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Zhang L, Yuan L, Xiang J, Liao Q, Zhang D, Liu J. Response of the microbial community structure to the environmental factors during the extreme flood season in Poyang Lake, the largest freshwater lake in China. Front Microbiol 2024; 15:1362968. [PMID: 38633691 PMCID: PMC11021660 DOI: 10.3389/fmicb.2024.1362968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/13/2024] [Indexed: 04/19/2024] Open
Abstract
Background Poyang Lake is the largest freshwater lake in China, and there are several studies on the composition and diversity of bacteria in Poyang Lake, while few quantitative studies were carried out on the response of the bacterial community to environmental factors during the extreme flood season in Poyang Lake. Methods The connected-lake heterogeneity of bacterial community composition (BCC) was investigated in Poyang Lake during the flood season in 2020. Illumina high-throughput sequencing technology was used in this study. Results The bacterial community structure in the water was different from that in the sediment of Poyang Lake during extreme flood seasons. The bacterial diversity in water was much lower than that in sediment. In the water column, the dominant phyla were Actinobacteriota, while the composition of bacteria in sediment was more complex than that in water, and the dominant phyla in sediment were Proteobacteria, Chloroflexi, Acidobacteriota, and Actinobacteriota. The bacterial diversity in the water of Poyang Lake showed seasonal dynamics, while no seasonal variation of bacterial communities in sediment was observed. The bacterial community structure in the sediment from the two bays and channel areas of Poyang Lake can be distinguished from each other. The microbial diversity in sediment gradually increased from the Sancha Bay to the Zhouxi Bay and then to the channel, but the total nitrogen (TN) concentration in sediment (STN) and the total phosphorus (TP) concentration in sediment (STP) showed opposite trends. This might be due to the anthropogenic disturbances from the extreme flood. The bacterial community structure in, water column was significantly correlated with WT, NH4-N, STP, SOM, Chl a, DO, TP, and Eh, while the bacterial community structure in sediment was significantly correlated with SOM and STP. Conclusion The bacterial community structure in water was greatly different from that in sediment in Poyang Lake during extreme flood seasons. The bacterial community structure in the water column was not only sensitive to the geochemical characteristics of the water but also affected by some nutrient concentrations in the sediment. During the wet seasons, bacterial diversity was only affected by SOM and STP.
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Affiliation(s)
- Li Zhang
- Institute of Quality & Safety and Standards of Agricultural Products Research, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Lijuan Yuan
- Institute of Quality & Safety and Standards of Agricultural Products Research, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Jianjun Xiang
- Institute of Quality & Safety and Standards of Agricultural Products Research, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Qiegen Liao
- Institute of Quality & Safety and Standards of Agricultural Products Research, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Dawen Zhang
- Institute of Quality & Safety and Standards of Agricultural Products Research, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Jutao Liu
- Jiangxi Provincial Institute of Water Sciences, Nanchang, Jiangxi, China
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2
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Li L, Huang D, Hu Y, Rudling NM, Canniffe DP, Wang F, Wang Y. Globally distributed Myxococcota with photosynthesis gene clusters illuminate the origin and evolution of a potentially chimeric lifestyle. Nat Commun 2023; 14:6450. [PMID: 37833297 PMCID: PMC10576062 DOI: 10.1038/s41467-023-42193-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
Photosynthesis is a fundamental biogeochemical process, thought to be restricted to a few bacterial and eukaryotic phyla. However, understanding the origin and evolution of phototrophic organisms can be impeded and biased by the difficulties of cultivation. Here, we analyzed metagenomic datasets and found potential photosynthetic abilities encoded in the genomes of uncultivated bacteria within the phylum Myxococcota. A putative photosynthesis gene cluster encoding a type-II reaction center appears in at least six Myxococcota families from three classes, suggesting vertical inheritance of these genes from an early common ancestor, with multiple independent losses in other lineages. Analysis of metatranscriptomic datasets indicate that the putative myxococcotal photosynthesis genes are actively expressed in various natural environments. Furthermore, heterologous expression of myxococcotal pigment biosynthesis genes in a purple bacterium supports that the genes can drive photosynthetic processes. Given that predatory abilities are thought to be widespread across Myxococcota, our results suggest the intriguing possibility of a chimeric lifestyle (combining predatory and photosynthetic abilities) in members of this phylum.
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Affiliation(s)
- Liuyang Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Danyue Huang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yaoxun Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Nicola M Rudling
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Daniel P Canniffe
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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3
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Saggu SK, Nath A, Kumar S. Myxobacteria: biology and bioactive secondary metabolites. Res Microbiol 2023; 174:104079. [PMID: 37169232 DOI: 10.1016/j.resmic.2023.104079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/22/2023] [Accepted: 05/04/2023] [Indexed: 05/13/2023]
Abstract
Myxobacteria are Gram-negative eubacteria and they thrive in a variety of habitats including soil rich in organic matter, rotting wood, animal dung and marine environment. Myxobacteria are a promising source of new compounds associated with diverse bioactive spectrum and unique mode of action. The genome information of myxobacteria has revealed many orphan biosynthetic pathways indicating that these bacteria can be the source of several novel natural products. In this review, we highlight the biology of myxobacteria with emphasis on their habitat, life cycle, isolation methods and enlist all the bioactive secondary metabolites purified till date and their mode of action.
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Affiliation(s)
- Sandeep Kaur Saggu
- Department of Biotechnology, Kanya Maha Vidyalaya, Jalandhar, Punjab, India - 144004.
| | - Amar Nath
- University Centre of Excellence in Research, Baba Farid University of Health Sciences, Faridkot, Punjab India 151203.
| | - Shiv Kumar
- Guru Gobind Singh Medical College, Baba Farid University of Health Sciences, Faridkot, Punjab India 151203.
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4
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Campa MF, Chen See JR, Unverdorben LV, Wright OG, Roth KA, Niles JM, Ressler D, Macatugal EMS, Putt AD, Techtmann SM, Righetti TL, Hazen TC, Lamendella R. Geochemistry and Multiomics Data Differentiate Streams in Pennsylvania Based on Unconventional Oil and Gas Activity. Microbiol Spectr 2022; 10:e0077022. [PMID: 35980272 PMCID: PMC9603415 DOI: 10.1128/spectrum.00770-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/15/2022] [Indexed: 12/30/2022] Open
Abstract
Unconventional oil and gas (UOG) extraction is increasing exponentially around the world, as new technological advances have provided cost-effective methods to extract hard-to-reach hydrocarbons. While UOG has increased the energy output of some countries, past research indicates potential impacts in nearby stream ecosystems as measured by geochemical and microbial markers. Here, we utilized a robust data set that combines 16S rRNA gene amplicon sequencing (DNA), metatranscriptomics (RNA), geochemistry, and trace element analyses to establish the impact of UOG activity in 21 sites in northern Pennsylvania. These data were also used to design predictive machine learning models to determine the UOG impact on streams. We identified multiple biomarkers of UOG activity and contributors of antimicrobial resistance within the order Burkholderiales. Furthermore, we identified expressed antimicrobial resistance genes, land coverage, geochemistry, and specific microbes as strong predictors of UOG status. Of the predictive models constructed (n = 30), 15 had accuracies higher than expected by chance and area under the curve values above 0.70. The supervised random forest models with the highest accuracy were constructed with 16S rRNA gene profiles, metatranscriptomics active microbial composition, metatranscriptomics active antimicrobial resistance genes, land coverage, and geochemistry (n = 23). The models identified the most important features within those data sets for classifying UOG status. These findings identified specific shifts in gene presence and expression, as well as geochemical measures, that can be used to build robust models to identify impacts of UOG development. IMPORTANCE The environmental implications of unconventional oil and gas extraction are only recently starting to be systematically recorded. Our research shows the utility of microbial communities paired with geochemical markers to build strong predictive random forest models of unconventional oil and gas activity and the identification of key biomarkers. Microbial communities, their transcribed genes, and key biomarkers can be used as sentinels of environmental changes. Slight changes in microbial function and composition can be detected before chemical markers of contamination. Potential contamination, specifically from biocides, is especially concerning due to its potential to promote antibiotic resistance in the environment. Additionally, as microbial communities facilitate the bulk of nutrient cycling in the environment, small changes may have long-term repercussions. Supervised random forest models can be used to identify changes in those communities, greatly enhance our understanding of what such impacts entail, and inform environmental management decisions.
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Affiliation(s)
- Maria Fernanda Campa
- University of Tennessee, Knoxville, Tennessee, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | | | | | | | | | | | | | - Andrew D. Putt
- University of Tennessee, Knoxville, Tennessee, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | | | - Terry C. Hazen
- University of Tennessee, Knoxville, Tennessee, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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5
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Kelleher SL, Alam S, Rivera OC, Barber-Zucker S, Zarivach R, Wagatsuma T, Kambe T, Soybel DI, Wright J, Lamendella R. Loss-of-function SLC30A2 mutants are associated with gut dysbiosis and alterations in intestinal gene expression in preterm infants. Gut Microbes 2022; 14:2014739. [PMID: 34965180 PMCID: PMC8726655 DOI: 10.1080/19490976.2021.2014739] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 11/17/2021] [Indexed: 02/04/2023] Open
Abstract
Loss of Paneth cell (PC) function is implicated in intestinal dysbiosis, mucosal inflammation, and numerous intestinal disorders, including necrotizing enterocolitis (NEC). Studies in mouse models show that zinc transporter ZnT2 (SLC30A2) is critical for PC function, playing a role in granule formation, secretion, and antimicrobial activity; however, no studies have investigated whether loss of ZnT2 function is associated with dysbiosis, mucosal inflammation, or intestinal dysfunction in humans. SLC30A2 was sequenced in healthy preterm infants (26-37 wks; n = 75), and structural analysis and functional assays determined the impact of mutations. In human stool samples, 16S rRNA sequencing and RNAseq of bacterial and human transcripts were performed. Three ZnT2 variants were common (>5%) in this population: H346Q, f = 19%; L293R, f = 7%; and a previously identified compound substitution in Exon7, f = 16%). H346Q had no effect on ZnT2 function or beta-diversity. Exon7 impaired zinc transport and was associated with a fractured gut microbiome. Analysis of microbial pathways suggested diverse effects on nutrient metabolism, glycan biosynthesis and metabolism, and drug resistance, which were associated with increased expression of host genes involved in tissue remodeling. L293R caused profound ZnT2 dysfunction and was associated with overt gut dysbiosis. Microbial pathway analysis suggested effects on nucleotide, amino acid and vitamin metabolism, which were associated with the increased expression of host genes involved in inflammation and immune response. In addition, L293R was associated with reduced weight gain in the early postnatal period. This implicates ZnT2 as a novel modulator of mucosal homeostasis in humans and suggests that genetic variants in ZnT2 may affect the risk of mucosal inflammation and intestinal disease.
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MESH Headings
- Animals
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- Cation Transport Proteins/deficiency
- Cation Transport Proteins/genetics
- Dysbiosis/genetics
- Dysbiosis/metabolism
- Dysbiosis/microbiology
- Exons
- Female
- Gastrointestinal Microbiome
- Humans
- Infant, Newborn
- Infant, Newborn, Diseases/genetics
- Infant, Newborn, Diseases/metabolism
- Infant, Newborn, Diseases/microbiology
- Infant, Premature/metabolism
- Intestines/metabolism
- Intestines/microbiology
- Loss of Function Mutation
- Male
- Mice, Knockout
- Mutation
- Mutation, Missense
- Polysaccharides/metabolism
- Mice
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Affiliation(s)
- Shannon L Kelleher
- Department of Cellular and Molecular Physiology, Penn State Hershey College of Medicine, Hershey, Pennsylvania, USA
- Department of Pharmacology, Penn State Hershey College of Medicine, Hershey, Pennsylvania, USA
- Department of Surgery, Penn State Hershey College of Medicine, Hershey, Pennsylvania, USA
- Department of Biomedical and Nutritional Sciences, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Samina Alam
- Department of Cellular and Molecular Physiology, Penn State Hershey College of Medicine, Hershey, Pennsylvania, USA
- Department of Surgery, Penn State Hershey College of Medicine, Hershey, Pennsylvania, USA
| | - Olivia C Rivera
- Department of Cellular and Molecular Physiology, Penn State Hershey College of Medicine, Hershey, Pennsylvania, USA
- Department of Surgery, Penn State Hershey College of Medicine, Hershey, Pennsylvania, USA
| | - Shiran Barber-Zucker
- Department of Life Sciences, The National Institute for Biotechnology in the Negev and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Raz Zarivach
- Department of Life Sciences, The National Institute for Biotechnology in the Negev and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Takumi Wagatsuma
- The Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Taiho Kambe
- The Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - David I Soybel
- Department of Surgery, Penn State Hershey College of Medicine, Hershey, Pennsylvania, USA
| | - Justin Wright
- Department of Biology, Juniata College, Huntingdon, Pennsylvania, USA
| | - Regina Lamendella
- Department of Biology, Juniata College, Huntingdon, Pennsylvania, USA
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6
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Genomes of Novel Myxococcota Reveal Severely Curtailed Machineries for Predation and Cellular Differentiation. Appl Environ Microbiol 2021; 87:e0170621. [PMID: 34524899 DOI: 10.1128/aem.01706-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cultured Myxococcota are predominantly aerobic soil inhabitants, characterized by their highly coordinated predation and cellular differentiation capacities. Little is currently known regarding yet-uncultured Myxococcota from anaerobic, nonsoil habitats. We analyzed genomes representing one novel order (o__JAFGXQ01) and one novel family (f__JAFGIB01) in the Myxococcota from an anoxic freshwater spring (Zodletone Spring) in Oklahoma, USA. Compared to their soil counterparts, anaerobic Myxococcota possess smaller genomes and a smaller number of genes encoding biosynthetic gene clusters (BGCs), peptidases, one- and two-component signal transduction systems, and transcriptional regulators. Detailed analysis of 13 distinct pathways/processes crucial to predation and cellular differentiation revealed severely curtailed machineries, with the notable absence of homologs for key transcription factors (e.g., FruA and MrpC), outer membrane exchange receptor (TraA), and the majority of sporulation-specific and A-motility-specific genes. Further, machine learning approaches based on a set of 634 genes informative of social lifestyle predicted a nonsocial behavior for Zodletone Myxococcota. Metabolically, Zodletone Myxococcota genomes lacked aerobic respiratory capacities but carried genes suggestive of fermentation, dissimilatory nitrite reduction, and dissimilatory sulfate-reduction (in f_JAFGIB01) for energy acquisition. We propose that predation and cellular differentiation represent a niche adaptation strategy that evolved circa 500 million years ago (Mya) in response to the rise of soil as a distinct habitat on Earth. IMPORTANCE The phylum Myxococcota is a phylogenetically coherent bacterial lineage that exhibits unique social traits. Cultured Myxococcota are predominantly aerobic soil-dwelling microorganisms that are capable of predation and fruiting body formation. However, multiple yet-uncultured lineages within the Myxococcota have been encountered in a wide range of nonsoil, predominantly anaerobic habitats, and the metabolic capabilities, physiological preferences, and capacity of social behavior of such lineages remain unclear. Here, we analyzed genomes recovered from a metagenomic analysis of an anoxic freshwater spring in Oklahoma, USA, that represent novel, yet-uncultured, orders and families in the Myxococcota. The genomes appear to lack the characteristic hallmarks for social behavior encountered in Myxococcota genomes and displayed a significantly smaller genome size and a smaller number of genes encoding biosynthetic gene clusters, peptidases, signal transduction systems, and transcriptional regulators. Such perceived lack of social capacity was confirmed through detailed comparative genomic analysis of 13 pathways associated with Myxococcota social behavior, as well as the implementation of machine learning approaches to predict social behavior based on genome composition. Metabolically, these novel Myxococcota are predicted to be strict anaerobes, utilizing fermentation, nitrate reduction, and dissimilarity sulfate reduction for energy acquisition. Our results highlight the broad patterns of metabolic diversity within the yet-uncultured Myxococcota and suggest that the evolution of predation and fruiting body formation in the Myxococcota has occurred in response to soil formation as a distinct habitat on Earth.
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7
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Community Profile and Drivers of Predatory Myxobacteria under Different Compost Manures. Microorganisms 2021; 9:microorganisms9112193. [PMID: 34835319 PMCID: PMC8622275 DOI: 10.3390/microorganisms9112193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022] Open
Abstract
Myxobacteria are unique predatory microorganisms with a distinctive social lifestyle. These taxa play key roles in the microbial food webs in different ecosystems and regulate the community structures of soil microbial communities. Compared with conditions under conventional management, myxobacteria abundance increases in the organic soil, which could be related to the presence of abundant myxobacteria in the applied compost manure during organic conditions. In the present study,16S rRNA genes sequencing technology was used to investigate the community profile and drivers of predatory myxobacteria in four common compost manures. According to the results, there was a significant difference in predatory myxobacteria community structure among different compost manure treatments (p < 0.05). The alpha-diversity indices of myxobacteria community under swine manure compost were the lowest (Observed OTU richness = 13.25, Chao1 = 14.83, Shannon = 0.61), and those under wormcast were the highest (Observed OTU richness = 30.25, Chao1 = 31.65, Shannon = 2.62). Bacterial community diversity and Mg2+ and Ca2+ concentrations were the major factors influencing the myxobacteria community under different compost manure treatments. In addition, organic carbon, pH, and total nitrogen influenced the community profile of myxobacteria in compost manure. The interaction between myxobacteria and specific bacterial taxa (Micrococcales) in compost manure may explain the influence of bacteria on myxobacteria community structure. Further investigations on the in-situ community profile of predatory myxobacteria and the key microorganism influencing their community would advance our understanding of the community profile and functions of predatory microorganisms in the microbial world.
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8
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Zhou Z, Hu R, Ni Y, Zhuang W, Luo Z, Huang W, Yan Q, He Z, Zhong Q, Wang C. Genetic Elucidation of Quorum Sensing and Cobamide Biosynthesis in Divergent Bacterial-Fungal Associations Across the Soil-Mangrove Root Interface. Front Microbiol 2021; 12:698385. [PMID: 34675891 PMCID: PMC8524053 DOI: 10.3389/fmicb.2021.698385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 09/15/2021] [Indexed: 11/13/2022] Open
Abstract
Plant roots in soil host a repertoire of bacteria and fungi, whose ecological interactions could improve their functions and plant performance. However, the potential microbial interactions and underlying mechanisms remain largely unknown across the soil-mangrove root interface. We herein analyzed microbial intra- and inter-domain network topologies, keystone taxa, and interaction-related genes across four compartments (non-rhizosphere, rhizosphere, episphere, and endosphere) from a soil-mangrove root continuum, using amplicon and metagenome sequencing technologies. We found that both intra- and inter-domain networks displayed notable differences in the structure and topology across four compartments. Compared to three peripheral compartments, the endosphere was a distinctive compartment harboring more dense co-occurrences with a higher average connectivity in bacterial-fungal network (2.986) than in bacterial (2.628) or fungal network (2.419), which could be related to three bacterial keystone taxa (Vibrio, Anaerolineae, and Desulfarculaceae) detected in the endosphere as they are known to intensify inter-domain associations with fungi and stimulate biofilm formation. In support of this finding, we also found that the genes involved in cell-cell communications by quorum sensing (rhlI, lasI, pqsH, and lasR) and aerobic cobamide biosynthesis (cobG, cobF, and cobA) were highly enriched in the endosphere, whereas anaerobic cobamide biosynthesis (encoded by cbiT and cbiE) was dominant in three peripheral compartments. Our results provide genetic evidence for the intensified bacterial-fungal associations of root endophytes, highlighting the critical role of the soil-root interface in structuring the microbial inter-domain associations.
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Affiliation(s)
- Zhengyuan Zhou
- 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
| | - Yanmei Ni
- Guangdong Agribusiness Tropical Agriculture Institute, Guangzhou, China
| | - Wei Zhuang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Zhiwen Luo
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Weiming Huang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 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
| | - 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
| | - Qiuping Zhong
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Cheng Wang
- 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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9
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Zhao M, Ma YT, He SY, Mou X, Wu L. Dynamics of bacterioplankton community structure in response to seasonal hydrological disturbances in Poyang Lake, the largest wetland in China. FEMS Microbiol Ecol 2020; 96:5863183. [DOI: 10.1093/femsec/fiaa064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 06/25/2020] [Indexed: 11/14/2022] Open
Abstract
ABSTRACT
Bacterioplankton communities play a critical role in biogeochemical cycling in freshwater environments, but how the hydrological regime impacts the assembly of bacterioplankton communities remains unclear. This study examined differences in bacterioplankton community structures between wet (July and September) and dry (October and November) seasons in two consecutive years (2016 and 2017) in Poyang Lake, the largest seasonal freshwater lake in China. Our results revealed no overall difference in bacterioplankton compositions and their predicted functions among spatially separated sites. However, bacterioplankton communities did show significant temporal shifts, mainly between samples in November and other months. Transitions from the dry to the wet season were observed in October in both sampling years. Meanwhile, insignificant spatial but significant temporal differences were also found for physicochemical variables. Moreover, redundancy analysis indicates that compared with water depth, water temperature was found to better explain changes in the bacterioplankton community. These findings consistently indicate that the bacterioplankton community in Poyang Lake is relatively less sensitive to annual hydrology shifts than water temperature and nutrient conditions.
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Affiliation(s)
- Man Zhao
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China
| | - Yan-tian Ma
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China
| | - Shi-yao He
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China
| | - Xiaozhen Mou
- Department of Biological Sciences, Kent State University, OH 44242, USA
| | - Lan Wu
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330022, China
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10
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Sun R, Tu Z, Fan L, Qiao Z, Liu X, Hu S, Zheng G, Wu Y, Wang R, Mi X. The correlation analyses of bacterial community composition and spatial factors between freshwater and sediment in Poyang Lake wetland by using artificial neural network (ANN) modeling. Braz J Microbiol 2020; 51:1191-1207. [PMID: 32406050 DOI: 10.1007/s42770-020-00285-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/23/2020] [Indexed: 02/06/2023] Open
Abstract
As one of the most important components of the lake ecosystem, microorganisms from the freshwater and sediment play an important role in many ecological processes. However, the difference and correlation of bacterial community between these two niches were not clear. This study investigated the diversity of microbial community of freshwater and sediment samples from fifteen locations in Poyang Lake wetland. The correlation between the bacterial community and physicochemical property of Poyang Lake wetland was analyzed by artificial neural network (ANN). Our results demonstrated that the freshwater and sediment bacterial community were dominated by groups of the Bacteroidetes (23.33%) and β-Proteobacteria (22.54%) separately, whereas, Canalipalpata, Bacillariophyta, Gemmatimonadetes, and Verrucomicrobia were detected in freshwater niches only. Phylogenetic analysis further indicated that bacterial composition in freshwater significantly differed with the sediment niches. There are 34 unique species accounted for 85% in fresh water samples and 28 unique species accounted for 82% in sediment samples. Cluster analysis further proved that all the samples from freshwater niches clustered closely together, far from the rest sediment samples. ANN analysis revealed that the freshwater with high N and P nutrients will greatly increase the diversity of the bacterial communities. In general, both environmental physicochemical properties, not each factor independently, contributed to the shift in the bacterial community structure. The five tributaries (Gan, Fu, Xin, Rao, Xiu Rivers) play a vital role in shaping the bacterial communities of Poyang Lake. This study provides new insights for understanding of microbial community compositions and structures of Poyang Lake wetland.
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Affiliation(s)
- Ran Sun
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'An, 710129, China.,School of Ecology and Environment, Northwestern Polytechnical University, Xi'An, 710129, China
| | - Zuxin Tu
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, 330029, China
| | - Lin Fan
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'An, 710129, China
| | - Zixia Qiao
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'An, 710129, China
| | - Xiaoyan Liu
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'An, 710129, China
| | - Sihai Hu
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'An, 710129, China
| | - Guohua Zheng
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, 330029, China.,Key Laboratory of Poyang Lake, Jiangxi Academy of Sciences, Nanchang, 330029, China
| | - Yaoguo Wu
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'An, 710129, China.
| | - Ruiwu Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'An, 710129, China.
| | - Xiaohui Mi
- School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'An, 710129, China
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11
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Staninska-Pięta J, Czarny J, Piotrowska-Cyplik A, Juzwa W, Wolko Ł, Nowak J, Cyplik P. Heavy Metals as a Factor Increasing the Functional Genetic Potential of Bacterial Community for Polycyclic Aromatic Hydrocarbon Biodegradation. Molecules 2020; 25:molecules25020319. [PMID: 31941126 PMCID: PMC7024319 DOI: 10.3390/molecules25020319] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/01/2020] [Accepted: 01/10/2020] [Indexed: 01/23/2023] Open
Abstract
The bioremediation of areas contaminated with hydrocarbon compounds and heavy metals is challenging due to the synergistic toxic effects of these contaminants. On the other hand, the phenomenon of the induction of microbial secretion of exopolysaccharides (EPS) under the influence of heavy metals may contribute to affect the interaction between hydrophobic hydrocarbons and microbial cells, thus increasing the bioavailability of hydrophobic organic pollutants. The purpose of this study was to analyze the impact of heavy metals on the changes in the metapopulation structure of an environmental consortium, with particular emphasis on the number of copies of orthologous genes involved in exopolysaccharide synthesis pathways and the biodegradation of hydrocarbons. The results of the experiment confirmed that the presence of heavy metals at concentrations of 50 mg·L-1 and 150 mg·L-1 resulted in a decrease in the metabolic activity of the microbial consortium and its biodiversity. Despite this, an increase in the biological degradation rate of polycyclic aromatic hydrocarbons was noted of 17.9% and 16.9%, respectively. An assessment of the estimated number of genes crucial for EPS synthesis and biodegradation of polycyclic aromatic hydrocarbons confirmed the relationship between the activation of EPS synthesis pathways and polyaromatic hydrocarbon biodegradation pathways. It was established that microorganisms that belong to the Burkholderiales order are characterized by a high representation of the analyzed orthologs and high application potential in areas contaminated with heavy metals and hydrocarbons.
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Affiliation(s)
- Justyna Staninska-Pięta
- Institute of Food Technology of Plant Origin, Poznan University of Life Sciences, Wojska Polskiego 31, 60-624 Poznań, Poland; (J.S.-P.); (A.P.-C.); (J.N.)
| | - Jakub Czarny
- Institute of Forensic Genetics, Al. Mickiewicza 3/4, 85-071 Bydgoszcz, Poland;
| | - Agnieszka Piotrowska-Cyplik
- Institute of Food Technology of Plant Origin, Poznan University of Life Sciences, Wojska Polskiego 31, 60-624 Poznań, Poland; (J.S.-P.); (A.P.-C.); (J.N.)
| | - Wojciech Juzwa
- Department Biotechnology and Food Microbiology, Poznan University of Life Sciences, Wojska Polskiego 48, 60-627 Poznan, Poland;
| | - Łukasz Wolko
- Department of Biochemistry and Biotechnology, Poznan University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland;
| | - Jacek Nowak
- Institute of Food Technology of Plant Origin, Poznan University of Life Sciences, Wojska Polskiego 31, 60-624 Poznań, Poland; (J.S.-P.); (A.P.-C.); (J.N.)
| | - Paweł Cyplik
- Department Biotechnology and Food Microbiology, Poznan University of Life Sciences, Wojska Polskiego 48, 60-627 Poznan, Poland;
- Correspondence: ; Tel.: +48-618466025
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12
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Evaluation of the Human Interference on the Microbial Diversity of Poyang Lake Using High-Throughput Sequencing Analyses. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16214218. [PMID: 31671714 PMCID: PMC6861916 DOI: 10.3390/ijerph16214218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/19/2019] [Accepted: 10/29/2019] [Indexed: 11/30/2022]
Abstract
The Poyang Lake Watershed (PLW) is regarded as an air temperature moderator, as well as a wind energy, food resources and good habitat in the Jiangxi Province, People’s Republic of China. However, with the increasing of anthropogenic disturbance on PLW, there are few studies focused on the effects of human activities on microbial composition in Poyang Lake. In the present study, a high-throughput sequencing method was used to identify the microbial composition in water and sludge in Dahuchi (DHC, sub-lake of Poyang Lake National Nature Reserve), Shahu (SH, sub-lake of Poyang Lake National Nature Reserve), Nanhu (NH, sub-lake out of Poyang Lake National Nature Reserve), Zhelinhu (ZLH, artificial reservoir), Sixiahu (SXH, sub-lake artificially isolated from Poyang Lake) and Qianhu (QH, urban lake). Results of the present study illustrated the various bacterial diversity between different lakes, for example, at the phylum level, Actinobacteria and Cyanobacteria showed low abundance in water samples of ZLH and QH, and high abundance in DHC. In addition, anthropogenic disturbance and human activities decreased the abundance of probiotic bacteria (Actinobacteria, Cyanobacteria, Chloroflexi and Acidobacteria) and increased the abundance of pathogenic bacteria (Acinetobacter, Aeromonas and Noviherbaspirillum). The enrichment of pathogenic bacteria in polluted lakes, in turn, may cause potential threats to human health.
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13
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Zhang H, Wan Z, Ding M, Wang P, Xu X, Jiang Y. Inherent bacterial community response to multiple heavy metals in sediment from river-lake systems in the Poyang Lake, China. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 165:314-324. [PMID: 30212732 DOI: 10.1016/j.ecoenv.2018.09.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/28/2018] [Accepted: 09/01/2018] [Indexed: 05/17/2023]
Abstract
Sediment is the one of most important storage of heavy metal. Microbiotas in sediment can be used as the effective indicators of heavy metals. The goal of this study was to understand the bacterial communities responding to heavy metal enrichment in sediments and prioritize some factors that affected significantly to bacterial community. Sediments were sampled from five river-lake systems in the Poyang Lake in dry season, and the bacterial community was analyzed using Illumina high-throughput sequencing. Relationships between sediment environment and the diversity and structure of bacterial communities were determined by correlation analysis and redundancy analysis (RDA). The result indicated that Cd and Sb were identified as the heavy metals of the great risk in sediments. Sediments from five river-lake systems shared 31.83% core operational taxonomic units (OTUs) of bacterial communities. Proteobacteria (33.54% of total sequences) and Actinobacteria (15.04%) were the dominant phyla across all sites. High enrichment of heavy metals (MRI and mCd) resulted in low diversity of bacterial communities (Simpson index). The RDA revealed pH, OC, mCd, and Efs of As, Pb, Cd were major factors related to bacterial community structure changes. The dominant phylum Actinobacteria was regarded as tolerant bacteria, while the dominant phylum Proteobacteria was named as resistant bacteria in sediment with high anthropogenic Cd enrichment.
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Affiliation(s)
- Hua Zhang
- Key Laboratory of Poyang Lake Wetland and Watershed Research, Ministry of Education, Jiangxi Normal University, Nanchang 330022, China; Jiangxi Provincial Key Laboratory of Poyang Lake Comprehensive Management and Resource Development, Jiangxi Normal University, Nanchang 330022, China.
| | - Zhiwei Wan
- Key Laboratory of Poyang Lake Wetland and Watershed Research, Ministry of Education, Jiangxi Normal University, Nanchang 330022, China
| | - Mingjun Ding
- Key Laboratory of Poyang Lake Wetland and Watershed Research, Ministry of Education, Jiangxi Normal University, Nanchang 330022, China
| | - Peng Wang
- Key Laboratory of Poyang Lake Wetland and Watershed Research, Ministry of Education, Jiangxi Normal University, Nanchang 330022, China; School of Geography and Environment, Jiangxi Normal University, Nanchang 330022, China.
| | - Xiaoling Xu
- Key Laboratory of Poyang Lake Wetland and Watershed Research, Ministry of Education, Jiangxi Normal University, Nanchang 330022, China; School of Geography and Environment, Jiangxi Normal University, Nanchang 330022, China
| | - Yinghui Jiang
- Key Laboratory of Poyang Lake Wetland and Watershed Research, Ministry of Education, Jiangxi Normal University, Nanchang 330022, China; School of Geography and Environment, Jiangxi Normal University, Nanchang 330022, China
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14
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Ji B, Qin H, Guo S, Chen W, Zhang X, Liang J. Bacterial communities of four adjacent fresh lakes at different trophic status. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 157:388-394. [PMID: 29649784 DOI: 10.1016/j.ecoenv.2018.03.086] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 03/26/2018] [Accepted: 03/28/2018] [Indexed: 05/20/2023]
Abstract
Knowing the microbial compositions in fresh lakes is significant to explore the mechanisms of eutrophication and algal blooms. This study reported on the bacterial communities of the four adjacent fresh lakes at different trophic status by Illumina MiSeq Platform, which were Tangxun Lake (J1), Qingling Lake (J2), Huangjia Lake (J3) and Niushan Lake (J4) in Wuhan, China. J1 had the highest salinity and phosphorus. J2 was abundant in TC (Total Carbon)/TOC (Total Organic Carbon.), calcium and magnesium. J3 had the highest content of nitrogen, iron and pollution of heavy metals. High-throughput sequencing analysis of the 16S rRNA gene revealed that the eutrophic lakes (J1, J2 and J3) were dominated by Cyanobacteria (46.1% for J1, 40.8% for J2, 33.4% for J3) and the oligotrophic lake (J4) was dominated by Actinobacteria (34.2%). An increase of Cyanobacteria could inhibit the growth of Proteobacteria, Actinobacteria and Bacteroidetes. Functional inferences from 16S rRNA sequences suggested that J4 had more abundant bacteria with regard to substrate metabolism than J1, J2, and J3. Burkholderia and Fluviicola might be a suggestion of good water quality. The results demonstrated that the bacterial community could well reflect the water quality of the four lakes.
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Affiliation(s)
- Bin Ji
- School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, China; Hubei Key Laboratory of Regional Development and Environmental Response (Hubei University), Wuhan 430062, China.
| | - Hui Qin
- School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Shaodong Guo
- School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Wei Chen
- School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Xuechun Zhang
- School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Jiechao Liang
- School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, China
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15
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Mohr KI. Diversity of Myxobacteria-We Only See the Tip of the Iceberg. Microorganisms 2018; 6:E84. [PMID: 30103481 PMCID: PMC6164225 DOI: 10.3390/microorganisms6030084] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/06/2018] [Accepted: 08/08/2018] [Indexed: 11/20/2022] Open
Abstract
The discovery of new antibiotics is mandatory with regard to the increasing number of resistant pathogens. One approach is the search for new antibiotic producers in nature. Among actinomycetes, Bacillus species, and fungi, myxobacteria have been a rich source for bioactive secondary metabolites for decades. To date, about 600 substances could be described, many of them with antibacterial, antifungal, or cytostatic activity. But, recent cultivation-independent studies on marine, terrestrial, or uncommon habitats unequivocally demonstrate that the number of uncultured myxobacteria is much higher than would be expected from the number of cultivated strains. Although several highly promising myxobacterial taxa have been identified recently, this so-called Great Plate Count Anomaly must be overcome to get broader access to new secondary metabolite producers. In the last years it turned out that especially new species, genera, and families of myxobacteria are promising sources for new bioactive metabolites. Therefore, the cultivation of the hitherto uncultivable ones is our biggest challenge.
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Affiliation(s)
- Kathrin I Mohr
- Microbial Drugs (MWIS), Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany.
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16
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Akins LN, Ayayee P, Leff LG. Composition and diversity of cyanobacteria-associated and free-living bacterial communities during cyanobacterial blooms. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1354-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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17
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Keshri J, Pradeep Ram AS, Sime-Ngando T. Distinctive Patterns in the Taxonomical Resolution of Bacterioplankton in the Sediment and Pore Waters of Contrasted Freshwater Lakes. MICROBIAL ECOLOGY 2018; 75:662-673. [PMID: 28920165 DOI: 10.1007/s00248-017-1074-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 09/08/2017] [Indexed: 06/07/2023]
Abstract
Bacteria assemblages in lake sediments play a key role in various biogeochemical processes, yet their association with interstitial pore waters has been scarcely investigated. In this study, we utilized Illumina next-generation amplicon sequencing of the 16S rRNA gene to characterize the seasonal bacterial communities in the sediments and pore waters of three contrasted temperate freshwater lakes, namely Pavin, Aydat, and Grangent (French Massif Central). Despite occupying seemingly similar habitats, bacterial communities differed substantially between sediments and pore waters at all seasons with low sharing of operational taxonomic units (OTUs, 6.7 to 20.3%) between them. Sediment-associated bacteria were more rich and diverse than pore water bacteria, indicating a high heterogeneity in the sediment microhabitat. The changes in both sediment and pore water bacterial communities were lake and season specific. The bacterial community showed distinct differences between the lakes, with larger presence of strict anaerobes such as Syntrophus, Syntrophorhabdus, and Sulfuricurvum in the pore water and sediments of Pavin responsible for carbon and sulfur cycling. In both Aydat and Grangent, the hgcI_clade dominated throughout the study period in the pore waters. The higher representation of lesser-known transient members of lake communities such as Methylotenera in the pore waters of Aydat, and Clostridium and Sulfuricurvum in the pore and sediments of Grangent, respectively, were observed during the period of temporary anoxia in summer caused by lake stratification. Our study revealed that in the investigated lakes, the prevailing environmental factors across time and space structured and influenced the adaptation of bacterial communities to specific ecological niches.
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Affiliation(s)
- J Keshri
- Laboratoire Microorganismes: Génome et Environnement, UMR CNRS 6023, Université Clermont-Auvergne, 1 Impasse Amélie Murat, BP 80026, 63178, Aubière Cedex, France
- Institute of Postharvest and Food Sciences, Agricultural Research Organization, Volcani Centre, 50250, Bet Dagan, Israel
| | - A S Pradeep Ram
- Laboratoire Microorganismes: Génome et Environnement, UMR CNRS 6023, Université Clermont-Auvergne, 1 Impasse Amélie Murat, BP 80026, 63178, Aubière Cedex, France.
| | - T Sime-Ngando
- Laboratoire Microorganismes: Génome et Environnement, UMR CNRS 6023, Université Clermont-Auvergne, 1 Impasse Amélie Murat, BP 80026, 63178, Aubière Cedex, France
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18
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Behera P, Mahapatra S, Mohapatra M, Kim JY, Adhya TK, Raina V, Suar M, Pattnaik AK, Rastogi G. Salinity and macrophyte drive the biogeography of the sedimentary bacterial communities in a brackish water tropical coastal lagoon. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 595:472-485. [PMID: 28395262 DOI: 10.1016/j.scitotenv.2017.03.271] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 03/28/2017] [Accepted: 03/29/2017] [Indexed: 06/07/2023]
Abstract
Brackish water coastal lagoons are least understood with respect to the seasonal and temporal variability in their sedimentary bacterial communities. These coastal lagoons are characterized by the steep environmental gradient and provide an excellent model system to decipher the biotic and abiotic factors that determine the bacterial community structure over time and space. Using Illumina sequencing of the 16S rRNA genes from a total of 100 bulk surface sediments, we investigated the sedimentary bacterial communities, their spatiotemporal distribution, and compared them with the rhizosphere sediment communities of a common reed; Phragmites karka and a native seagrass species; Halodule uninervis in Chilika Lagoon. Spatiotemporal patterns in bacterial communities were linked to specific biotic factors (e.g., presence and type of macrophyte) and abiotic factors (e.g., salinity) that drove the community composition. Comparative assessment of communities highlighted bacterial lineages that were responsible for segregating the sediment communities over distinct salinity regimes, seasons, locations, and presence and type of macrophytes. Several bacterial taxa were specific to one of these ecological factors suggesting that species-sorting processes drive specific biogeographical patterns in the bacterial populations. Modeling of proteobacterial lineages against salinity gradient revealed that α- and γ-Proteobacteria increased with salinity, whereas β-Proteobacteria displayed the opposite trend. The wide variety of biogeochemical functions performed by the rhizosphere microbiota of P. karka must be taken into consideration while formulating the management and conservation plan for this reed. Overall, this study provides a comprehensive understanding of the spatiotemporal dynamics and functionality of sedimentary bacterial communities and highlighted the role of biotic and abiotic factors in generating the biogeographical patterns in the bacterial communities of a tropical brackish water coastal lagoon.
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Affiliation(s)
- Pratiksha Behera
- Wetland Research and Training Centre, Chilika Development Authority, Barkul, Balugaon, 752030, Odisha, India
| | - Sofia Mahapatra
- Wetland Research and Training Centre, Chilika Development Authority, Barkul, Balugaon, 752030, Odisha, India
| | - Madhusmita Mohapatra
- Wetland Research and Training Centre, Chilika Development Authority, Barkul, Balugaon, 752030, Odisha, India
| | - Ji Yoon Kim
- Department of Integrated Biological Science, Pusan National University, Geumjeong-gu, 46241 Busan, South Korea
| | - Tapan K Adhya
- School of Biotechnology, KIIT University, Patia, Bhubaneswar, 751024, Odisha, India
| | - Vishakha Raina
- School of Biotechnology, KIIT University, Patia, Bhubaneswar, 751024, Odisha, India
| | - Mrutyunjay Suar
- School of Biotechnology, KIIT University, Patia, Bhubaneswar, 751024, Odisha, India
| | - Ajit K Pattnaik
- Wetland Research and Training Centre, Chilika Development Authority, Barkul, Balugaon, 752030, Odisha, India
| | - Gurdeep Rastogi
- Wetland Research and Training Centre, Chilika Development Authority, Barkul, Balugaon, 752030, Odisha, India.
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19
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Ettinger CL, Voerman SE, Lang JM, Stachowicz JJ, Eisen JA. Microbial communities in sediment from Zostera marina patches, but not the Z. marina leaf or root microbiomes, vary in relation to distance from patch edge. PeerJ 2017; 5:e3246. [PMID: 28462046 PMCID: PMC5410140 DOI: 10.7717/peerj.3246] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/29/2017] [Indexed: 12/31/2022] Open
Abstract
Background Zostera marina (also known as eelgrass) is a foundation species in coastal and marine ecosystems worldwide and is a model for studies of seagrasses (a paraphyletic group in the order Alismatales) that include all the known fully submerged marine angiosperms. In recent years, there has been a growing appreciation of the potential importance of the microbial communities (i.e., microbiomes) associated with various plant species. Here we report a study of variation in Z. marina microbiomes from a field site in Bodega Bay, CA. Methods We characterized and then compared the microbial communities of root, leaf and sediment samples (using 16S ribosomal RNA gene PCR and sequencing) and associated environmental parameters from the inside, edge and outside of a single subtidal Z. marina patch. Multiple comparative approaches were used to examine associations between microbiome features (e.g., diversity, taxonomic composition) and environmental parameters and to compare sample types and sites. Results Microbial communities differed significantly between sample types (root, leaf and sediment) and in sediments from different sites (inside, edge, outside). Carbon:Nitrogen ratio and eelgrass density were both significantly correlated to sediment community composition. Enrichment of certain taxonomic groups in each sample type was detected and analyzed in regard to possible functional implications (especially regarding sulfur metabolism). Discussion Our results are mostly consistent with prior work on seagrass associated microbiomes with a few differences and additional findings. From a functional point of view, the most significant finding is that many of the taxa that differ significantly between sample types and sites are closely related to ones commonly associated with various aspects of sulfur and nitrogen metabolism. Though not a traditional model organism, we believe that Z. marina can become a model for studies of marine plant-microbiome interactions.
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Affiliation(s)
| | - Sofie E Voerman
- Climate Change Cluster, University of Technology Sydney, Sydney, Australia.,School of Life Sciences, University of Technology Sydney, Sydney, Australia
| | - Jenna M Lang
- Genome Center, University of California, Davis, CA, United States.,Trace Genomics, San Francisco, CA, United States
| | - John J Stachowicz
- Department of Evolution and Ecology, University of California, Davis, CA, United States
| | - Jonathan A Eisen
- Genome Center, University of California, Davis, CA, United States.,Department of Evolution and Ecology, University of California, Davis, CA, United States.,Department of Medical Microbiology and Immunology, University of California, Davis, Davis, CA, United States
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20
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Han I, Yoo K, Wee GN, No JH, Park J, Min SJ, Kim SH, Leea TK. Short-term Effects of Great Cormorant Droppings on Water Quality and Microbial Community of an Artificial Agricultural Reservoir. JOURNAL OF ENVIRONMENTAL QUALITY 2017; 46:470-476. [PMID: 28380549 DOI: 10.2134/jeq2016.11.0459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Agricultural reservoirs are established to improve the management of water resources. Waterbirds in protected waters have become a nuisance, however, as nutrients from fecal deposits transported by the waterbirds have served to severely deteriorate water quality. Despite the importance of clean water resources, the microecology of small agricultural reservoirs regularly colonized by transitory waterbirds are seldom reviewed. To improve our understanding of the influence of waterbirds on small bodies of water, a microcosm study was conducted using water and sediment from an agricultural reservoir inhabited by 300 to 500 great cormorants. Temporal changes in total nitrogen, total phosphorous, chemical oxygen demand, NH-N, PO-P, and chlorophyll-a concentrations, in addition to the microbial community, were evaluated for microcosms containing 0, 0.5, 1.0, and 5.0 g of feces collected from a great cormorant colony. Chemical analysis of the water microcosm revealed that all microcosms showed both immediate and prolonged increases in nutrients due to the addition of feces. Additionally, a mere 0.5 g of feces doubled the concentration of chlorophyll-a from 2.1 ± 0.99 to 5.2 ± 1.1 μg L within 1 mo. Nonmetric multidimensional scaling of the microbial community structure revealed disturbances in both water and sediment microcosms. Disturbances to the microbial community in the water microcosm were significant only when 5.0 g of feces was added; however, disturbances to sediment microbial communities were induced by a smaller mass of feces. These results confirm the short-term water quality impairment and shift in microbial community structure caused by waterbird droppings and bird colony surface runoff in an agricultural reservoir.
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