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Banerjee A, Dhal MK, Madhu K, Chah CN, Rattan B, Katiyar V, Sekharan S, Sarmah AK. Landfill-mined soil-like fraction (LMSF) use in biopolymer composting: Material pre-treatment, bioaugmentation and agricultural prospects. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 355:124255. [PMID: 38815894 DOI: 10.1016/j.envpol.2024.124255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 05/06/2024] [Accepted: 05/25/2024] [Indexed: 06/01/2024]
Abstract
Polylactic Acid (PLA) based compostable bioplastic films degrade under thermophilic composting conditions. The purpose of our study was to understand whether sample pre-treatment along with bioaugmentation of the degradation matrix could reduce the biodegradation time under a simulated composting environment. Sepcifically, we also explored whether the commercial composts could be replaced by landfill-mined soil-like fraction (LMSF) for the said application. The effect of pre-treatment on the material was analysed by tests like tensile strength analysis, hydrophobicity analysis, morphological analysis, thermal degradation profiling, etc. Subsequently, the degradation experiment was performed in a simulated composting environment following the ASTM D5338 standard, along with bioaugmentation in selected experimental setups. When the novel approach of material pre-treatment and bioaugmentation were applied in combination, the time necessary for 90% degradation was reduced by 27% using compost and by 23% using LMSF. Beyond the improvement in degradation rate, the water holding capacity increased significantly for the degradation matrices. With pH, C: N ratio and microbial diversity tested to be favourable through 16s metabarcoding studies, material pre-treatment and bioaugmentation allow LMSF to not only replace commercial compost in polymer degradation but also find immense application in the agricultural sector of drought-affected areas (for better water retention) after it has been used for PLA degradation.
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Affiliation(s)
- Arnab Banerjee
- Department of Civil Engineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India; Centre for Sustainable Polymers, Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Manoj Kumar Dhal
- Centre for Sustainable Polymers, Institute of Technology Guwahati, Guwahati, 781039, Assam, India; Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Kshitij Madhu
- Centre for Sustainable Polymers, Institute of Technology Guwahati, Guwahati, 781039, Assam, India; Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Charakho N Chah
- Department of Civil Engineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Bharat Rattan
- Department of Civil Engineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Vimal Katiyar
- Centre for Sustainable Polymers, Institute of Technology Guwahati, Guwahati, 781039, Assam, India; Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Sreedeep Sekharan
- Department of Civil Engineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India; Centre for Sustainable Polymers, Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Ajit K Sarmah
- Department of Civil and Environmental Engineering, The Faculty of Engineering, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand; Centre for Sustainable Water Research, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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Ewerling A, May-Simera HL. Evolutionary trajectory for nuclear functions of ciliary transport complex proteins. Microbiol Mol Biol Rev 2024:e0000624. [PMID: 38995044 DOI: 10.1128/mmbr.00006-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024] Open
Abstract
SUMMARYCilia and the nucleus were two defining features of the last eukaryotic common ancestor. In early eukaryotic evolution, these structures evolved through the diversification of a common membrane-coating ancestor, the protocoatomer. While in cilia, the descendants of this protein complex evolved into parts of the intraflagellar transport complexes and BBSome, the nucleus gained its selectivity by recruiting protocoatomer-like proteins to the nuclear envelope to form the selective nuclear pore complexes. Recent studies show a growing number of proteins shared between the proteomes of the respective organelles, and it is currently unknown how ciliary transport proteins could acquire nuclear functions and vice versa. The nuclear functions of ciliary proteins are still observable today and remain relevant for the understanding of the disease mechanisms behind ciliopathies. In this work, we review the evolutionary history of cilia and nucleus and their respective defining proteins and integrate current knowledge into theories for early eukaryotic evolution. We postulate a scenario where both compartments co-evolved and that fits current models of eukaryotic evolution, explaining how ciliary proteins and nucleoporins acquired their dual functions.
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Affiliation(s)
- Alexander Ewerling
- Faculty of Biology, Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
| | - Helen Louise May-Simera
- Faculty of Biology, Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
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Ning X, Hu J, Yue J, Tang T, Zhang B. Microbial community structure of an anaerobic side-stream coupled anoxic-aerobic membrane bioreactor (AOMBR-ASSR) for an in-situ sludge reduction process. Bioprocess Biosyst Eng 2024; 47:1027-1037. [PMID: 38777954 DOI: 10.1007/s00449-024-03019-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/10/2024] [Indexed: 05/25/2024]
Abstract
With the anoxic-aerobic membrane bioreactor (AO-MBR, CP) as a reference, high-throughput sequencing technology was used to reveal the characteristics of the microbial community structure in the anaerobic side-stream anoxic-aerobic membrane bioreactor sludge reduction process (AOMBR-ASSR, SRP). After the stable operation of two processes for 120 days, the average removal efficiencies of TN and TP in the effluent of SRP were increased by 5.6% and 29.8%, respectively. The observed sludge yields (Yobs) of the two processes were 0.14 and 0.17 gMLSS/(gCOD), respectively, and the sludge reduction rate of the SRP was 19.5%. Compared to the CP, the microbial richness and diversity index of SRP increased significantly. Chloroflexi, which is responsible for the degradation of organic substances under an anaerobic condition, seemed to be reduced in the SRP. Meanwhile, other phyla that involved in the nitrogen cycle, such as Nitrospirae and Planctomycetes, were found to be more abundant in the SRP than in the CP. A total of 21 identified classes were observed, and primarily hydrolyzed fermented bacteria (Sphingobacteriia, Betaproteobacteria, Actinobacteria and Deltaproteobacteria) and slow-growing microorganisms (Bacilli) were accumulated in the SRP. At the genus level, the inserted anaerobic side-stream reactor favored the hydrolyzed bacteria (Saprospiraceae, Rhodobacter and Candidatus_Competibacter), fermented bacteria (Lactococcus and Trichococcus), and slow-growing microorganisms (Dechloromonas and Haliangium), which play a crucial role in the sludge reduction. Furthermore, the enrichment of bacterial species related to nitrogen (Nitrospir and Azospira) provided the potential for nitrogen removal, while the anaerobic environment of the side-stream reactor promoted the enrichment of phosphorus-accumulating organisms.
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Affiliation(s)
- Xinqiang Ning
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin, 644000, China
| | - Jialun Hu
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin, 644000, China
| | - Jiao Yue
- School of Food and Biotechnology, Xihua University, Chengdu, 610039, China
- Environmental Water Construction Co. Ltd., Chengdu Environment Group, Chengdu, 610000, China
| | - Tang Tang
- College of Bioengineering, Sichuan University of Science & Engineering, Yibin, 644000, China
| | - Bin Zhang
- School of Food and Biotechnology, Xihua University, Chengdu, 610039, China.
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Wang Q, Yu J, Li X, Zhang Y, Zhang J, Wang J, Mu J, Yu X, Hui R. Seasonal and anthropogenic influences on bacterioplankton communities: ecological impacts in the coastal waters of Qinhuangdao, Northern China. Front Microbiol 2024; 15:1431548. [PMID: 38962120 PMCID: PMC11220261 DOI: 10.3389/fmicb.2024.1431548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Accepted: 06/06/2024] [Indexed: 07/05/2024] Open
Abstract
Marine bacterioplankton play a crucial role in the cycling of carbon, nitrogen, and phosphorus in coastal waters. And the impact of environmental factors on bacterial community structure and ecological functions is a dynamic ongoing process. To systematically assess the relationship between environmental changes and bacterioplankton communities, this study delved into the spatiotemporal distribution and predicted metabolic characteristics of bacterioplankton communities at two estuarine beaches in Northern China. Coastal water samples were collected regularly in spring, summer, and autumn, and were analyzed in combination with environmental parameters and bacterioplankton community. Results indicated significant seasonal variations in bacterioplankton communities as Bacteroidetes and Actinobacteria were enriched in spring, Cyanobacteria proliferated in summer. While Pseudomonadota and microorganisms associated with organic matter decomposition prevailed in autumn, closely linked to seasonal variation of temperature, light and nutrients such as nitrogen and phosphorus. Particularly in summer, increased tourism activities and riverine inputs significantly raised nutrient levels, promoting the proliferation of specific photosynthetic microorganisms, potentially linked to the occurrence of phytoplankton blooms. Spearman correlation analysis further revealed significant correlations between bacterioplankton communities and environmental factors such as salinity, chlorophyll a, and total dissolved phosphorus (TDP). Additionally, the metabolic features of the spring bacterioplankton community were primarily characterized by enhanced activities in the prokaryotic carbon fixation pathways, reflecting rapid adaptation to increased light and temperature, as well as significant contributions to primary productivity. In summer, the bacterial communities were involved in enhanced glycolysis and biosynthetic pathways, reflecting high energy metabolism and responses to increased light and biomass. In autumn, microorganisms adapted to the accelerated decomposition of organic matter and the seasonal changes in environmental conditions through enhanced amino acid metabolism and material cycling pathways. These findings demonstrate that seasonal changes and human activities significantly influence the structure and function of bacterioplankton communities by altering nutrient dynamics and physical environmental conditions. This study provides important scientific insights into the marine biological responses under global change.
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Affiliation(s)
- Qiuzhen Wang
- Ocean College, Hebei Agricultural University, Qinhuangdao, China
- Hebei Key Laboratory of Nutrition Regulation and Disease Control for Aquaculture, Qinhuangdao, China
| | - Jia Yu
- Ocean College, Hebei Agricultural University, Qinhuangdao, China
| | - Xiaofang Li
- Ocean College, Hebei Agricultural University, Qinhuangdao, China
| | - Yong Zhang
- Department of Ocean Survey, Qinhuangdao Marine Center of the Ministry of Natural Resources, Qinhuangdao, China
| | - Jianle Zhang
- Department of Ocean Survey, Qinhuangdao Marine Center of the Ministry of Natural Resources, Qinhuangdao, China
| | - Jianyan Wang
- Department of Life Sciences, National Natural History Museum of China, Beijing, China
| | - Jiandong Mu
- Ecological Environment Research Department, Hebei Ocean and Fisheries Science Research Institute, Qinhuangdao, China
| | - Xinping Yu
- Ocean College, Hebei Agricultural University, Qinhuangdao, China
| | - Ruixue Hui
- Ocean College, Hebei Agricultural University, Qinhuangdao, China
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Clagnan E, Petrini S, Pioli S, Piergiacomo F, Chowdhury AA, Brusetti L, Foladori P. Conventional activated sludge vs. photo-sequencing batch reactor for enhanced nitrogen removal in municipal wastewater: Microalgal-bacterial consortium and pathogenic load insights. BIORESOURCE TECHNOLOGY 2024; 401:130735. [PMID: 38670293 DOI: 10.1016/j.biortech.2024.130735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/02/2024] [Accepted: 04/23/2024] [Indexed: 04/28/2024]
Abstract
Municipal wastewater treatment plants are mostly based on traditional activated sludge (AS) processes. These systems are characterised by major drawbacks: high energy consumption, large amount of excess sludge and high greenhouse gases emissions. Treatment through microalgal-bacterial consortia (MBC) is an alternative and promising solution thanks to lower energy consumption and emissions, biomass production and water sanitation. Here, microbial difference between a traditional anaerobic sludge (AS) and a consortium-based system (photo-sequencing batch reactor (PSBR)) with the same wastewater inlet were characterised through shotgun metagenomics. Stable nitrification was achieved in the PSBR ensuring ammonium removal > 95 % and significant total nitrogen removal thanks to larger flocs enhancing denitrification. The new system showed enhanced pathogen removal, a higher abundance of photosynthetic and denitrifying microorganisms with a reduced emissions potential identifying this novel PSBR as an effective alternative to AS.
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Affiliation(s)
- Elisa Clagnan
- Free University of Bolzano, Faculty of Science and Technology, Piazza Università 1, 39100 Bolzano, Italy; Department for Sustainability, Biotechnologies and Agroindustry Division, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, Via Anguillarese 301 00123 Rome, Italy; Gruppo Ricicla Labs, Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia (DiSAA), Università Degli Studi di Milano, Via Celoria 2 20133 Milano, Italy
| | - Serena Petrini
- University of Trento, Department of Civil, Environmental and Mechanical Engineering, Via Mesiano 77 38123, Trento, Italy
| | - Silvia Pioli
- Free University of Bolzano, Faculty of Science and Technology, Piazza Università 1, 39100 Bolzano, Italy; Institute of Research on Terrestrial Ecosystems (IRET), National Research Council (CNR), Monterotondo Scalo RM, Italy
| | - Federica Piergiacomo
- Free University of Bolzano, Faculty of Science and Technology, Piazza Università 1, 39100 Bolzano, Italy
| | - Atif Aziz Chowdhury
- Free University of Bolzano, Faculty of Science and Technology, Piazza Università 1, 39100 Bolzano, Italy
| | - Lorenzo Brusetti
- Free University of Bolzano, Faculty of Science and Technology, Piazza Università 1, 39100 Bolzano, Italy.
| | - Paola Foladori
- University of Trento, Department of Civil, Environmental and Mechanical Engineering, Via Mesiano 77 38123, Trento, Italy
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Odelgard A, Hägglund E, Guy L, Andersson SGE. Phylogeny and Expansion of Serine/Threonine Kinases in Phagocytotic Bacteria in the Phylum Planctomycetota. Genome Biol Evol 2024; 16:evae068. [PMID: 38547507 PMCID: PMC11032199 DOI: 10.1093/gbe/evae068] [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] [Accepted: 03/23/2024] [Indexed: 04/22/2024] Open
Abstract
The recently isolated bacterium "Candidatus Uabimicrobium amorphum" is the only known prokaryote that can engulf other bacterial cells. Its proteome contains a high fraction of proteins involved in signal transduction systems, which is a feature normally associated with multicellularity in eukaryotes. Here, we present a protein-based phylogeny which shows that "Ca. Uabimicrobium amorphum" represents an early diverging lineage that clusters with the Saltatorellus clade within the phylum Planctomycetota. A gene flux analysis indicated a gain of 126 protein families for signal transduction functions in "Ca. Uabimicrobium amorphum", of which 66 families contained eukaryotic-like Serine/Threonine kinases with Pkinase domains. In total, we predicted 525 functional Serine/Threonine kinases in "Ca. Uabimicrobium amorphum", which represent 8% of the proteome and is the highest fraction of Serine/Threonine kinases in a bacterial proteome. The majority of Serine/Threonine kinases in this species are membrane proteins and 30% contain long, tandem arrays of WD40 or TPR domains. The pKinase domain was predicted to be located in the cytoplasm, while the WD40 and TPR domains were predicted to be located in the periplasm. Such domain combinations were also identified in the Serine/Threonine kinases of other species in the Planctomycetota, although in much lower abundances. A phylogenetic analysis of the Serine/Threonine kinases in the Planctomycetota inferred from the Pkinase domain alone provided support for lineage-specific expansions of the Serine/Threonine kinases in "Ca. Uabimicrobium amorphum". The results imply that expansions of eukaryotic-like signal transduction systems are not restricted to multicellular organisms, but have occurred in parallel in prokaryotes with predatory lifestyles and phagocytotic-like behaviors.
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Affiliation(s)
- Anna Odelgard
- Molecular Evolution, Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Emil Hägglund
- Molecular Evolution, Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lionel Guy
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala University, Uppsala, Sweden
| | - Siv G E Andersson
- Molecular Evolution, Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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Huang H, Shi Y, Gong Z, Wang J, Zheng L, Gao S. Revealing the characteristics of biofilms on different polypropylene plastic products: Comparison between disposable masks and takeaway boxes. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133400. [PMID: 38198871 DOI: 10.1016/j.jhazmat.2023.133400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024]
Abstract
The increasingly severe plastic pollution issue was intensified by the enormous plastic emissions into ecosystems during the Covid-19 pandemic. Plastic wastes entering the environment were swiftly exposed to microorganisms and colonized by biofilms, and the plastic-biofilm combined effects further influenced the ecosystem. However, the non-woven structure of disposable masks discarded carelessly during the COVID-19 pandemic was different from those of plastics with flat surface. To reveal the potential effects of plastic structure on colonized biofilms, white disposable surgical masks (DM) and transparent takeaway boxes (TB), both made of polyethylene, were selected for the incubation of organic conditioning films and biofilms. The results indicated that the non-woven structure of disposable mask was destroyed by the influence of water infiltration and biofilm colonization. The influence of surface structure on conditioning films led to a relatively higher proportion of tryptophan-like substances on DM than those on TB samples. Therefore, biofilms with significantly higher microbial biomass and carbon metabolic capacity were formed on DM than those on TB samples owing to the combined effects of their differences in surface structure and conditioning films. Moreover, abundant functional microorganisms associated with stress tolerance, carbon metabolism and biofilm formation were observed in biofilms on disposable mask. Combining with the results of partial least squares regression analysis, the selective colonization of functional microorganisms on disposable masks with uneven surface longitudinal fluctuation was revealed. Although the predicted functions of biofilms on disposable masks and takeaway boxes showed more similarity to each other than to those of free-living aquatic microorganisms owing to the existence of the plastisphere, biofilms on disposable masks may potentially trigger environmental risks different from those of takeaway boxes by unique carbon metabolism and abundant biomass.
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Affiliation(s)
- Hexinyue Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, People's Republic of China
| | - Yanqi Shi
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, People's Republic of China
| | - Zhimin Gong
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jiahao Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, People's Republic of China
| | - Lezhou Zheng
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, People's Republic of China
| | - Shixiang Gao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, People's Republic of China.
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8
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Zheng R, Wang C, Liu R, Cai R, Sun C. Physiological and metabolic insights into the first cultured anaerobic representative of deep-sea Planctomycetes bacteria. eLife 2024; 12:RP89874. [PMID: 38265071 PMCID: PMC10945688 DOI: 10.7554/elife.89874] [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] [Indexed: 01/25/2024] Open
Abstract
Planctomycetes bacteria are ubiquitously distributed across various biospheres and play key roles in global element cycles. However, few deep-sea Planctomycetes members have been cultivated, limiting our understanding of Planctomycetes in the deep biosphere. Here, we have successfully cultured a novel strain of Planctomycetes (strain ZRK32) from a deep-sea cold seep sediment. Our genomic, physiological, and phylogenetic analyses indicate that strain ZRK32 is a novel species, which we propose be named: Poriferisphaera heterotrophicis. We show that strain ZRK32 replicates using a budding mode of division. Based on the combined results from growth assays and transcriptomic analyses, we found that rich nutrients, or supplementation with NO3- or NH4+ promoted the growth of strain ZRK32 by facilitating energy production through the tricarboxylic acid cycle and the Embden-Meyerhof-Parnas glycolysis pathway. Moreover, supplementation with NO3- or NH4+ induced strain ZRK32 to release a bacteriophage in a chronic manner, without host cell lysis. This bacteriophage then enabled strain ZRK32, and another marine bacterium that we studied, to metabolize nitrogen through the function of auxiliary metabolic genes. Overall, these findings expand our understanding of deep-sea Planctomycetes bacteria, while highlighting their ability to metabolize nitrogen when reprogrammed by chronic viruses.
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Affiliation(s)
- Rikuan Zheng
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center of Ocean Mega-Science, Chinese Academy of SciencesQingdaoChina
| | - Chong Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center of Ocean Mega-Science, Chinese Academy of SciencesQingdaoChina
| | - Rui Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center of Ocean Mega-Science, Chinese Academy of SciencesQingdaoChina
| | - Ruining Cai
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center of Ocean Mega-Science, Chinese Academy of SciencesQingdaoChina
- College of Earth Science, University of Chinese Academy of SciencesBeijingChina
| | - Chaomin Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center of Ocean Mega-Science, Chinese Academy of SciencesQingdaoChina
- College of Earth Science, University of Chinese Academy of SciencesBeijingChina
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9
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Bao Y, Ruan Y, Wu J, Wang WX, Leung KMY, Lee PKH. Metagenomics-Based Microbial Ecological Community Threshold and Indicators of Anthropogenic Disturbances in Estuarine Sediments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:780-794. [PMID: 38118133 DOI: 10.1021/acs.est.3c08076] [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: 12/22/2023]
Abstract
Assessing the impacts of cumulative anthropogenic disturbances on estuarine ecosystem health is challenging. Using spatially distributed sediments from the Pearl River Estuary (PRE) in southern China, which are significantly influenced by anthropogenic activities, we demonstrated that metagenomics-based surveillance of benthic microbial communities is a robust approach to assess anthropogenic impacts on estuarine benthic ecosystems. Correlational and threshold analyses between microbial compositions and environmental conditions indicated that anthropogenic disturbances in the PRE sediments drove the taxonomic and functional variations in the benthic microbial communities. An ecological community threshold of anthropogenic disturbances was identified, which delineated the PRE sediments into two groups (H and L) with distinct taxa and functional traits. Group H, located nearshore and subjected to a higher level of anthropogenic disturbances, was enriched with pollutant degraders, putative human pathogens, fecal pollution indicators, and functional traits related to stress tolerance. In contrast, Group L, located offshore and subjected to a lower level of anthropogenic disturbances, was enriched with halotolerant and oligotrophic taxa and functional traits related to growth and resource acquisition. The machine learning random forest model identified a number of taxonomic and functional indicators that could differentiate PRE sediments between Groups H and L. The identified ecological community threshold and microbial indicators highlight the utility of metagenomics-based microbial surveillance in assessing the adverse impacts of anthropogenic disturbances in estuarine sediments, which can assist environmental management to better protect ecosystem health.
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Affiliation(s)
- Yingyu Bao
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
| | - Yuefei Ruan
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
| | - Jiaxue Wu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
| | - Wen-Xiong Wang
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
- Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| | - Kenneth M Y Leung
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
- Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| | - Patrick K H Lee
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
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10
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Zhang Y, Wang M, Cheng W, Huang C, Ren J, Wan T, Gao K. Effects of water environmental factors and antibiotics on bacterial community in urban landscape lakes. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 265:106740. [PMID: 37925787 DOI: 10.1016/j.aquatox.2023.106740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/11/2023] [Accepted: 10/28/2023] [Indexed: 11/07/2023]
Abstract
The presence of antibiotics can affect the natural microbial community and exert selective pressure on the environment's microorganisms. This study focused on three types of urban landscape lakes in Xi'an that were closely related to human activities. By combining basic water quality indicators, antibiotic occurrence status, bacterial communities and their potential metabolic functions, Spearman correlation coefficient and redundancy analysis were used to explore the relationship between them, and further explore the impact mechanism of environmental factors and antibiotics on bacterial community structure. The results showed that ofloxacin, erythromycin, and roxithromycin were the main types of antibiotics in the three landscape lakes, with low ecological risks, and there was a clear clustering of antibiotic occurrence. Proteobacteria was the most abundant bacterial phylum, and each lake had its own unique dominant bacteria, which indicates that they are influenced by varying water sources, pollution, and other nearby environments. Statistical analysis showed that pH and nitrogen nutrients were the most critical environmental factors affecting bacterial communities (P<0.01), while tetracyclines and lincomycins were the antibiotics that had a significant impact on bacterial communities (P<0.05). Antibiotics mainly promote defense- and signal transduction-related functions, and inhibit the metabolic activity of bacterial communities. However, the impact of antibiotics on bacterial diversity, community structure, and potential metabolic function in the three urban lakes was less than that of environmental factors. These results help to clarify the mechanism and degree of impact of different interference factors (environmental factors, conventional pollutants, and antibiotics) on bacterial communities in the water environment and are important for the management of urban landscape lake water environments.
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Affiliation(s)
- Yutong Zhang
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China; Institute of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, China
| | - Min Wang
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China; Institute of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, China
| | - Wen Cheng
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China; Institute of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, China.
| | - Chen Huang
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China; Institute of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, China
| | - Jiehui Ren
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China; Institute of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, China
| | - Tian Wan
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China; Institute of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, China
| | - Kangyi Gao
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, China; Institute of Water Resources and Hydro-Electric Engineering, Xi'an University of Technology, Xi'an, China
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11
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Conesa HM, Párraga-Aguado I, Jiménez-Cárceles FJ, Risueño Y. Evaluation of the rhizospheric microbiome of the native colonizer Piptatherum miliaceum in semiarid mine tailings. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2023; 45:9359-9371. [PMID: 36074214 PMCID: PMC10673988 DOI: 10.1007/s10653-022-01357-y] [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: 02/28/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
The study of the rhizospheric microbiome in native plants should be a prerequisite before carrying out the phytomanagement of mine tailings. The goal of this work was to evaluate the rhizospheric microbiome of Piptatherum miliaceum in semiarid mine tailings. A comprehensive edaphic characterization was performed including the description of soil microbial composition in the rhizosphere of P. miliaceum growing at a mine tailings pile and at a control site. Plant nutritional and isotopic compositions were also determined. Neutral pH of the tailings (7.3) determined low metal extractability in 0.01 M CaCl2 (e.g. < 1 mg/kg for Zn). In spite of the contrasting edaphic fertility conditions of both sites, N (~ 15 g kg-1) and P (~ 400 mg kg-1) leaf concentrations were similar. The lower δ15N at the tailings plants (- 4.50‰) compared to the control (6.42‰) indicated greater efficiency of P. miliaceum for uptaking N under the low fertility conditions of the tailings (0.1% total soil nitrogen). The presence at the tailings of bacterial orders related to the cycling of N, such as Rhizobiales, could have contributed to enhance N acquisition. The lower leaf δ13C values at the tailings (- 30.22‰) compared to the control (- 28.47‰) indicated lower water use efficiency of the tailing plants. Some organotrophic bacterial and fungal groups in the tailings' rhizospheres were also found in the control site (e.g. Cytophagales, Sphingobacteriales for bacteria; Hypocreales, Pleosporales for fungi). This may indicate that P. miliaceum is able to shape its own specific microbiome at the tailings independently from the initial microbial composition of the tailings.
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Affiliation(s)
- Héctor M Conesa
- Departamento de Ingeniería Agronómica, Escuela Técnica Superior de Ingeniería Agronómica, Universidad Politécnica de Cartagena, Paseo Alfonso XIII, 48, 30203, Cartagena, Spain
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12
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Bolik S, Schlaich A, Mukhina T, Amato A, Bastien O, Schneck E, Demé B, Jouhet J. Lipid bilayer properties potentially contributed to the evolutionary disappearance of betaine lipids in seed plants. BMC Biol 2023; 21:275. [PMID: 38017456 PMCID: PMC10685587 DOI: 10.1186/s12915-023-01775-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/21/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND Many organisms rely on mineral nutrients taken directly from the soil or aquatic environment, and therefore, developed mechanisms to cope with the limitation of a given essential nutrient. For example, photosynthetic cells have well-defined responses to phosphate limitation, including the replacement of cellular membrane phospholipids with non-phosphorous lipids. Under phosphate starvation, phospholipids in extraplastidial membranes are replaced by betaine lipids in microalgae. In higher plants, the synthesis of betaine lipid is lost, driving plants to other strategies to cope with phosphate starvation where they replace their phospholipids by glycolipids. RESULTS The aim of this work was to evaluate to what extent betaine lipids and PC lipids share physicochemical properties and could substitute for each other. By neutron diffraction experiments and dynamic molecular simulation of two synthetic lipids, the dipalmitoylphosphatidylcholine (DPPC) and the dipalmitoyl-diacylglyceryl-N,N,N-trimethylhomoserine (DP-DGTS), we found that DP-DGTS bilayers are thicker than DPPC bilayers and therefore are more rigid. Furthermore, DP-DGTS bilayers are more repulsive, especially at long range, maybe due to unexpected unscreened electrostatic contribution. Finally, DP-DGTS bilayers could coexist in the gel and fluid phases. CONCLUSION The different properties and hydration responses of PC and DGTS provide an explanation for the diversity of betaine lipids observed in marine organisms and for their disappearance in seed plants.
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Affiliation(s)
- Stéphanie Bolik
- Laboratoire Physiologie Cellulaire Et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, Grenoble, France
- Large Scale Structures Group, Institut Laue-Langevin, 38000, Grenoble, France
| | - Alexander Schlaich
- Institute for Computational Physics, Universität Stuttgart, Stuttgart, Germany
- Stuttgart Center for Simulation Science (SimTech), Universität Stuttgart, Stuttgart, Germany
| | - Tetiana Mukhina
- Institute for Condensed Matter Physics, Darmstadt, Darmstadt, TU, Germany
| | - Alberto Amato
- Laboratoire Physiologie Cellulaire Et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, Grenoble, France
| | - Olivier Bastien
- Laboratoire Physiologie Cellulaire Et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, Grenoble, France
| | - Emanuel Schneck
- Institute for Condensed Matter Physics, Darmstadt, Darmstadt, TU, Germany
| | - Bruno Demé
- Large Scale Structures Group, Institut Laue-Langevin, 38000, Grenoble, France.
| | - Juliette Jouhet
- Laboratoire Physiologie Cellulaire Et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG, Grenoble, France.
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13
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Gogoleva N, Chervyatsova O, Balkin A, Kuzmina L, Shagimardanova E, Kiseleva D, Gogolev Y. Microbial tapestry of the Shulgan-Tash cave (Southern Ural, Russia): influences of environmental factors on the taxonomic composition of the cave biofilms. ENVIRONMENTAL MICROBIOME 2023; 18:82. [PMID: 37990336 PMCID: PMC10662634 DOI: 10.1186/s40793-023-00538-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/09/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND Cave biotopes are characterized by stable low temperatures, high humidity, and scarcity of organic substrates. Despite the harsh oligotrophic conditions, they are often inhabited by rich microbial communities. Abundant fouling with a wide range of morphology and coloration of colonies covers the walls of the Shulgan-Tash cave in the Southern Urals. This cave is also famous for the unique Paleolithic painting discovered in the middle of the last century. We aimed to investigate the diversity, distribution, and potential impact of these biofilms on the cave's Paleolithic paintings, while exploring how environmental factors influence the microbial communities within the cave. RESULTS The cave's biofilm morphotypes were categorized into three types based on the ultrastructural similarities. Molecular taxonomic analysis identified two main clusters of microbial communities, with Actinobacteria dominating in most of them and a unique "CaveCurd" community with Gammaproteobacteria prevalent in the deepest cave sections. The species composition of these biofilms reflects changes in environmental conditions, such as substrate composition, temperature, humidity, ventilation, and CO2 content. Additionally, it was observed that cave biofilms contribute to biocorrosion on cave wall surfaces. CONCLUSIONS The Shulgan-Tash cave presents an intriguing example of a stable extreme ecosystem with diverse microbiota. However, the intense dissolution and deposition of carbonates caused by Actinobacteria pose a potential threat to the preservation of the cave's ancient rock paintings.
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Affiliation(s)
- Natalia Gogoleva
- Research Department for Limnology, Mondsee, Universität Innsbruck, Mondsee, 5310, Austria.
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia.
| | | | - Alexander Balkin
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia
- Institute for Cellular and Intracellular Symbiosis, Ural Branch of the Russian Academy of Sciences, Orenburg, 460000, Russia
| | - Lyudmila Kuzmina
- Ufa Institute of Biology, Ufa Federal Research Center, Russian Academy of Sciences, Ufa, 450054, Russia
| | - Elena Shagimardanova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia
- Loginov Moscow Clinical Scientific Center, Moscow, 111123, Russia
| | - Daria Kiseleva
- Institute of Geology and Geochemistry, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, 620016, Russia
- Institute of Fundamental Education, Ural Federal University named after the first President of Russia B.N. Yeltsin, Ekaterinburg, 620002, Russia
| | - Yuri Gogolev
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", Kazan, 420111, Russia
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14
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Verma K, Manisha M, Shivali NU, Santrupt RM, Anirudha TP, Ramesh N, Chanakya HN, Parama VRR, Mohan Kumar MS, Rao L. Investigating the effects of irrigation with indirectly recharged groundwater using recycled water on soil and crops in semi-arid areas. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 337:122516. [PMID: 37690469 DOI: 10.1016/j.envpol.2023.122516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/18/2023] [Accepted: 09/04/2023] [Indexed: 09/12/2023]
Abstract
The utilization of direct wastewater for irrigation poses many environmental problems such as soil quality deterioration due to the accumulation of salts, heavy metals, micro-pollutants, and health risks due to undesirable microorganisms. This hampers its agricultural reuse in arid and semi-arid regions. To address these concerns, the present study introduces a recent approach that involves using indirectly recharged groundwater (GW) with secondary treated municipal wastewater (STW) for irrigation through a Soil Aquifer Treatment-based system (SAT). This method aims to mitigate freshwater scarcity in semi-arid regions. The study assessed GW levels, physicochemical properties, and microbial diversity of GW, and soil in both impacted (receiving recycled water) and non-impacted (not receiving recycled water) areas, before recycling (2015-2018) and after recycling (2019-2022) period of the project. The results indicated a significant increase of 68-70% in GW levels of the studied boreholes in the impacted areas. Additionally, the quality of indirectly recharged GW in the impacted areas improved notably in terms of electrical conductivity (EC), hardness, total dissolved solids (TDS), sodium adsorption ratio (SAR), along with certain cations and anions (hard water to soft water). No significant difference was observed in soil properties and microbial diversity of the impacted areas, except for EC and SAR, which were reduced by 50% and 39%, respectively, after the project commenced. The study also monitored specific microbial species, including total coliforms, Escherichia coli (as indicator organisms), Shigella, and Klebsiella in some of the harvested crops (beetroot, tomato, and spinach). However, none of the analysed crops exhibited the presence of the studied microorganisms. Overall, the study concludes that indirectly recharged GW using STW is a better sustainable and safe irrigation alternative compared to direct wastewater use or extracted hard GW from deep aquifers.
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Affiliation(s)
- Kavita Verma
- Center for Sustainable Technologies, Indian Institute of Science, Bengaluru, India.
| | - Manjari Manisha
- Center for Sustainable Technologies, Indian Institute of Science, Bengaluru, India
| | - N U Shivali
- Center for Sustainable Technologies, Indian Institute of Science, Bengaluru, India
| | - R M Santrupt
- Center for Sustainable Technologies, Indian Institute of Science, Bengaluru, India
| | - T P Anirudha
- Center for Sustainable Technologies, Indian Institute of Science, Bengaluru, India
| | - N Ramesh
- Center for Sustainable Technologies, Indian Institute of Science, Bengaluru, India
| | - H N Chanakya
- Center for Sustainable Technologies, Indian Institute of Science, Bengaluru, India
| | - V R R Parama
- Department of Soil Science & Agricultural Chemistry, College of Agriculture, UAS, GKVK, Bengaluru, India
| | - M S Mohan Kumar
- Formerly @ Department of Civil Engineering, Indian Institute of Science, Bengaluru, India; Currently @ Gitam University, Bengaluru, India
| | - Lakshminarayana Rao
- Center for Sustainable Technologies, Indian Institute of Science, Bengaluru, India
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Chauhan S, Yadav U, Bano N, Kumar S, Fatima T, Anshu, Dubey A, Singh PC. Carbendazim Modulates the Metabolically Active Bacterial Populations in Soil and Rhizosphere. Curr Microbiol 2023; 80:280. [PMID: 37439951 DOI: 10.1007/s00284-023-03391-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 06/26/2023] [Indexed: 07/14/2023]
Abstract
The impact of fungicide residues on non-target soil bacterial communities is relatively unexplained. We hypothesize that the persistence of fungicide residues in the soil will affect the soil bacterial populations. Persistence depends on biotic and abiotic factors, primarily determined by agricultural activities. Activities such as fallow soil (F), farmyard manure (FYM) amendment, rice straw (RS) mulching, and cultivation of maize (Zea mays) and clover (Trifolium alexandrinum) were used as treatments. The soil CO2 efflux showed no effect of Carbendazim on dormant bacteria (unwatered condition). However, in irrigated condition, Carbendazim enhanced the CO2 efflux by 8, 164, 131, 249, and 182% in fallow, FYM, RS, maize, and Trifolium treatments, respectively. However, 16S rRNA metagenome study after 30 days of carbendazim treatment showed that maize rhizosphere microflora was most susceptible, decreasing the Shannon diversity index from 0.321 to 0.165. Diversity indices generally increased in maize and RS treatments, and Proteobacteria was the most prominent bacterial phyla in the maize rhizosphere. The microbial communities separated into distinct groups on the Principal Co-ordinate analysis (PCoA) plot. The separation on scale 1 (35%) and scale 2 (13%) was based, respectively, on microbial activity and carbendazim treatments. Functionally Maize+Carbendazim treatment showed the highest enzyme activities dehydrogenase (82.25%), acid phosphatase (78.10%), alkaline phosphatase (48.26%), β-glucosidase (59.99%), protease (126.65%), and urease (50.66%) compared to fallow soil. Overall, Carbendazim enhanced non-target bacterial activity in metabolically active niches, while it did not affect the dormant microflora. Thus, organic amendments and cultivation of fungicide-contaminated soil may help render the contaminant through bacterial activity.
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Affiliation(s)
- Soni Chauhan
- Microbial Technology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Department of Biosciences, Integral University, Kursi Rd, Lucknow, 226026, India
| | - Udit Yadav
- Microbial Technology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | - Nasreen Bano
- Microbial Technology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | - Sanjeev Kumar
- Microbial Technology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | - Touseef Fatima
- Microbial Technology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
- Department of Biosciences, Integral University, Kursi Rd, Lucknow, 226026, India
| | - Anshu
- Microbial Technology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India
| | - Amita Dubey
- Department of Biosciences, Integral University, Kursi Rd, Lucknow, 226026, India
| | - Poonam C Singh
- Microbial Technology Division, CSIR-National Botanical Research Institute, Lucknow, 226001, India.
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16
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Ng CWW, Liao JX, Lau SY, So PS, Hau BCH, Peprah-Manu D. Coupled effects of elevated CO 2 and biochar on microbial communities of vegetated soil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 342:118136. [PMID: 37196620 DOI: 10.1016/j.jenvman.2023.118136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/20/2023] [Accepted: 05/08/2023] [Indexed: 05/19/2023]
Abstract
Soil microbial communities are important for plant growth and establishing healthy ecosystems. Although biochar is widely adopted as a sustainable fertilizer, its influence on soil ecological functions is still unclear, especially under climate change such as elevated carbon dioxide concentration (eCO2). This study explores the coupled effects between eCO2 and biochar on microbial communities in soil planted with tree seedlings of Schefflera heptaphylla. Root characteristics and soil microbial communities were examined and interpreted with statistical analysis. Results show that biochar application at ambient carbon dioxide concentration (aCO2) always improves plant growth, which is further promoted under eCO2. Similarly, β-glucosidase, urease and phosphatase activities are enhanced by biochar at aCO2 (p < 0.05). In contrast, only urease activity increases with biochar added at eCO2 (p < 0.05). The beneficial effects of biochar on soil enzyme activities become less significant at eCO2. Depending on biochar type, biochar can increase bacterial diversity and fungal richness at aCO2. However, at eCO2, biochar does not significantly affect microbial richness (p > 0.05) while microbial diversity is reduced by peanut shell biochar (p < 0.05). Owing to better plant growth under biochar application and eCO2, plants are likely to become more dominant in specializing the microbial communities that are favourable to them. In such community, the abundance of Proteobacteria is the greatest and increases after biochar addition at eCO2. The most abundant fungus also shifts from Rozellomycota to Ascomycota and Basidiomycota. These microbes can improve soil fertility. Even though the microbial diversity is reduced, using biochar at eCO2 can further promote plant growth, which in turn enhances carbon sequestration. Thus, biochar application can be an effective strategy to facilitate ecological restoration under climate change and relieve the problem of eCO2.
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Affiliation(s)
- Charles Wang Wai Ng
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong Special Administrative Region of China.
| | - Jia Xin Liao
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong Special Administrative Region of China.
| | - Sze Yu Lau
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong Special Administrative Region of China.
| | - Pui San So
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong Special Administrative Region of China.
| | - Billy Chi Hang Hau
- School of Biological Sciences, The University of Hong Kong, Hong Kong Special Administrative Region of China.
| | - Daniel Peprah-Manu
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong Special Administrative Region of China.
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17
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Das S, Najar IN, Sherpa MT, Kumar S, Sharma P, Mondal K, Tamang S, Thakur N. Baseline metagenome-assembled genome (MAG) data of Sikkim hot springs from Indian Himalayan geothermal belt (IHGB) showcasing its potential CAZymes, and sulfur-nitrogen metabolic activity. World J Microbiol Biotechnol 2023; 39:179. [PMID: 37133792 DOI: 10.1007/s11274-023-03631-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 04/26/2023] [Indexed: 05/04/2023]
Abstract
Here we present the construction and characterization of metagenome assembled genomes (MAGs) from two hot springs residing in the vicinity of Indian Himalayan Geothermal Belt (IHGB). A total of 78 and 7 taxonomic bins were obtained for Old Yume Samdong (OYS) and New Yume Samdong (NYS) hot springs respectively. After passing all the criteria only 21 and 4 MAGs were further studied based on the successful prediction of their 16 S rRNA. Various databases were used such as GTDB, Kaiju, EzTaxon, BLAST XY Plot and NCBI BLAST to get the taxonomic classification of various 16 S rRNA predicted MAGs. The bacterial genomes found were from both thermophilic and mesophilic bacteria among which Proteobacteria, Chloroflexi, Bacteroidetes and Firmicutes were the abundant phyla. However, in case of OYS, two genomes belonged to archaeal Methanobacterium and Methanocaldococcus. Functional characterization revealed the richness of CAZymes such as Glycosyl Transferase (GT) (56.7%), Glycoside Hydrolase (GH) (37.4%), Carbohydrate Esterase family (CE) (8.2%), and Polysaccharide Lyase (PL) (1.9%). There were negligible antibiotic resistance genes in the MAGs however, a significant heavy metal tolerance gene was found in the MAGs. Thus, it may be assumed that there is no coexistence of antibiotic and heavy metal resistance genes in these hot spring microbiomes. Since the selected hot springs possess good sulfur content thus, we also checked the presence of genes for sulfur and nitrogen metabolism. It was found that MAGs from both the hot springs possess significant number of genes related to sulfur and nitrogen metabolism.
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Affiliation(s)
- Sayak Das
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India
- Department of Life Science and Bioinformatics, Hargobind Khurana School of Life Sciences, Assam University, Silchar, Assam, 788011, India
| | - Ishfaq Nabi Najar
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India
| | - Mingma Thundu Sherpa
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India
| | - Santosh Kumar
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India
| | - Prayatna Sharma
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India
| | - Krishnendu Mondal
- Department of Microbiology, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Sonia Tamang
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India
| | - Nagendra Thakur
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India.
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18
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Liu C, Liu C, Gao F, Wang A, Wang H, Yang Y, He L. Composition of Particulate Matter and Bacterial Community in Gut Contents and Surrounding Sediments of Three Sipunculan Species ( Siphonosoma australe, Phascolosoma arcuatum, and Sipunculus nudus). Int J Mol Sci 2023; 24:ijms24066001. [PMID: 36983074 PMCID: PMC10054262 DOI: 10.3390/ijms24066001] [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: 12/23/2022] [Revised: 03/16/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
Siphonosoma australe, Phascolosoma arcuatum, and Sipunculus nudus are three important sipunculan species in tropical intertidal zones. In this study, the particle size, organic matter content, and bacterial community composition in the gut contents of three different sipunculans and their surrounding sediments were analyzed. The grain size fractions of sipunculans' guts were significantly different from those of their surrounding sediments; particle size fractions < 500 μm were favored by the sipunculans. As for the total organic matter (TOM), higher contents of organic matter were observed in the guts than in the surrounding sediments in all three sipunculan species. The bacterial community composition of all the samples was investigated by 16S rRNA gene sequencing, in which a total of 8974 OTUs were obtained from 24 samples based on a 97% threshold. The predominant phylum identified from the gut contents of three sipunculans was Planctomycetota, while the predominant phylum in their surrounding sediments was Proteobacteria. At the genus level, the most abundant genus was Sulfurovum (average 4.36%) in the surrounding sediments, while the most abundant genus was Gplla (average 12.76%) in the gut contents. The UPGMA tree showed that the samples from the guts of three different sipunculans and their surrounding sediments were clustered separately into two groups, which showed that these three sipunculans had a different bacterial community composition with their surrounding sediments. The grain size and total organic matter (TOM) had the greatest impacts on the bacterial community composition at both the phylum and genus levels. In conclusion, the differences in particle size fractions, organic matter content, and bacterial community composition between the gut contents and surrounding sediments in these three sipunculan species might be caused by their selective ingestion.
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Affiliation(s)
- Chunsheng Liu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
- College of Marine Science, Hainan University, Haikou 570228, China
| | - Chuang Liu
- College of Marine Science, Hainan University, Haikou 570228, China
| | - Fei Gao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
- College of Marine Science, Hainan University, Haikou 570228, China
| | - Aimin Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
- College of Marine Science, Hainan University, Haikou 570228, China
| | - Haiqing Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
- College of Marine Science, Hainan University, Haikou 570228, China
| | - Yumei Yang
- College of Marine Science, Hainan University, Haikou 570228, China
| | - Linwen He
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
- College of Marine Science, Hainan University, Haikou 570228, China
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19
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Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates. Mar Drugs 2023; 21:md21030165. [PMID: 36976214 PMCID: PMC10054348 DOI: 10.3390/md21030165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/21/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Marine invertebrate microbiomes have been a rich source of bioactive compounds and interesting genomic features. In cases where the achievable amounts of metagenomic DNA are too low for direct sequencing, multiple displacement amplification (MDA) can be used for whole genome amplification. However, MDA has known limitations which can affect the quality of the resulting genomes and metagenomes. In this study, we evaluated the conservation of biosynthetic gene clusters (BGCs) and enzymes in MDA products from low numbers of prokaryotic cells (estimated 2–850). Marine invertebrate microbiomes collected from Arctic and sub-Arctic areas served as source material. The cells were separated from the host tissue, lysed, and directly subjected to MDA. The MDA products were sequenced by Illumina sequencing. Corresponding numbers of bacteria from a set of three reference strains were treated the same way. The study demonstrated that useful information on taxonomic, BGC, and enzyme diversities was obtainable from such marginal quantities of metagenomic material. Although high levels of assembly fragmentation resulted in most BGCs being incomplete, we conclude that this genome mining approach has the potential to reveal interesting BGCs and genes from hard-to-reach biological sources.
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Chiriac MC, Haber M, Salcher MM. Adaptive genetic traits in pelagic freshwater microbes. Environ Microbiol 2023; 25:606-641. [PMID: 36513610 DOI: 10.1111/1462-2920.16313] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022]
Abstract
Pelagic microbes have adopted distinct strategies to inhabit the pelagial of lakes and oceans and can be broadly categorized in two groups: free-living, specialized oligotrophs and patch-associated generalists or copiotrophs. In this review, we aim to identify genomic traits that enable pelagic freshwater microbes to thrive in their habitat. To do so, we discuss the main genetic differences of pelagic marine and freshwater microbes that are both dominated by specialized oligotrophs and the difference to freshwater sediment microbes, where copiotrophs are more prevalent. We phylogenomically analysed a collection of >7700 metagenome-assembled genomes, classified habitat preferences on different taxonomic levels, and compared the metabolic traits of pelagic freshwater, marine, and freshwater sediment microbes. Metabolic differences are mainly associated with transport functions, environmental information processing, components of the electron transport chain, osmoregulation and the isoelectric point of proteins. Several lineages with known habitat transitions (Nitrososphaeria, SAR11, Methylophilaceae, Synechococcales, Flavobacteriaceae, Planctomycetota) and the underlying mechanisms in this process are discussed in this review. Additionally, the distribution, ecology and genomic make-up of the most abundant freshwater prokaryotes are described in details in separate chapters for Actinobacteriota, Bacteroidota, Burkholderiales, Verrucomicrobiota, Chloroflexota, and 'Ca. Patescibacteria'.
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Affiliation(s)
| | - Markus Haber
- Institute of Hydrobiology, Biology Centre CAS, Ceske Budejovice, Czechia
| | - Michaela M Salcher
- Institute of Hydrobiology, Biology Centre CAS, Ceske Budejovice, Czechia
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21
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Structure and Function Analysis of Cultivated Meconopsis integrifolia Soil Microbial Community Based on High-Throughput Sequencing and Culturability. BIOLOGY 2023; 12:biology12020160. [PMID: 36829439 PMCID: PMC9952792 DOI: 10.3390/biology12020160] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/14/2023] [Accepted: 01/16/2023] [Indexed: 01/22/2023]
Abstract
(1) Background: The structure, function, and community interactions of soil microbial communities of cultivated Meconopsis integrifolia were characterized by studying this alpine flower and traditional endangered Tibetan medicine. (2) Methods: Soil bacteria and fungi were studied based on high-throughput sequencing technology. Bacteria were isolated using culturomics and functionally identified as IAA-producing, organic phosphorus-dissolving, inorganic phosphorus-dissolving, and iron-producing carriers. (3) Results: The dominant bacterial phyla were found to be Proteobacteria and Acidobacteria, and unclassified_Rhizobiales was the most abundant genus. Ascomycota and Mortierellomycota were the dominant fungal phyla. The bacteria were mainly carbon and nitrogen metabolizers, and the fungi were predominantly Saprotroph-Symbiotroph. The identified network was completely dominated by positive correlations, but the fungi were more complex than the bacteria, and the bacterial keystones were unclassified_Caulobacteraceae and Pedobacter. Most of the keystones of fungi belonged to the phyla Ascomycetes and Basidiomycota. The highest number of different species of culturable bacteria belonged to the genus Streptomyces, with three strains producing IAA, 12 strains solubilizing organic phosphorus, one strain solubilizing inorganic phosphorus, and nine strains producing iron carriers. (4) Conclusions: At the cost of reduced ecological stability, microbial communities increase cooperation toward promoting overall metabolic efficiency and enabling their survival in the extreme environment of the Tibetan Plateau. These pioneering results have value for the protection of endangered Meconopsis integrifolia under global warming and the sustainable utilization of its medicinal value.
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22
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Raiyani NM, Singh SP. Microbial community and predictive functionalities associated with the marine sediment of Coastal Gujarat. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:43245-43266. [PMID: 36650368 DOI: 10.1007/s11356-023-25196-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 01/04/2023] [Indexed: 01/19/2023]
Abstract
Marine sediments are complex ecosystems where structures and functions constantly change due to natural and anthropogenic influences. In this investigation, a comprehensive and comparative analysis of the bacterial communities and their functional potential of the pristine and polluted marine sediments were carried out using MiSeq. The phylum Proteobacteria was dominant in all study sites. Other phyla were Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Chloroflexi, Nitrospirae, Cyanobacteria, Verrucomicrobia, Tenericutes, and Chlorobi. Interestingly, about 50% of genera belong to the unclassified categories. The key genera were identified as Acinetobacter, Bacillus, Pseudomona, Idiomarina, Thalassospira, and Marinobacter, Halomonas, Planctomyces, Psychrobacter, and Vogesella. PICRUSt analysis revealed that major functions are associated with the metabolism category. Additionally, metabolism related to amino acids, carbohydrates, energy generation, xenobiotics degradation, nitrogen, sulfate, and methane were prominent. Similarly, the predicted metabolisms by COG and KEGG were observed in the microbial communities of the marine sediments. To date, a comprehensive description of the microbial life with metabolic potential in these study sites has not been investigated. This study therefore significantly adds to our understanding of the microbiome and its functional attributes of marine sediments.
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Affiliation(s)
- Nirali M Raiyani
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot, 360 005, Gujarat, India
| | - Satya P Singh
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot, 360 005, Gujarat, India.
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23
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Howe KL, Seitz KW, Campbell LG, Baker BJ, Thrash JC, Rabalais NN, Rogener MK, Joye SB, Mason OU. Metagenomics and metatranscriptomics reveal broadly distributed, active, novel methanotrophs in the Gulf of Mexico hypoxic zone and in the marine water column. FEMS Microbiol Ecol 2022; 99:6909064. [PMID: 36520069 PMCID: PMC9874027 DOI: 10.1093/femsec/fiac153] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/17/2022] [Accepted: 12/20/2022] [Indexed: 12/23/2022] Open
Abstract
The northern Gulf of Mexico (nGOM) hypoxic zone is a shallow water environment where methane, a potent greenhouse gas, fluxes from sediments to bottom water and remains trapped due to summertime stratification. When the water column is destratified, an active planktonic methanotrophic community could mitigate the efflux of methane, which accumulates to high concentrations, to the atmosphere. To investigate the possibility of such a biofilter in the nGOM hypoxic zone we performed metagenome assembly, and metagenomic and metatranscriptomic read mapping. Methane monooxygenase (pmoA) was an abundant transcript, yet few canonical methanotrophs have been reported in this environment, suggesting a role for non-canonical methanotrophs. To determine the identity of these methanotrophs, we reconstructed six novel metagenome-assembled genomes (MAGs) in the Planctomycetota, Verrucomicrobiota and one putative Latescibacterota, each with at least one pmoA gene copy. Based on ribosomal protein phylogeny, closely related microbes (mostly from Tara Oceans) and isolate genomes were selected and co-analyzed with the nGOM MAGs. Gene annotation and read mapping suggested that there is a large, diverse and unrecognized community of active aerobic methanotrophs in the nGOM hypoxic zone and in the global ocean that could mitigate methane flux to the atmosphere.
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Affiliation(s)
- Kathryn L Howe
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, 32306, Tallahassee, United States
| | - Kiley W Seitz
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, 78373, Port Aransas, United States
| | - Lauren G Campbell
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, 32306, Tallahassee, United States
| | - Brett J Baker
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, 78373, Port Aransas, United States,Department of Integrative Biology, University of Texas at Austin, 78712, Austin, United States
| | - J Cameron Thrash
- Department of Biological Sciences, University of Southern California, 90089, Los Angeles, United States
| | - Nancy N Rabalais
- Department of Oceanography and Coastal Sciences, Louisiana State University, 70803, Baton Rouge, United States,Louisiana Universities Marine Consortium, 70344, Chauvin, United States
| | - Mary-Kate Rogener
- Department of Marine Sciences, University of Georgia, 30602, Athens, United States
| | - Samantha B Joye
- Department of Marine Sciences, University of Georgia, 30602, Athens, United States
| | - Olivia U Mason
- Corresponding author: Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL 32306, United States. E-mail:
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24
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Fu JJ, Wang Y, Yang JH, Huang DQ, Zhang Q, Huang Y, Chen JR, Fan NS, Jin RC. Mitigating the detrimental effects of salt stress on anammox process: A comparison between glycine betaine and mannitol. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158221. [PMID: 36041620 DOI: 10.1016/j.scitotenv.2022.158221] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/18/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
The use of seawater to alleviate water shortages causes an increase of salinity in municipal pipe networks, posing challenges for biological wastewater treatment. The impacts of two compatible solutes on the anammox process under salt stress (20 g L-1) were compared here at the genetic and microbial levels. The findings revealed that both 0.3 mM glycine betaine (GB) and mannitol (MA) could alleviate the salt stress on anammox process, with GB exhibiting a better effect. Specifically, the addition of GB recovered the nitrogen removal efficiency (NRE) from 40 % to >80 % within 13 days. The addition of MA caused the reduction of the absolute abundance of hdh and hzsA, implying that 0.6 mM was not the optimal concentration. Moreover, salt stress induced an increase in the absolute abundance of nitrification functional genes and a decrease in the abundance of denitrification functional genes. Notably, compared with the initial level, the abundance of Candidatus Kuenenia increased by 7.1 % and 4.3 % after adding GB and MA, respectively. According to the network analysis, two compatible solutes promoted the bacterial interactions in anammox systems, which promoted the nitrogen circulation and further the nitrogen removal performance. This work provides a feasible strategy to relieve the salt stress on anammox process and then facilitates its application for treating saline wastewater.
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Affiliation(s)
- Jin-Jin Fu
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; School of Engineering, Hangzhou Normal University, Hangzhou 310018, China
| | - Ye Wang
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; School of Engineering, Hangzhou Normal University, Hangzhou 310018, China
| | - Jun-Hui Yang
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; School of Engineering, Hangzhou Normal University, Hangzhou 310018, China
| | - Dong-Qi Huang
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; School of Engineering, Hangzhou Normal University, Hangzhou 310018, China
| | - Quan Zhang
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; School of Engineering, Hangzhou Normal University, Hangzhou 310018, China
| | - Yong Huang
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; School of Engineering, Hangzhou Normal University, Hangzhou 310018, China
| | - Jin-Rong Chen
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; School of Engineering, Hangzhou Normal University, Hangzhou 310018, China
| | - Nian-Si Fan
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; School of Engineering, Hangzhou Normal University, Hangzhou 310018, China.
| | - Ren-Cun Jin
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; School of Engineering, Hangzhou Normal University, Hangzhou 310018, China
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25
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The Effect of Date Palm Genotypes on Rhizobacterial Community Structures under Saline Environments. BIOLOGY 2022; 11:biology11111666. [DOI: 10.3390/biology11111666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/11/2022] [Accepted: 11/12/2022] [Indexed: 11/18/2022]
Abstract
Some genotypes of date palms (Phoenix dactylifera L.) are salt-tolerant; however, salinity significantly affects others. This study aimed to determine the root epiphytic bacterial contributions to the salt tolerance mechanism in the date palm and to verify if the salt-tolerant “Umsila” and the salt-susceptible “Zabad” cultivars have different bacterial communities. Therefore, the epiphytic bacterial community structures were investigated in both cultivars when grown under control and salinity conditions. The proximal soils of the roots were collected, the DNA was extracted, and a culture-independent approach using Illumina® MiSeq™ sequence analysis was carried out to identify the changes in the bacterial community structures in the soil samples due to the changes in salinity and the genotypes of the plants based on 16S rRNA gene sequencing. While salt tolerance response differences were evident between the two cultivars, the 16S rRNA gene sequencing results revealed 771 operational taxonomic units (OTUs), including 62 that were differentially accumulated in response to salinity. The ordination analysis showed significant (p = 0.001) changes among the communities in response to salinity in both cultivars. However, the results showed that the two cultivars had distinct bacterial communities when grown under controlled conditions, whereas they had a more similar bacterial community structure when grown under salinity conditions. The plant genotype does not affect the epiphyte bacterial community structure under salinity, probably because salinity affects the plant-microbe interaction similarly in both cultivars. Also, the identified rhizospheric bacteria are not directly associated with the root’s physiological processes in response to salinity.
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26
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Pin Viso ND, Rizzo PF, Young BJ, Gabioud E, Bres P, Riera NI, Merino L, Farber MD, Crespo DC. The Use of Raw Poultry Waste as Soil Amendment Under Field Conditions Caused a Loss of Bacterial Genetic Diversity Together with an Increment of Eutrophic Risk and Phytotoxic Effects. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02119-0. [PMID: 36197502 DOI: 10.1007/s00248-022-02119-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Poultry waste has been used as fertilizer to avoid soil degradation caused by the long-term application of chemical fertilizer. However, few studies have evaluated field conditions where livestock wastes have been used for extended periods of time. In this study, physicochemical parameters, metabarcoding of the 16S rRNA gene, and ecotoxicity indexes were used for the characterization of chicken manure and poultry litter to examine the effect of their application to agricultural soils for 10 years. Poultry wastes showed high concentrations of nutrients and increased electrical conductivity leading to phytotoxic effects on seeds. The bacterial communities were dominated by typical members of the gastrointestinal tract, noting the presence of pathogenic bacteria. Soils subjected to poultry manure applications showed statistically higher values of total and extractable phosphorous, increasing the risk of eutrophication. Moreover, while the soil bacterial community remained dominated by the ones related to the biogeochemical cycles of nutrients and plant growth promotion, losses of alpha diversity were observed on treated soils. Altogether, our work would contribute to understand the effects of common local agricultural practices and support the adoption of the waste treatment process in compliance with environmental sustainability guidelines.
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Affiliation(s)
- Natalia D Pin Viso
- Instituto de Agrobiotecnología y Biología Molecular, IABiMo, INTA-CONICET, Calle Las Cabañas y Los Reseros s/n, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz 2290, 1425, Ciudad Autónoma de Buenos Aires, Argentina
- Universidad Nacional de Hurlingham, Tte. Origone 151, 1688, Hurlingham, Buenos Aires, Argentina
| | - Pedro F Rizzo
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola (IMyZA), Calle Las Cabañas y Los Reseros S/N, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina
| | - Brian J Young
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola (IMyZA), Calle Las Cabañas y Los Reseros S/N, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina
| | - Emmanuel Gabioud
- Instituto Nacional de Tecnología Agropecuaria (INTA), Estación Experimental Agropecuaria Paraná, Ruta 11 Km 12.5, 3101, Oro Verde, Entre Ríos, Argentina
| | - Patricia Bres
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola (IMyZA), Calle Las Cabañas y Los Reseros S/N, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina
| | - Nicolás I Riera
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola (IMyZA), Calle Las Cabañas y Los Reseros S/N, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina
| | - Lina Merino
- Universidad Nacional de Hurlingham, Tte. Origone 151, 1688, Hurlingham, Buenos Aires, Argentina
| | - Marisa D Farber
- Instituto de Agrobiotecnología y Biología Molecular, IABiMo, INTA-CONICET, Calle Las Cabañas y Los Reseros s/n, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz 2290, 1425, Ciudad Autónoma de Buenos Aires, Argentina.
- Universidad Nacional de Hurlingham, Tte. Origone 151, 1688, Hurlingham, Buenos Aires, Argentina.
| | - Diana C Crespo
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz 2290, 1425, Ciudad Autónoma de Buenos Aires, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola (IMyZA), Calle Las Cabañas y Los Reseros S/N, Casilla de Correo 25, 1712, Hurlingham, Buenos Aires, Argentina
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27
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Scicchitano D, Lo Martire M, Palladino G, Nanetti E, Fabbrini M, Dell’Anno A, Rampelli S, Corinaldesi C, Candela M. Microbiome network in the pelagic and benthic offshore systems of the northern Adriatic Sea (Mediterranean Sea). Sci Rep 2022; 12:16670. [PMID: 36198901 PMCID: PMC9535000 DOI: 10.1038/s41598-022-21182-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/23/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractBecause of their recognized global importance, there is now the urgent need to map diversity and distribution patterns of marine microbial communities. Even if available studies provided some advances in the understanding the biogeographical patterns of marine microbiomes at the global scale, their degree of plasticity at the local scale it is still underexplored, and functional implications still need to be dissected. In this scenario here we provide a synoptical study on the microbiomes of the water column and surface sediments from 19 sites in a 130 km2 area located 13.5 km afar from the coast in the North-Western Adriatic Sea (Italy), providing the finest-scale mapping of marine microbiomes in the Mediterranean Sea. Pelagic and benthic microbiomes in the study area showed sector specific-patterns and distinct assemblage structures, corresponding to specific variations in the microbiome network structure. While maintaining a balanced structure in terms of potential ecosystem services (e.g., hydrocarbon degradation and nutrient cycling), sector-specific patterns of over-abundant modules—and taxa—were defined, with the South sector (the closest to the coast) characterized by microbial groups of terrestrial origins, both in the pelagic and the benthic realms. By the granular assessment of the marine microbiome changes at the local scale, we have been able to describe, to our knowledge at the first time, the integration of terrestrial microorganisms in the marine microbiome networks, as a possible natural process characterizing eutrophic coastal area. This raises the question about the biological threshold for terrestrial microorganisms to be admitted in the marine microbiome networks, without altering the ecological balance.
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28
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Li C, Maqbool T, Kang H, Zhang Z. In-Situ Sludge Reduction Performance and Mechanism in Sulfidogenic Anoxic-Oxic-Anoxic Membrane Bioreactors. MEMBRANES 2022; 12:865. [PMID: 36135885 PMCID: PMC9502630 DOI: 10.3390/membranes12090865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/31/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Abstract
The excess sludge generated from the activated sludge process remains a big issue. Sustainable approaches that achieve in situ sludge reduction with satisfactory effluent quality deserve attention. This study explored the sludge reduction performance of sulfidogenic anoxic-oxic-anoxic (AOA) membrane bioreactors. The dynamics of the microbial community and metabolic pathways were further analyzed to elucidate the internal mechanism of sludge reduction. Compared with the conventional anoxic-oxic-oxic membrane bioreactor (MBRcontrol), AOAS150 (150 mg/L SO42- in the membrane tank) and AOAS300 (300 mg/L SO42- in the membrane tank) reduced biomass production by 40.39% and 47.45%, respectively. The sulfide reduced from sulfate could enhance the sludge decay rate and decrease sludge production. Extracellular polymeric substances (EPSs) destruction and aerobic lysis contributed to sludge reduction in AOA bioreactors. The relative abundance of Bacteroidetes (phylum), sulfate-reducing bacteria (SRB, genus), and Ignavibacterium (genus) increased in AOA bioreactors compared with MBRcontrol. Our metagenomic analysis indicated that the total enzyme-encoding genes involved in glycolysis, denitrification, and sulfate-reduction processes decreased over time in AOAS300 and were lower in AOAS300 than AOAS150 at the final stage of operation. The excess accumulation of sulfide in AOAS300 may inactive the functional bacteria, and sulfide inhibition induced sludge reduction.
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Affiliation(s)
- Chengyue Li
- Institute of Environmental Engineering & Nano-Technology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Guangdong Provincial Engineering Research Centre for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Tahir Maqbool
- Institute of Environmental Engineering & Nano-Technology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Guangdong Provincial Engineering Research Centre for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Hongyu Kang
- Institute of Environmental Engineering & Nano-Technology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Guangdong Provincial Engineering Research Centre for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Zhenghua Zhang
- Institute of Environmental Engineering & Nano-Technology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Guangdong Provincial Engineering Research Centre for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- School of Environment, Tsinghua University, Beijing 100084, China
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29
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Lou T, Peng Z, Jiang K, Niu N, Wang J, Liu A. Nitrogen removal characteristics of biofilms in each area of a full-scale AAO oxidation ditch process. CHEMOSPHERE 2022; 302:134871. [PMID: 35551942 DOI: 10.1016/j.chemosphere.2022.134871] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 04/30/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
Plastic carriers were installed in different areas of a full-scale anaerobic/anoxic/aerobic (AAO) oxidation ditch process, and the dynamics of nitrogen removal, biofilm morphologies, and microorganism species were investigated. The results showed that the biofilm at the front of the aerobic area (dissolved oxygen [DO] = 0.93 mg L-1) provided the best denitrification, with specific nitrate and nitrite reduction rates of 10.16 and 3.78 mg·(g·h)-1, respectively. The biofilm in the middle of the aerobic area (DO = 1.27 mg L-1) exhibited the best nitrification performance, with a maximum specific ammonia oxidation rate of 3.21 mg·(g·h)-1. The biofilm at the end of the aerobic area (DO = 0.01 mg L-1) exhibited the highest anammox potential with a maximum specific anammox rate of 0.67 mg·(g·h)-1. No correlation was observed between the specific nitrogen removal rates and abundance of nitrogen-removing microorganisms at the genus level. Biofilm denitrification during the process was primarily completed by heterotrophic denitrifying bacteria (Thauera, Acinetobacter, Hyphomicrobium, and Thermomonas). Aerobic denitrifying bacteria (0.19% Thauera and 0.34% Hyphomicrobium) were identified as the main denitrifying bacteria in the middle of the aerobic area. The dominant nitrifying microorganisms in the middle of the aerobic area were Nitrosomonas (0.50%) and Nitrospira (1.04%). A biofilm in the end of the aerobic area exhibited specific anammox potential, which may have been related to the dominance of 0.024% Candidatus Brocadia. Kinetic analysis revealed that adding plastic carriers to the front and middle of the aerobic area contributed to stable nitrogen removal efficiency.
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Affiliation(s)
- Tianyu Lou
- School of Water Conservancy and Engineering, Zhengzhou University, Zhengzhou, 450001, China
| | - Zhaoxu Peng
- School of Water Conservancy and Engineering, Zhengzhou University, Zhengzhou, 450001, China.
| | - Kun Jiang
- School of Water Conservancy and Engineering, Zhengzhou University, Zhengzhou, 450001, China
| | - Ningqi Niu
- School of Water Conservancy and Engineering, Zhengzhou University, Zhengzhou, 450001, China
| | - Ju Wang
- School of Water Conservancy and Engineering, Zhengzhou University, Zhengzhou, 450001, China
| | - Ao Liu
- School of Water Conservancy and Engineering, Zhengzhou University, Zhengzhou, 450001, China
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30
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Pescador DS, Delgado-Baquerizo M, Fiore-Donno AM, Singh BK, Bonkowski M, Maestre FT. Ecological clusters of soil taxa within bipartite networks are highly sensitive to climatic conditions in global drylands. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210387. [PMID: 35757878 PMCID: PMC9234812 DOI: 10.1098/rstb.2021.0387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/19/2022] [Indexed: 12/18/2022] Open
Abstract
Determining the influence of climate in driving the global distribution of soil microbial communities is fundamental to help predict potential shifts in soil food webs and ecosystem functioning under global change scenarios. Herein, we used a global survey including 80 dryland ecosystems from six continents, and found that the relative abundance of ecological clusters formed by taxa involved in bacteria-fungi and bacteria-cercozoa bipartite networks was highly sensitive to changes in temperature and aridity. Importantly, such a result was maintained when controlling for soil, geographical location and vegetation attributes, being pH and soil organic carbon important determinants of the relative abundance of the ecological clusters. We also identified potential global associations between important soil microbial taxa, which can be useful to support the conservation of terrestrial ecosystems under global change scenarios. Our results suggest that increases in temperature and aridity such as those forecasted for the next decades in drylands could potentially lead to drastic changes in the community composition of functionally important bipartite networks within soil food webs. This could have important but unknown implications for the provision of key ecosystem functions and associated services driven by the organisms forming these networks if other taxa cannot cope with them. This article is part of the theme issue 'Ecological complexity and the biosphere: the next 30 years'.
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Affiliation(s)
- David S. Pescador
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Madrid, Spain
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, E-41012, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Anna Maria Fiore-Donno
- Department of Biology, Institute of Zoology, University of Cologne, 50674 Cologne, Germany
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia
| | - Michael Bonkowski
- Department of Biology, Institute of Zoology, University of Cologne, 50674 Cologne, Germany
| | - Fernando T. Maestre
- Instituto Multidisciplinar para el Estudio del Medio ‘Ramón Margalef’, Universidad de Alicante, San Vicente del Raspeig, Spain
- Departamento de Ecología, Universidad de Alicante, San Vicente del Raspeig, Spain
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31
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An In Situ Study to Understand Community Structure of Estuarine Microbes on the Plastisphere. Microorganisms 2022; 10:microorganisms10081543. [PMID: 36013961 PMCID: PMC9415314 DOI: 10.3390/microorganisms10081543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/19/2022] [Accepted: 07/19/2022] [Indexed: 02/01/2023] Open
Abstract
Microplastics are defined as pieces of plastic that are smaller than 5 mm and they are now considered one of the most abundant ubiquitous plastic debris. Microbial communities that settle on particles can potentially lead to the transport of pathogenic and harmful bloom-forming species, as well as have an impact on global biogeochemical cycles. However, little is known about the acclimation of microbes to different types of microplastic in the estuarine environment. In this study, 16S ribosomal RNA sequencing and analysis was performed on biofilm samples from three different types of microplastic beads placed in Baltimore’s Inner Harbor. Microbial communities associated with microplastic particles and glass bead control were monitored throughout the 28-day incubation time. A significant taxonomic composition dissimilarity was observed between particles-associated and free-living communities, suggesting a unique microbial adaptation to these biofilms. The polymer types, however, did not significantly influence the microbial community composition. Some families with interesting potential metabolism were identified in the plastisphere samples, including Cyanobacteria, Planctomycetes, Desulfobacteriota, and Firmicutes, leading into speculation of their ecological responses and metabolic roles in the estuarine environment. It is crucial to understand the microorganisms that inhabit plastic debris in estuarine systems and their potential metabolic capacity and how it may differ from its marine counterparts in order to assess their roles in global nutrient cycles and if they have ability to be utilized in bioremediation for plastic pollution.
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32
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Prasitwuttisak W, Hoshiko Y, Maeda T, Haraguchi A, Yanagawa K. Microbial Community Structures and Methanogenic Functions in Wetland Peat Soils. Microbes Environ 2022; 37. [PMID: 35851269 PMCID: PMC9530717 DOI: 10.1264/jsme2.me22004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methane metabolism in wetlands involves diverse groups of bacteria and archaea, which are responsible for the biological decomposition of organic matter under certain anoxic conditions. Recent advances in environmental omics revealed the phylogenetic diversity of novel microbial lineages, which have not been previously placed in the traditional tree of life. The present study aimed to verify the key players in methane production, either well-known archaeal members or recently identified lineages, in peat soils collected from wetland areas in Japan. Based on an analysis of microbial communities using 16S rRNA gene sequencing and the molecular cloning of the functional gene, mcrA, a marker gene for methanogenesis, methanogenic archaea belonging to Methanomicrobiales, Methanosarcinales, Methanobacteriales, and Methanomassiliicoccales were detected in anoxic peat soils, suggesting the potential of CH4 production in this natural wetland. “Candidatus Bathyarchaeia”, archaea with vast metabolic capabilities that is widespread in anoxic environments, was abundant in subsurface peat soils (up to 96% of the archaeal community) based on microbial gene quantification by qPCR. These results emphasize the importance of discovering archaea members outside of traditional methanogenic lineages that may have significant functions in the wetland biogeochemical cycle.
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Affiliation(s)
| | - Yuki Hoshiko
- Department of Biological Functions Engineering, Graduate School of Life Sciences and Systems Engineering, Kyushu Institute of Technology
| | - Toshinari Maeda
- Department of Biological Functions Engineering, Graduate School of Life Sciences and Systems Engineering, Kyushu Institute of Technology
| | - Akira Haraguchi
- Faculty of Environmental Engineering, The University of Kitakyushu
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33
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Wang Y, Cheng X, Wang H, Zhou J, Liu X, Tuovinen OH. The Characterization of Microbiome and Interactions on Weathered Rocks in a Subsurface Karst Cave, Central China. Front Microbiol 2022; 13:909494. [PMID: 35847118 PMCID: PMC9277220 DOI: 10.3389/fmicb.2022.909494] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Karst caves are a natural oligotrophic subsurface biosphere widely distributed in southern China. Despite the progress in bacterial and fungal diversity, the knowledge about interactions between bacteria, fungi, and minerals is still limited in caves. Hence, for the first time, we investigated the interaction between bacteria and fungi living on weathered rocks in the Heshang Cave via high-throughput sequencing of 16S rRNA and ITS1 genes, and co-occurrence analysis. The mineral compositions of weathered rocks were analyzed by X-ray diffraction. Bacterial communities were dominated by Actinobacteria (33.68%), followed by Alphaproteobacteria (8.78%), and Planctomycetia (8.73%). In contrast, fungal communities were dominated by Sordariomycetes (21.08%) and Dothideomycetes (14.06%). Mineral substrata, particularly phosphorus-bearing minerals, significantly impacted bacterial (hydroxyapatite) and fungal (fluorapatite) communities as indicated by the redundancy analysis. In comparison with fungi, the development of bacterial communities was more controlled by the environmental selection indicated by the overwhelming contribution of deterministic processes. Co-occurrence network analysis showed that all nodes were positively linked, indicating ubiquitous cooperation within bacterial groups and fungal groups, as well as between bacteria and fungi under oligotrophic conditions in the subsurface biosphere. In total, 19 bacterial ASVs and 34 fungal OTUs were identified as keystone taxa, suggesting the fundamental role of fungi in maintaining the microbial ecosystem on weathered rocks. Ascomycota was most dominant in keystone taxa, accounting for 26.42%, followed by Actinobacteria in bacteria (24.53%). Collectively, our results confirmed the highly diverse bacterial and fungal communities on weathered rocks, and their close cooperation to sustain the subsurface ecosystem. Phosphorus-bearing minerals were of significance in shaping epipetreous bacterial and fungal communities. These observations provide new knowledge about microbial interactions between bacteria, fungi, and minerals in the subterranean biosphere.
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Affiliation(s)
- Yiheng Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China.,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xiaoyu Cheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China.,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China.,School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Jianping Zhou
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Xiaoyan Liu
- School of Environmental Studies, China University of Geosciences, Wuhan, China
| | - Olli H Tuovinen
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
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34
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Ferrarezi RS, Lin X, Gonzalez Neira AC, Tabay Zambon F, Hu H, Wang X, Huang JH, Fan G. Substrate pH Influences the Nutrient Absorption and Rhizosphere Microbiome of Huanglongbing-Affected Grapefruit Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:856937. [PMID: 35646029 PMCID: PMC9141052 DOI: 10.3389/fpls.2022.856937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/04/2022] [Indexed: 06/15/2023]
Abstract
The substrate pH directly affects nutrient availability in the rhizosphere and nutrient uptake by plants. Macronutrients such as nitrogen, potassium, calcium, magnesium, and sulfur are highly available at pH 6.0-6.5, while micronutrients become less available at higher, alkaline pH (pH > 7.0). Recent research has indicated that low pHs can enhance nutrient uptake and improve sweet orange (Citrus sinensis) tree health. We designed a study to understand the influence of a wide range of substrate pH values on plant size and biomass, nutrient availability, leaf gas exchange, and rhizosphere microbiome of grapefruit (Citrus paradisi) affected by Huanglongbing (HLB). Two-year-old "Ray Ruby" grapefruit plants grafted on sour orange (Citrus aurantium) rootstock were cultivated indoors in 10-cm wide × 40-cm tall pots with peat:perlite commercial substrate (80:20 v/v). We tested two disease statuses [HLB-free or healthy (negative, HLB-) and HLB-affected (positive, HLB+)] and six substrate pH values (4, 5, 6, 7, 8, 9) in a 2 × 6 factorial arranged on a complete randomized design with four replications. The canopy volume of HLB+ plants was 20% lower than healthy plants, with pHs 7 and 9 resulting in 44% less canopy volume. The root and shoot ratio of dry weight was 25.8% lower in HLB+ than in healthy plants. Poor root growth and a decrease in fibrous roots were found, especially in pH 5 and 6 treatments in HLB+ plants (p < 0.0001). The disease status and the substrate pHs influenced the leaf nutrient concentration (p < 0.05). High substrate pH affects nutrient availability for root uptake, influencing the nutrient balance throughout the plant system. pH values did not affect plant photosynthesis, indicating that pH does not recover HLB+ plants to the photosynthetic levels of healthy plants-even though high pH positively influenced internal CO2. There were collectively over 200 rhizobacterial identified by the 16S rRNA gene sequencing in individual phylogenetic trees. Most rhizobacteria reads were identified in pH 9. Our results indicated no effect of substrate pHs on the plant disease status induced by enhanced nutrient uptake.
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Affiliation(s)
- Rhuanito Soranz Ferrarezi
- Department of Horticulture, University of Georgia, Athens, GA, United States
- Horticultural Sciences Department, Indian River Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Fort Pierce, FL, United States
| | - Xiongjie Lin
- Fruit Research Institute, Fujian Academy of Agricultural Sciences/Fujian Key Laboratory of Plant Nutrition and Fertilizer, Fuzhou, China
| | - Andres C. Gonzalez Neira
- Horticultural Sciences Department, Indian River Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Fort Pierce, FL, United States
| | - Flavia Tabay Zambon
- Horticultural Sciences Department, Indian River Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Fort Pierce, FL, United States
| | - Hanqing Hu
- Fruit Research Institute, Fujian Academy of Agricultural Sciences/Fujian Key Laboratory of Plant Nutrition and Fertilizer, Fuzhou, China
| | - Xianda Wang
- Fruit Research Institute, Fujian Academy of Agricultural Sciences/Fujian Key Laboratory of Plant Nutrition and Fertilizer, Fuzhou, China
| | - Jing-Hao Huang
- Fruit Research Institute, Fujian Academy of Agricultural Sciences/Fujian Key Laboratory of Plant Nutrition and Fertilizer, Fuzhou, China
| | - Guocheng Fan
- Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, China
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35
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Wongkiew S, Chaikaew P, Takrattanasaran N, Khamkajorn T. Evaluation of nutrient characteristics and bacterial community in agricultural soil groups for sustainable land management. Sci Rep 2022; 12:7368. [PMID: 35513414 PMCID: PMC9072534 DOI: 10.1038/s41598-022-09818-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/28/2022] [Indexed: 11/09/2022] Open
Abstract
The soil bacterial community is critical for understanding biological processes in soils and is used for agricultural soil management. The understanding of microorganisms and ecology in different soil groups classified based on soil properties (e.g., minerals, soil texture, location, nitrogen, phosphorus, organic carbon and pH, among others), is limited. To suggest soil management strategies using bacterial data, we classified soils into four groups based on physical-chemical characteristics and elucidated their relationships with soil nutrient characteristics and the bacterial community in agricultural fields in Saraburi Province, Thailand. Results show that soil groups with high bacterial diversity had positive correlations with total Kjeldahl nitrogen and available phosphorus but were negatively affected by total organic carbon and pH levels. Dominant bacterial genera included Lactobacillus, Phascolarctobacterium, Prevotella, Clostridium, Gaiellales and Blautia. Significant key biomarkers were found (p < 0.05). Nutrient-rich soil groups (high available P, acidic pH) were found with genus Agromyces, while low nutrient soil groups (low available P, basic pH) were found with Hydrogenispora, Ignavibacterium and Bauldia. Based on co-occurrence networks, organic degrading bacteria functioned with other bacteria at high degrees of interconnections, suggesting organic amendment, biostimulation and biodegradation using nutrient-rich organic substrates could be used for agricultural soil improvements.
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Affiliation(s)
- Sumeth Wongkiew
- Department of Environmental Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Water Science and Technology for Sustainable Environment Research Group, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Pasicha Chaikaew
- Department of Environmental Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
| | - Natta Takrattanasaran
- Land Development Department, Land Development Regional Office 1, Pathum Thani, 12110, Thailand
| | - Thanachanok Khamkajorn
- Land Development Department, Land Development Regional Office 1, Pathum Thani, 12110, Thailand
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36
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Cai M, Zhang H, Zhang Y, Wu H. Bioelectrochemical assisted landfill technology for the stabilization and valorization of food waste anaerobic digestate. BIORESOURCE TECHNOLOGY 2022; 351:126935. [PMID: 35247563 DOI: 10.1016/j.biortech.2022.126935] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/24/2022] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
Anaerobic digestion provides an important approach for food waste treatment and valorization, yet a considerable amount of digestate is produced. The appropriate management and utilization of food waste anaerobic digestate is highly desirable for solving both environmental and economic concerns currently. This work innovatively develops a natural potential difference assisted landfill technology (shown as BESAL) for food waste digestate treatment and energy recovery. The results demonstrate the electrochemical assistant accelerates the stabilization of digestate, provides extra 14.89% of organic matter removal and 20.92 mW/m2 of electrical energy recovery over conventional treatment. BESAL promotes the removal of soluble matters in digestate extraction, prevents 13.07 mg/g ammonium-N and 32.87% of total VFAs from accumulation. BESAL also performs gene level stabilization by inhibiting/eliminating microbial and pathogenic gene to ensure the biosafety in its product. Integrated landfill with bioelectrochemical assistance provides a promising option for organic waste stabilization and valorization.
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Affiliation(s)
- Mengyu Cai
- Hebei Key Laboratory of Heavy Metal Deep-Remediation in Water and Resource Reuse and Key Laboratory of Applied Chemistry, Yanshan University, Qinhuangdao 066004, China
| | - Haoran Zhang
- Comprehensive Administrative Law Enforcement Detachment, Bureau of Marine and Fishery of Qinhuangdao, Qinhuangdao 066004, China
| | - Yingchao Zhang
- Hebei Key Laboratory of Heavy Metal Deep-Remediation in Water and Resource Reuse and Key Laboratory of Applied Chemistry, Yanshan University, Qinhuangdao 066004, China
| | - Hao Wu
- Hebei Key Laboratory of Heavy Metal Deep-Remediation in Water and Resource Reuse and Key Laboratory of Applied Chemistry, Yanshan University, Qinhuangdao 066004, China.
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37
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Kaluzhnaya OV, Itskovich VB. Features of Diversity of Polyketide Synthase Genes in the Community of Freshwater Sponge Baikalospongia fungiformis. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422030061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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38
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Wang X, Shang Y, Wei Q, Wu X, Dou H, Zhang H, Zhou S, Sha W, Sun G, Ma S, Zhang H. Comparative Analyses of the Gut Microbiome of Two Fox Species, the Red Fox (Vulpes Vulpes) and Corsac Fox (Vulpes Corsac), that Occupy Different Ecological Niches. MICROBIAL ECOLOGY 2022; 83:753-765. [PMID: 34189610 DOI: 10.1007/s00248-021-01806-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
The gut microbiome is integral for the host's living and environmental adaptation and crucially important for understanding host adaptive mechanisms. The red fox (Vulpes vulpes) dominates a wider ecological niche and more complicated habitat than that of the corsac fox (V. corsac). However, the adaptive mechanisms (in particular, the gut microbiome responsible for this kind of difference) are still unclear. Therefore, we investigated the gut microbiome of these two species in the Hulunbuir grassland, China, and evaluated their microbiome composition, function, and adaptive mechanisms. We profiled the gut microbiome and metabolism function of red and corsac foxes via 16S rRNA gene and metagenome sequencing. The foxes harbored species-specific microbiomes and functions that were related to ecological niche and habitat. The red fox had abundant Bacteroides, which leads to significant enrichment of metabolic pathways (K12373 and K21572) and enzymes related to chitin and carbohydrate degradation that may help the red fox adapt to a wider niche. The corsac fox harbored large proportions of Blautia, Terrisporobacter, and ATP-binding cassette (ABC) transporters (K01990, K02003, and K06147) that can help maintain corsac fox health, allowing it to live in harsh habitats. These results indicate that the gut microbiome of the red and corsac foxes may have different abilities which may provide these species with differing capabilities to adapt to different ecological niches and habitats, thus providing important microbiome data for understanding the mechanisms of host adaptation to different niches and habitats.
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Affiliation(s)
- Xibao Wang
- College of Life Science, Qufu Normal University, Qufu, China
| | - Yongquan Shang
- College of Life Science, Qufu Normal University, Qufu, China
| | - Qinguo Wei
- College of Life Science, Qufu Normal University, Qufu, China
| | - Xiaoyang Wu
- College of Life Science, Qufu Normal University, Qufu, China
| | - Huashan Dou
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir, China
| | - Huanxin Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Shengyang Zhou
- College of Life Science, Qufu Normal University, Qufu, China
| | - Weilai Sha
- College of Life Science, Qufu Normal University, Qufu, China
| | - Guolei Sun
- College of Life Science, Qufu Normal University, Qufu, China
| | - Shengchao Ma
- College of Life Science, Qufu Normal University, Qufu, China
| | - Honghai Zhang
- College of Life Science, Qufu Normal University, Qufu, China.
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39
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The Changes in Soil Microbial Communities across a Subalpine Forest Successional Series. FORESTS 2022. [DOI: 10.3390/f13020289] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Knowledge regarding changes in soil microbial communities with forest succession is vital to understand soil microbial community shifts under global change scenarios. The composition and diversity of soil microbial communities across a subalpine forest successional series were therefore investigated in the Wanglang National Nature Reserve on the eastern Qinghai-Tibet Plateau, China. The calculated diversity indices of soil bacteria (8.598 to 9.791 for Shannon-Wiener, 0.997 to 0.974 for Simpson, 4131 to 4974 for abundance-based coverage estimator (ACE) and 3007 to 3511 for Species richness indices), and ACE (1323 to 921) and Species richness (1251 to 879) indices of soil fungi decreased from initial to terminal succession stages, but Shannon-Wiener and Simpson of soil fungi indices varied slightly with forest succession. Meanwhile, the composition and structure of soil microbial communities varied markedly with forest succession. The relative abundance of the dominant bacterial phyla (Acidobacteria, Firmicutes and Actinobacteria) and fungal taxa (Mortierellomycota, Rozellomycota and unassigned phylum clade GS01) varied considerably with forest succession. However, regardless of successional stage, Proteobacteria and Acidobacteria dominated soil bacterial communities and Ascomycota and Basidiomycota dominated soil fungal communities. Moreover, the changes in soil microbial diversity with forest succession were significantly affected by soil pH, soil organic carbon, soil temperature, altitude, and non-woody debris stock. Importantly, soil pH was the dominant driver of soil microbial community shift with forest succession. In conclusion, the forests at different succession stages not only conserve same microbial populations, but also nurse unique microbial diversity across the forest succession series; and the biodiversity of soil bacterial and fungal communities has differential responses to forest succession.
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40
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Santos-Aberturas J, Vior NM. Beyond Soil-Dwelling Actinobacteria: Fantastic Antibiotics and Where to Find Them. Antibiotics (Basel) 2022; 11:195. [PMID: 35203798 PMCID: PMC8868522 DOI: 10.3390/antibiotics11020195] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/27/2022] [Accepted: 01/29/2022] [Indexed: 12/10/2022] Open
Abstract
Bacterial secondary metabolites represent an invaluable source of bioactive molecules for the pharmaceutical and agrochemical industries. Although screening campaigns for the discovery of new compounds have traditionally been strongly biased towards the study of soil-dwelling Actinobacteria, the current antibiotic resistance and discovery crisis has brought a considerable amount of attention to the study of previously neglected bacterial sources of secondary metabolites. The development and application of new screening, sequencing, genetic manipulation, cultivation and bioinformatic techniques have revealed several other groups of bacteria as producers of striking chemical novelty. Biosynthetic machineries evolved from independent taxonomic origins and under completely different ecological requirements and selective pressures are responsible for these structural innovations. In this review, we summarize the most important discoveries related to secondary metabolites from alternative bacterial sources, trying to provide the reader with a broad perspective on how technical novelties have facilitated the access to the bacterial metabolic dark matter.
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Affiliation(s)
| | - Natalia M. Vior
- Department of Molecular Microbiology, John Innes Centre, Norwich NR7 4UH, UK
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41
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Pabst M, Grouzdev DS, Lawson CE, Kleikamp HBC, de Ram C, Louwen R, Lin YM, Lücker S, van Loosdrecht MCM, Laureni M. A general approach to explore prokaryotic protein glycosylation reveals the unique surface layer modulation of an anammox bacterium. THE ISME JOURNAL 2022; 16:346-357. [PMID: 34341504 PMCID: PMC8776859 DOI: 10.1038/s41396-021-01073-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 07/09/2021] [Accepted: 07/19/2021] [Indexed: 02/07/2023]
Abstract
The enormous chemical diversity and strain variability of prokaryotic protein glycosylation makes their large-scale exploration exceptionally challenging. Therefore, despite the universal relevance of protein glycosylation across all domains of life, the understanding of their biological significance and the evolutionary forces shaping oligosaccharide structures remains highly limited. Here, we report on a newly established mass binning glycoproteomics approach that establishes the chemical identity of the carbohydrate components and performs untargeted exploration of prokaryotic oligosaccharides from large-scale proteomics data directly. We demonstrate our approach by exploring an enrichment culture of the globally relevant anaerobic ammonium-oxidizing bacterium Ca. Kuenenia stuttgartiensis. By doing so we resolve a remarkable array of oligosaccharides, which are produced by two seemingly unrelated biosynthetic routes, and which modify the same surface-layer protein simultaneously. More intriguingly, the investigated strain also accomplished modulation of highly specialized sugars, supposedly in response to its energy metabolism-the anaerobic oxidation of ammonium-which depends on the acquisition of substrates of opposite charges. Ultimately, we provide a systematic approach for the compositional exploration of prokaryotic protein glycosylation, and reveal a remarkable example for the evolution of complex oligosaccharides in bacteria.
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Affiliation(s)
- Martin Pabst
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| | | | - Christopher E. Lawson
- grid.184769.50000 0001 2231 4551DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA USA
| | - Hugo B. C. Kleikamp
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| | - Carol de Ram
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| | - Rogier Louwen
- grid.5645.2000000040459992XDepartment of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Yue Mei Lin
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| | - Sebastian Lücker
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | - Mark C. M. van Loosdrecht
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| | - Michele Laureni
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
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42
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Hu B, Gu X, Wang Y, Leng J, Zhang K, Zhao J, Wu P, Li X, Wan C, Xu J. Revealing the effects of static magnetic field on the anoxic/oxic sequencing batch reactor from the perspective of electron transport and microbial community shifts. BIORESOURCE TECHNOLOGY 2022; 345:126535. [PMID: 34896533 DOI: 10.1016/j.biortech.2021.126535] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
The effects of static magnetic field (SMF) on an anoxic/oxic sequencing batch reactor were investigated from the perspective of electron transport via determining the variations of reduced/oxidized nicotinamide adenine dinucleotide (NADH/NAD+) ratio, NADH concentration, electron transport system activity (ETSA), poly-β-hydroxybutyrate (PHB), extracellular polymeric substances (EPS), as well as the gene expression under different conditions. Moreover, the shifts of microbial community were also analyzed. The application of SMF with an appropriate intensity significantly improved the performance of the process, the abundance of the anoxic denitrifiers, and the activity of the aerobic denitrifiers. The NADH content, as well as ETSA were also enhanced, therefore, the total nitrogen removal efficiency of the process was increased. However, the overhigh SMF intensity resulted in the change of microbial community, meanwhile, had negative effects on the metabolism of microorganisms. Selecting a proper intensity is crucial for the SMF-enhanced biological wastewater treatment process.
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Affiliation(s)
- Bo Hu
- School of Civil Engineering, Chang' an University, Xi'an, China; Key Laboratory of Water Supply & Sewage Engineering, Ministry of Housing and Urban-rural Development, Xi'na, China.
| | - Xin Gu
- School of Civil Engineering, Chang' an University, Xi'an, China; Key Laboratory of Water Supply & Sewage Engineering, Ministry of Housing and Urban-rural Development, Xi'na, China
| | - Yilin Wang
- School of Civil Engineering, Chang' an University, Xi'an, China; Bureau of Housing and Urban-Rural Development of Chencang District, Baoji City, China
| | - Juntong Leng
- School of Civil Engineering, Chang' an University, Xi'an, China; Key Laboratory of Water Supply & Sewage Engineering, Ministry of Housing and Urban-rural Development, Xi'na, China
| | - Kai Zhang
- School of Civil Engineering, Chang' an University, Xi'an, China; Key Laboratory of Water Supply & Sewage Engineering, Ministry of Housing and Urban-rural Development, Xi'na, China
| | - Jianqiang Zhao
- Key Laboratory of Water Supply & Sewage Engineering, Ministry of Housing and Urban-rural Development, Xi'na, China; School of Water and Environment, Chang' an University, Xi'an, China; Key Laboratory of Environmental Protection & Pollution and Remediation of Water and Soil of Shaanxi Province, Xi'an, China
| | - Pei Wu
- School of Civil Engineering, Chang' an University, Xi'an, China; Key Laboratory of Water Supply & Sewage Engineering, Ministry of Housing and Urban-rural Development, Xi'na, China
| | - Xiaoling Li
- School of Civil Engineering, Chang' an University, Xi'an, China; Key Laboratory of Water Supply & Sewage Engineering, Ministry of Housing and Urban-rural Development, Xi'na, China
| | - Chengjie Wan
- School of Civil Engineering, Chang' an University, Xi'an, China; Key Laboratory of Water Supply & Sewage Engineering, Ministry of Housing and Urban-rural Development, Xi'na, China
| | - Jingtong Xu
- School of Civil Engineering, Chang' an University, Xi'an, China; Key Laboratory of Water Supply & Sewage Engineering, Ministry of Housing and Urban-rural Development, Xi'na, China
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Kallscheuer N, Jogler C, Peeters SH, Boedeker C, Jogler M, Heuer A, Jetten MSM, Rohde M, Wiegand S. Mucisphaera calidilacus gen. nov., sp. nov., a novel planctomycete of the class Phycisphaerae isolated in the shallow sea hydrothermal system of the Lipari Islands. Antonie van Leeuwenhoek 2022; 115:407-420. [PMID: 35050438 PMCID: PMC8882080 DOI: 10.1007/s10482-021-01707-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 12/29/2021] [Indexed: 02/07/2023]
Abstract
For extending the current collection of axenic cultures of planctomycetes, we describe in this study the isolation and characterisation of strain Pan265T obtained from a red biofilm in the hydrothermal vent system close to the Lipari Islands in the Tyrrhenian Sea, north of Sicily, Italy. The strain forms light pink colonies on solid medium and grows as a viscous colloid in liquid culture, likely as the result of formation of a dense extracellular matrix observed during electron microscopy. Cells of the novel isolate are spherical, motile and divide by binary fission. Strain Pan265T is mesophilic (temperature optimum 30-33 °C), neutrophilic (pH optimum 7.0-8.0), aerobic and heterotrophic. The strain has a genome size of 3.49 Mb and a DNA G + C content of 63.9%. Phylogenetically, the strain belongs to the family Phycisphaeraceae, order Phycisphaerales, class Phycisphaerae. Our polyphasic analysis supports the delineation of strain Pan265T from the known genera in this family. Therefore, we conclude to assign strain Pan265T to a novel species within a novel genus, for which we propose the name Mucisphaera calidilacus gen. nov., sp. nov. The novel species is the type species of the novel genus and is represented by strain Pan265T (= DSM 100697T = CECT 30425T) as type strain.
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Affiliation(s)
- Nicolai Kallscheuer
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands.
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany.
| | - Stijn H Peeters
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | | | - Mareike Jogler
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Anja Heuer
- Leibniz Institute DSMZ, Braunschweig, Germany
| | - Mike S M Jetten
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sandra Wiegand
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
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44
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Li Y, Wang Y, Shen C, Xu L, Yi S, Zhao Y, Zuo W, Gu C, Shan Y, Bai Y. Structural and Predicted Functional Diversities of Bacterial Microbiome in Response to Sewage Sludge Amendment in Coastal Mudflat Soil. BIOLOGY 2021; 10:biology10121302. [PMID: 34943217 PMCID: PMC8698727 DOI: 10.3390/biology10121302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 11/16/2022]
Abstract
The study investigated the influence of sewage sludge application at rates of 0 (CK), 30 (ST), 75 (MT), and 150 (HT) t ha−1 to mudflats on bacterial community diversity and predicted functions using amplicon-based sequencing. Soils under sewage sludge treatments, especially the HT treatment, exhibited lower pH, salinity and higher nutrient contents (C, N, and P). Moreover, restructured bacterial communities with significantly higher diversities and distinct core and unique microbiomes were observed in all sewage sludge-amended soils as compared to the control. Specifically, core bacterial families, such as Hyphomicrobiaceae, Cytophagaceae, Pirellulaceae Microbacteriaceae, and Phyllobacteriaceae, were significantly enriched in sewage sludge-amended soils. In addition, sewage sludge amendment significantly improved predicted functional diversities of core microbiomes, with significantly higher accumulative relative abundances of functions related to carbon and nitrogen cycling processes compared to the unamended treatment. Correlation analyses showed that modified soil physicochemical properties were conducive for the improvement of diversities of bacterial communities and predicted functionalities. These outcomes demonstrated that sewage sludge amendment not only alleviated saline–sodic and nutrient deficiency conditions, but also restructured bacterial communities with higher diversities and versatile functions, which may be particularly important for the fertility formation and development of mudflat soils.
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Affiliation(s)
- Yunlong Li
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; (Y.L.); (Y.W.); (C.S.); (L.X.); (S.Y.); (Y.Z.); (W.Z.); (Y.S.)
| | - Yimin Wang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; (Y.L.); (Y.W.); (C.S.); (L.X.); (S.Y.); (Y.Z.); (W.Z.); (Y.S.)
| | - Chao Shen
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; (Y.L.); (Y.W.); (C.S.); (L.X.); (S.Y.); (Y.Z.); (W.Z.); (Y.S.)
| | - Lu Xu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; (Y.L.); (Y.W.); (C.S.); (L.X.); (S.Y.); (Y.Z.); (W.Z.); (Y.S.)
| | - Siqiang Yi
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; (Y.L.); (Y.W.); (C.S.); (L.X.); (S.Y.); (Y.Z.); (W.Z.); (Y.S.)
| | - Yilin Zhao
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; (Y.L.); (Y.W.); (C.S.); (L.X.); (S.Y.); (Y.Z.); (W.Z.); (Y.S.)
| | - Wengang Zuo
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; (Y.L.); (Y.W.); (C.S.); (L.X.); (S.Y.); (Y.Z.); (W.Z.); (Y.S.)
| | - Chuanhui Gu
- Environmental Research Center, Duke Kunshan University, Kunshan 215316, China;
| | - Yuhua Shan
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; (Y.L.); (Y.W.); (C.S.); (L.X.); (S.Y.); (Y.Z.); (W.Z.); (Y.S.)
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210095, China
| | - Yanchao Bai
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou 225127, China; (Y.L.); (Y.W.); (C.S.); (L.X.); (S.Y.); (Y.Z.); (W.Z.); (Y.S.)
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210095, China
- Correspondence:
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45
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Xiao X, Zhu Y, Gao C, Zhang Y, Gao Y, Zhao Y. Microbial inoculations improved rice yields by altering the presence of soil rare bacteria. Microbiol Res 2021; 254:126910. [PMID: 34768028 DOI: 10.1016/j.micres.2021.126910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 08/26/2021] [Accepted: 10/25/2021] [Indexed: 10/20/2022]
Abstract
Microbial inoculation is a promising way to improve crop yields in an eco-friendly and economic manner. However, the effects of inoculation on soil resident rare species, representing most of the diversity, are still not well documented and need further assessment. Here, we conducted a pot experiment to test the effects of single-strain and co-inoculants of Rhodopseudomonas palustris and Bacillus subtilis on soil rare and abundant bacteria through sequencing 16S ribosomal RNA gene amplicons. The results showed that microbial inoculations significantly improved the rice yields up to 17.73 %, and R. palustris and B. subtilis co-inoculation showed synergistic effects on rice yields. The inoculations exerted significant modification in soil bacterial community structure, with a more pronounced influence on the rare community than the abundant. The large shifts in rare community structure induced the increase of beneficial rare members and enhanced the membrane transporters and signal transduction together with the increase of some essential metabolism pathways. According to the random forest modeling, relative abundance of the subgroups of rare and abundant communities could explain 61.37-63.09 % of the variations in the rice yields. Structural equation modeling further demonstrated the potential predominant role of rare bacteria in impacting the crop yields (r = 0.95). Overall, our study proved the effectiveness of the co-inoculant in promoting the rice yields through mediating the soil rare bacteria of microbial community. These findings expand current understanding of the microbial inoculation impacts on subsequent crop yield and the underlying microbial mechanisms in agricultural ecosystem.
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Affiliation(s)
- Xian Xiao
- School of Environmental and Safety Engineering, Changzhou University, Changzhou 213164, China; Jiangsu Petrochemical Safety and Environmental Engineering Research Center, Changzhou 213164, China
| | - Yan Zhu
- School of Environmental and Safety Engineering, Changzhou University, Changzhou 213164, China
| | - Chenxin Gao
- School of Environmental and Safety Engineering, Changzhou University, Changzhou 213164, China
| | - Yimin Zhang
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection of China, Nanjing 210042, China
| | - Yuexiang Gao
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection of China, Nanjing 210042, China
| | - Yuan Zhao
- School of Environmental and Safety Engineering, Changzhou University, Changzhou 213164, China.
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46
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Seeger C, Dyrhage K, Mahajan M, Odelgard A, Lind SB, Andersson SGE. The Subcellular Proteome of a Planctomycetes Bacterium Shows That Newly Evolved Proteins Have Distinct Fractionation Patterns. Front Microbiol 2021; 12:643045. [PMID: 34745019 PMCID: PMC8567305 DOI: 10.3389/fmicb.2021.643045] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/25/2021] [Indexed: 11/13/2022] Open
Abstract
The Planctomycetes bacteria have unique cell architectures with heavily invaginated membranes as confirmed by three-dimensional models reconstructed from FIB-SEM images of Tuwongella immobilis and Gemmata obscuriglobus. The subcellular proteome of T. immobilis was examined by differential solubilization followed by LC-MS/MS analysis, which identified 1569 proteins in total. The Tris-soluble fraction contained mostly cytoplasmic proteins, while inner and outer membrane proteins were found in the Triton X-100 and SDS-soluble fractions, respectively. For comparisons, the subcellular proteome of Escherichia coli was also examined using the same methodology. A notable difference in the overall fractionation pattern of the two species was a fivefold higher number of predicted cytoplasmic proteins in the SDS-soluble fraction in T. immobilis. One category of such proteins is represented by innovations in the Planctomycetes lineage, including unique sets of serine/threonine kinases and extracytoplasmic sigma factors with WD40 repeat domains for which no homologs are present in E. coli. Other such proteins are members of recently expanded protein families in which the newly evolved paralog with a new domain structure is recovered from the SDS-soluble fraction, while other paralogs may have similar domain structures and fractionation patterns as the single homolog in E. coli. The expanded protein families in T. immobilis include enzymes involved in replication-repair processes as well as in rRNA and tRNA modification and degradation. These results show that paralogization and domain shuffling have yielded new proteins with distinct fractionation characteristics. Understanding the molecular intricacies of these adaptive changes might aid in the development of a model for the evolution of cellular complexity.
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Affiliation(s)
- Christian Seeger
- Science for Life Laboratory, Molecular Evolution, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Karl Dyrhage
- Science for Life Laboratory, Molecular Evolution, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Mayank Mahajan
- Science for Life Laboratory, Molecular Evolution, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Anna Odelgard
- Science for Life Laboratory, Molecular Evolution, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Sara Bergström Lind
- Department of Chemistry-BMC, Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - Siv G E Andersson
- Science for Life Laboratory, Molecular Evolution, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
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47
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Dubé CE, Ziegler M, Mercière A, Boissin E, Planes S, Bourmaud CAF, Voolstra CR. Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition. Nat Commun 2021; 12:6402. [PMID: 34737272 PMCID: PMC8568919 DOI: 10.1038/s41467-021-26543-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/04/2021] [Indexed: 02/07/2023] Open
Abstract
Coral microbiomes are critical to holobiont functioning, but much remains to be understood about how prevailing environment and host genotype affect microbial communities in ecosystems. Resembling human identical twin studies, we examined bacterial community differences of naturally occurring fire coral clones within and between contrasting reef habitats to assess the relative contribution of host genotype and environment to microbiome structure. Bacterial community composition of coral clones differed between reef habitats, highlighting the contribution of the environment. Similarly, but to a lesser extent, microbiomes varied across different genotypes in identical habitats, denoting the influence of host genotype. Predictions of genomic function based on taxonomic profiles suggest that environmentally determined taxa supported a functional restructuring of the microbial metabolic network. In contrast, bacteria determined by host genotype seemed to be functionally redundant. Our study suggests microbiome flexibility as a mechanism of environmental adaptation with association of different bacterial taxa partially dependent on host genotype.
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Affiliation(s)
- C. E. Dubé
- grid.11642.300000 0001 2111 2608UMR 9220 ENTROPIE, UR-IRD-CNRS-UNC-IFREMER, Université de La Réunion, 15 Avenue René Cassin, CS 92003, 97744 Saint-Denis Cedex, La Réunion France ,grid.11136.340000 0001 2192 5916PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia ,grid.23856.3a0000 0004 1936 8390Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, G1V 0A6 Canada
| | - M. Ziegler
- grid.8664.c0000 0001 2165 8627Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 IFZ, 35392 Giessen, Germany ,grid.45672.320000 0001 1926 5090Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955 Saudi Arabia
| | - A. Mercière
- grid.11136.340000 0001 2192 5916PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia
| | - E. Boissin
- grid.11136.340000 0001 2192 5916PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia
| | - S. Planes
- grid.11136.340000 0001 2192 5916PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia
| | - C. A. -F. Bourmaud
- grid.11642.300000 0001 2111 2608UMR 9220 ENTROPIE, UR-IRD-CNRS-UNC-IFREMER, Université de La Réunion, 15 Avenue René Cassin, CS 92003, 97744 Saint-Denis Cedex, La Réunion France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia
| | - C. R. Voolstra
- grid.45672.320000 0001 1926 5090Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955 Saudi Arabia ,grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, 78457 Konstanz, Germany
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48
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Chen P, Huang J, Rao L, Zhu W, Yu Y, Xiao F, Chen X, Yu H, Wu Y, Xu K, Zheng X, Hu R, He Z, Yan Q. Resistance and Resilience of Fish Gut Microbiota to Silver Nanoparticles. mSystems 2021; 6:e0063021. [PMID: 34519523 PMCID: PMC8547456 DOI: 10.1128/msystems.00630-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/30/2021] [Indexed: 11/20/2022] Open
Abstract
Understanding mechanisms governing the resistance and resilience of microbial communities is essential for predicting their ecological responses to environmental disturbances. Although we have a good understanding of such issues for soil and lake ecosystems, how ecological resistance and resilience regulate the microbiota in the fish gut ecosystem remains unclear. Using the zebrafish model, we clarified the potential mechanisms governing the gut microbiota after exposure to silver nanoparticles (AgNPs). Here, we explored the ecological resistance and resilience of gut microbiota in zebrafish exposed to different concentrations of AgNPs (i.e., 10, 33 and 100 μg/liter) for 15, 45, 75 days. The high-throughput sequencing analysis of the 16S rRNA gene showed that AgNP exposure significantly reduced the α-diversity of gut microbiota and resulted in obvious dynamics of community composition and structure. However, the rebound of zebrafish gut microbiota was pushed toward an alternative state after 15 days of AgNP exposure. We found that homogeneous selection was a more prevalent contributor in driving gut community recovery after AgNP exposure. The resilience and resistance of gut microbiota responses to AgNP disturbance might be mainly determined by the predominant keystone taxa such as Acinetobacter and Gemmata. This study not only expanded our understanding of fish gut microbiota's responses to pollutants but also provided new insights into maintaining host-microbiome stability during environmental perturbations. IMPORTANCE Understanding the ecological mechanisms governing the resistance and resilience of microbial communities is a key issue to predict their responses to environmental disturbances. Using the zebrafish model, we wanted to clarify the potential mechanisms governing the resistance and resilience of gut microbiota after exposure to silver nanoparticles (AgNPs). We found that AgNP contamination significantly reduced the α-diversity of gut microbiota and resulted in obvious changes in community composition. The resilience and resistance of gut microbiota to AgNPs might be associated with the predominant keystone taxa (e.g., Acinetobacter and Gemmata). This study greatly expanded our understanding of how fish gut microbiota responds to environmental perturbations and maintains stability.
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Affiliation(s)
- Pubo Chen
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Jie Huang
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Liuyu Rao
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Wengen Zhu
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yuhe Yu
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Fanshu Xiao
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xiaojuan Chen
- Key Laboratory of Ecological Impacts of Hydraulic-Projects and Restoration of Aquatic Ecosystem of Ministry of Water Resources, Institute of Hydroecology, Ministry of Water Resources and Chinese Academy of Sciences, Wuhan, China
| | - Huang Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Yongjie Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Kui Xu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xiafei Zheng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
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49
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Srinivasan R, Kannappan A, Shi C, Lin X. Marine Bacterial Secondary Metabolites: A Treasure House for Structurally Unique and Effective Antimicrobial Compounds. Mar Drugs 2021; 19:md19100530. [PMID: 34677431 PMCID: PMC8539464 DOI: 10.3390/md19100530] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/12/2021] [Accepted: 09/15/2021] [Indexed: 02/06/2023] Open
Abstract
The prevalence of antimicrobial resistance reduces the effectiveness of antimicrobial drugs in preventing and treating infectious diseases caused by pathogenic organisms, such as bacteria, fungi, and viruses. Because of the burgeoning growth of microbes with antimicrobial-resistant traits, there is a dire need to identify and develop novel and effective antimicrobial agents to treat infections from antimicrobial-resistant strains. The marine environment is rich in ecological biodiversity and can be regarded as an untapped resource for prospecting novel bioactive compounds. Therefore, exploring the marine environment for antimicrobial agents plays a significant role in drug development and biomedical research. Several earlier scientific investigations have proven that bacterial diversity in the marine environment represents an emerging source of structurally unique and novel antimicrobial agents. There are several reports on marine bacterial secondary metabolites, and many are pharmacologically significant and have enormous promise for developing effective antimicrobial drugs to combat microbial infections in drug-resistant pathogens. In this review, we attempt to summarize published articles from the last twenty-five years (1996–2020) on antimicrobial secondary metabolites from marine bacteria evolved in marine environments, such as marine sediment, water, fauna, and flora.
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Affiliation(s)
- Ramanathan Srinivasan
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (R.S.); (X.L.)
| | - Arunachalam Kannappan
- State Key Laboratory of Microbial Metabolism, MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (A.K.); (C.S.)
| | - Chunlei Shi
- State Key Laboratory of Microbial Metabolism, MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (A.K.); (C.S.)
| | - Xiangmin Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (R.S.); (X.L.)
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50
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Franke JD, Fuerst JA, Poole AM. Editorial: Structure, Function and Evolution of Complex Cellular Organization in Bacteria and Archaea. Front Microbiol 2021; 12:751416. [PMID: 34526983 PMCID: PMC8435829 DOI: 10.3389/fmicb.2021.751416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 08/10/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Josef D Franke
- Department of Biology, Creighton University, Omaha, NE, United States
| | - John A Fuerst
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Anthony M Poole
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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