory nitrogen cycling including nitrogen fixation and nitrate reduction was primarily predicted in the chemocline. Heterotrophic archaeal populations with predicted activity for sulfide oxidation related to uncultured Thermoplasmatales dominated in the deep layer. Abundant sulfate-reducing Desulfomonile and Ca. Acidulodesulfobacterium populations were active in the chemocline. In the deep layer, uncultured populations from the bacterial phyla Actinobacteria, Chloroflexi, and Nitrospirae contributed to both sulfate reduction and sulfide oxidation. Based on this information we evaluated the potential for sulfide mineral precipitation in the deep layer as a tool for remediation. We argue that sulfide precipitation is not limited by microbial genetic potential but rather by the quantity and quality of organic carbon reaching the deep layer as well as by oxygen additions to the groundwater enabling sulfur oxidation. Addition of organic carbon and elemental sulfur should stimulate sulfate reduction and limit reoxidation of sulfide minerals.
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Affiliation(s)
- Diana Ayala-Muñoz
- Department of Civil and Environmental Engineering, The Pennsylvania State University, 212 Sackett Building, University Park, PA, 16802, USA.
| | - Jennifer L Macalady
- Department of Geosciences, The Pennsylvania State University, 211 Deike Building University Park, University Park, PA, 16802, USA
| | - Javier Sánchez-España
- Centro Nacional Instituto Geológico Minero de España (IGME), CSIC, Calera 1, 28760 Tres Cantos, Madrid, Spain
| | - Carmen Falagán
- School of Biological Sciences, University of Portsmouth, King Henry Building, King Henry 1st St., Portsmouth, PO1 2DY, UK
| | - Estelle Couradeau
- Department of Ecosystem Science and Management, The Pennsylvania State University, 50 ASI University Park, University Park, PA, 16802, USA
| | - William D Burgos
- Department of Civil and Environmental Engineering, The Pennsylvania State University, 212 Sackett Building, University Park, PA, 16802, USA.
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Yu Z, Chen J, Tan Y, Shen Y, Zhu L, Yu P. Phage Predation Promotes Filamentous Bacterium Piscinibacter Colonization and Improves Structural and Hydraulic Stability of Microbial Aggregates. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:16230-16239. [PMID: 36173693 DOI: 10.1021/acs.est.2c04745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Although bacteria-phage interactions have broad environmental applications and ecological implications, the influence of phage predation on bacterial aggregation and structural stability remains largely unexplored. Herein, we demonstrate that inefficient lytic phage predation can promote host filamentous bacterium Piscinibacter colonization onto non-host Thauera aggregates, improving the structural and hydraulic stability of the dual-species aggregates. Specifically, phage predation at 103-104 PFU/mL (i.e., multiplication of infection at 0.01-0.1) promoted initial Piscinibacter colonization by 10-15 folds and resulted in 29-31% higher abundance of Piscinibacter in the stabilized aggregates than that in the control aggregates without phage predation. Transcriptomic analysis revealed upregulated genes related to quorum sensing (by 15-92 folds) and polysaccharide secretion (by 10-90 folds) within the treated aggregates, which was consistent with 120-172% higher content of polysaccharides for the treated dual-species aggregates. Confocal laser scanning microscopic images further confirmed the increase of filamentous bacteria and polysaccharides (both with wider distribution) within the dual-species aggregates. Accordlingly, the aggregates' structural strength (via atomic force microscopes) and shear resistance (via hydraulic stress tests) increased by 77 and 42%, respectively, relative to the control group. In the long-term experiments, the enhanced hydraulic stability of the treated aggregates could facilitate dwelling bacteria propagation in flow-through conditions. Overall, our study demonstrates that phage predation can promote bacterial aggregation and enhance aggregate structural stability, revealing the beneficial role of lytic phage predation on bacterial symbiosis and environmental adaptivity.
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Affiliation(s)
- Zhuodong Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Juhong Chen
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Yixiao Tan
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yun Shen
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, United States
| | - Liang Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Pingfeng Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
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Kelly LC, Rivett DW, Pakostova E, Creer S, Cotterell T, Johnson DB. Mineralogy affects prokaryotic community composition in an acidic metal mine. Microbiol Res 2022; 266:127257. [DOI: 10.1016/j.micres.2022.127257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 11/06/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022]
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Chen Z, Fei YH, Liu WS, Ding K, Lu J, Cai X, Cui T, Tang YT, Wang S, Chao Y, Qiu R. Untangling microbial diversity and assembly patterns in rare earth element mine drainage in South China. WATER RESEARCH 2022; 225:119172. [PMID: 36191530 DOI: 10.1016/j.watres.2022.119172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/23/2022] [Accepted: 09/24/2022] [Indexed: 06/16/2023]
Abstract
Ion-adsorption rare earth element (REE) deposits are the main reservoirs of REEs worldwide, and are widely exploited in South China. Microbial diversity is essential for maintaining the performance and function of mining ecosystems. Investigating the ecological patterns underlying the REE mine microbiome is essential to understand ecosystem responses to environmental changes and to improve the bioremediation of mining areas. We applied 16S rRNA and ITS gene sequence analyses to investigate the composition characteristics of prokaryotic (bacteria, archaea) and fungal communities in a river impacted by REE acid mine drainage (REE-AMD). The river formed a unique micro-ecosystem, including the main prokaryotic taxa of Proteobacteria, Acidobacteria, Crenarchaeota, and Euryarchaeota, as well as the main fungal taxa of Ascomycota, Basidiomycota, and Chytridiomycota. Analysis of microbial diversity showed that, unlike prokaryotic communities that responded drastically to pollution disturbances, fungal communities were less affected by REE-AMD, but fluctuated significantly in different seasons. Ecological network analysis revealed that fungal communities have lower connectivity and centrality, and higher modularity than prokaryotic networks, indicating that fungal communities have more stable network structures. The introduction of REE-AMD mainly reduced the complexity of the community network and the number of keystone species, while the proportion of negative prokaryotic-fungal associations in the network increased. Ecological process analysis revealed that, compared to the importance of environmental selection for prokaryotes, stochastic processes might have contributed primarily to fungal communities in REE mining areas. These findings confirm that the different assembly mechanisms of prokaryotic and fungal communities are key to the differences in their responses to environmental perturbations. The findings also provide the first insights into microbiota assembly patterns in REE-AMD and important ecological knowledge for the formation and development of microbial communities in REE mining areas.
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Affiliation(s)
- Ziwu Chen
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; National-level Nanchang Economic and Technical Development Zone, Nanchang 330000, China
| | - Ying-Heng Fei
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Wen-Shen Liu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China
| | - Kengbo Ding
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China
| | - Jianan Lu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Xuan Cai
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Tuantuan Cui
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Ye-Tao Tang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China
| | - Shizhong Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuanqing Chao
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China.
| | - Rongliang Qiu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
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Jia Y, Wang P, Ou Y, Yan Y, Zhou S, Sun L, Lu H. Insights into the microbial response mechanisms to ciprofloxacin during sulfur-mediated biological wastewater treatment using a metagenomics approach. WATER RESEARCH 2022; 223:118995. [PMID: 36007398 DOI: 10.1016/j.watres.2022.118995] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
The fate and removal of ciprofloxacin, a class of fluoroquinolone antibiotic, during sulfur-mediated biological wastewater treatment has been recently well documented. However, little is known regarding the genetic response of microorganisms to ciprofloxacin. Here, a lab-scale anaerobic sulfate-reducing bioreactor was continuously operated over a long term for ciprofloxacin-contaminated wastewater treatment to investigate the response of the microorganisms to ciprofloxacin by adopting a metagenomics approach. It was found that total organic carbon (TOC) removal and sulfate reduction were promoted by approximately 10% under ciprofloxacin stress, along with the enrichment of functional genera (e.g., Desulfobacter, Geobacter) involved in carbon and sulfur metabolism. The metagenomic analytical results demonstrated that ciprofloxacin triggered the microbial SOS response, as demonstrated by the up-regulation of the multidrug efflux pump genes (8-125-fold higher than that of the control) and ciprofloxacin-degrading genes (4-33-fold higher than that of the control). Moreover, the contents of ATP, NADH, and cytochrome C, as well as related functional genes (including genes involved in energy generation, electron transport, carbon metabolism, and sulfur metabolism) were markedly increased under ciprofloxacin stress. This demonstrated that the carbon and sulfur metabolisms were enhanced for energy (ATP) generation and electron transport in response to ciprofloxacin-induced stress. Interestingly, the microbes tended to cooperate while being subjected exposure to exogenous ciprofloxacin according to the reconstructed metabolic network using the NetSeed model. Particularly, the species with higher complementarity indices played more pivotal roles in strengthening microbial metabolism and the SOS response under long-term ciprofloxacin stress. This study characterized the response mechanisms of microorganisms to ciprofloxacin at the genetic level in sulfur-mediated biological wastewater treatment. These new understandings will contribute the scientific basis for improving and optimizing the sulfur-mediated bioprocess for antibiotics-laden wastewater treatment.
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Affiliation(s)
- Yanyan Jia
- School of Ecology, Sun Yat-sen University, Guangzhou, PR China
| | - Pandeng Wang
- School of Ecology, Sun Yat-sen University, Guangzhou, PR China
| | - Yuyi Ou
- School of Ecology, Sun Yat-sen University, Guangzhou, PR China
| | - Yujian Yan
- School of Ecology, Sun Yat-sen University, Guangzhou, PR China
| | - Sining Zhou
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou, PR China
| | - Lianpeng Sun
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou, PR China
| | - Hui Lu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou, PR China.
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45
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Ku Y, Lei Y, Han X, Peng J, Zhu Y, Zhao Z. Spatial Patterns and Composition Traits of Soil Microbial Nitrogen-Metabolism Genes in the Robinia pseudoacacia Forests at a Regional Scale. Front Microbiol 2022; 13:918134. [PMID: 35814641 PMCID: PMC9263705 DOI: 10.3389/fmicb.2022.918134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/02/2022] [Indexed: 11/16/2022] Open
Abstract
Microbial-driven processes related to the nitrogen-metabolism (N-metabolism) in soil are critical for ecosystem functioning and stability. There are spatial patterns of microbial-mediated nitrogen processes, but we still lack an overview of the soil N-metabolism genes of single nitrogen-fixing tree species pure forests at a regional scale. Here, we investigated the spatial variation and drivers of microbial N-metabolism genes in the rhizosphere soil of Robinia pseudoacacia on the Loess Plateau by metagenomic technology. We found that the distance-decay of soil N functional gene similarities in Robinia pseudoacacia forests on the Loess Plateau spanning a geographic distance of 230 km was significant (p < 0.001). The gene composition and co-occurrence patterns in the process of soil microbial N-metabolism were very different, and they were mainly driven by soil pH and MAP (mean annual precipitation). The proportion of positive links and edges co-occurrence networks between N functional genes increased with increasing pH, suggesting that increasing pH promoted connections between functional genes. The relative frequencies of N-metabolism pathways were consistent on the Loess Plateau, the abundance of ammonia assimilation pathway was highest, and the abundance of the nitrogen fixation pathway was the lowest; only the abundance of the nitrogen fixation pathway was not significantly different. The bacterial and archaeal communities involved in soil nitrogen metabolism were significantly different. Structural equation modeling showed that decreases in soil pH and MAP mainly affected the increase in nitrogen functional gene abundance through an increase in the diversity of N-metabolism microorganisms. In conclusion, this study provides a baseline for biogeographic studies of soil microbe functional genes.
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Affiliation(s)
- Yongli Ku
- Key Comprehensive Laboratory of Forestry, Northwest A&F University, Yangling, China
| | - Yuting Lei
- Key Comprehensive Laboratory of Forestry, Northwest A&F University, Yangling, China
| | - Xiaoting Han
- Key Comprehensive Laboratory of Forestry, Northwest A&F University, Yangling, China
| | - Jieying Peng
- Key Comprehensive Laboratory of Forestry, Northwest A&F University, Yangling, China
| | - Ying Zhu
- Key Laboratory of Soil and Water Conservation and Ecological Restoration of State Forestry and Grassland Administration, Shaanxi Academy of Forestry, Xi’an, China
| | - Zhong Zhao
- Key Comprehensive Laboratory of Forestry, Northwest A&F University, Yangling, China
- Key Laboratory of Silviculture on the Loess Plateau State Forestry Administration, Northwest A&F University, Yangling, China
- *Correspondence: Zhong Zhao, ;
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Narsing Rao MP, Luo ZH, Dong ZY, Li Q, Liu BB, Guo SX, Nie GX, Li WJ. Metagenomic analysis further extends the role of Chloroflexi in fundamental biogeochemical cycles. ENVIRONMENTAL RESEARCH 2022; 209:112888. [PMID: 35143804 DOI: 10.1016/j.envres.2022.112888] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/02/2022] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Chloroflexi members are ubiquitous and have been extensively studied; however, the evolution and metabolic pathways of Chloroflexi members have long been debated. In the present study, the evolution and the metabolic potentials of 17 newly obtained Chloroflexi metagenome-assembled genomes (MAGs) were evaluated using genome and horizontal gene transfer (HGT) analysis. Taxonomic analysis suggests that the MAGs of the present study might be novel. One MAG encodes genes for anoxygenic phototrophy. The HGT analysis suggest that genes responsible for anoxygenic phototrophy in the MAG might have been transferred from Proteobacteria/Chlorobi. The evolution of anaerobic photosynthesis, which has long been questioned, has now been shown to be the result of HGT events. An incomplete Wood-Ljungdahl pathway (with missing genes metF, acsE, fdh, and acsA) was reported in Dehalococcoidetes members. In the present study, MAGs that were not the Dehalococcoidetes members encode genes acsA, acsB, metF and acsE. The genes responsible for sulfate reduction (sat, cysC and sir), dissimilatory sulfite reductase (dsrA and dsrB), and aerobic and anaerobic carbon monoxide oxidation (coxSML and cooSF) were detected in the present study MAGs. The present study expands our knowledge of the possible metabolic potentials of the phylum Chloroflexi and clarifies the evolution of anaerobic photosynthesis.
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Affiliation(s)
- Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Zhen-Hao Luo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Zhou-Yan Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China; Department of Pathogenic Biology, Binzhou Medical University, Yantai, 264003, PR China
| | - Qi Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Bing-Bing Liu
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, PR China
| | - Shu-Xian Guo
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, College of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, 473004, PR China
| | - Guo-Xin Nie
- College of Fisheries, Henan Normal University, Xinxiang, 453007, PR China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China.
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47
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Multikingdom interactions govern the microbiome in subterranean cultural heritage sites. Proc Natl Acad Sci U S A 2022; 119:e2121141119. [PMID: 35344401 PMCID: PMC9169738 DOI: 10.1073/pnas.2121141119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceThe conservation of historical relics against microbial biodeterioration is critical to preserving cultural heritages. One major challenge is our limited understanding of microorganisms' dispersal, colonization, and persistence on relics after excavation and opening to external environments. Here, we investigate the ecological and physiological profiles of the microbiome within and outside the Dahuting Han Dynasty Tomb with a 1,800-y history. Actinobacteria dominate the microbiome in this tomb. Via interkingdom signaling mutualism, springtails carry Actinobacteria as one possible source into the tomb from surrounding environments. Subsequently, Actinobacteria produce cellulases combined with antimicrobial substances, which helps them to colonize and thrive in the tomb via intrakingdom competition. Our findings unravel the ecology of the microbiomes colonizing historical relics and provide help for conservation practices.
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48
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Shu WS, Huang LN. Microbial diversity in extreme environments. Nat Rev Microbiol 2022; 20:219-235. [PMID: 34754082 DOI: 10.1038/s41579-021-00648-y] [Citation(s) in RCA: 107] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2021] [Indexed: 01/02/2023]
Abstract
A wide array of microorganisms, including many novel, phylogenetically deeply rooted taxa, survive and thrive in extreme environments. These unique and reduced-complexity ecosystems offer a tremendous opportunity for studying the structure, function and evolution of natural microbial communities. Marker gene surveys have resolved patterns and ecological drivers of these extremophile assemblages, revealing a vast uncultured microbial diversity and the often predominance of archaea in the most extreme conditions. New omics studies have uncovered linkages between community function and environmental variables, and have enabled discovery and genomic characterization of major new lineages that substantially expand microbial diversity and change the structure of the tree of life. These efforts have significantly advanced our understanding of the diversity, ecology and evolution of microorganisms populating Earth's extreme environments, and have facilitated the exploration of microbiota and processes in more complex ecosystems.
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Affiliation(s)
- Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, People's Republic of China.
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China.
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49
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OUIDIR T, GABRIEL B, CHABANE YNAIT. Overview of multi-species biofilms in different ecosystems: wastewater treatment, soil and oral cavity. J Biotechnol 2022; 350:67-74. [DOI: 10.1016/j.jbiotec.2022.03.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 01/27/2023]
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50
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Xu R, Zhang M, Lin H, Gao P, Yang Z, Wang D, Sun X, Li B, Wang Q, Sun W. Response of soil protozoa to acid mine drainage in a contaminated terrace. JOURNAL OF HAZARDOUS MATERIALS 2022; 421:126790. [PMID: 34358973 DOI: 10.1016/j.jhazmat.2021.126790] [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: 03/12/2021] [Revised: 07/28/2021] [Accepted: 07/28/2021] [Indexed: 05/28/2023]
Abstract
Acid mine drainage (AMD) system represents one of the most unfavorable habitats for microorganisms due to its low pH and high concentrations of metals. Compared to bacteria and fungi, our understanding regarding the response of soil protozoa to such extremely acidic environments remains limited. This study characterized the structures of protozoan communities inhabiting a terrace heavily contaminated by AMD. The sharp environmental gradient of this terrace was generated by annual flooding from an AMD lake located below, which provided a natural setting to unravel the environment-protozoa interactions. Previously unrecognized protozoa, such as Apicomplexa and Euglenozoa, dominated the extremely acidic soils, rather than the commonly recognized members (e.g., Ciliophora and Cercozoa). pH was the most important factor regulating the abundance of protozoan taxa. Metagenomic analysis of protozoan metabolic potential showed that many functional genes encoding for the alleviation of acid stress and various metabolic pathways were enriched, which may facilitate the survival and adaptation of protozoa to acidic environments. In addition, numerous co-occurrences between protozoa and bacterial or fungal taxa were observed, suggesting shared environmental preferences or potential bio-interactions among them. Future studies are required to confirm the ecological roles of these previously unrecognized protozoa as being important soil microorganisms.
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Affiliation(s)
- Rui Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, PR China
| | - Miaomiao Zhang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, PR China
| | - Hanzhi Lin
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, PR China
| | - Pin Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, PR China
| | - Zhaohui Yang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Dongbo Wang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, PR China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, PR China
| | - Qi Wang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, PR China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China; Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, PR China; School of Environment, Henan Normal University, PR China; Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, PR China.
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