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Liu J, Qian Y, Yang W, Yang M, Zhang Y, Duan B, Yang Y, Tao A, Xia C. Elucidating the interaction of rhizosphere microorganisms and environmental factors influencing the quality of Polygonatum kingianum Coll. et Hemsl. Sci Rep 2024; 14:19092. [PMID: 39154075 PMCID: PMC11330475 DOI: 10.1038/s41598-024-69673-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 08/07/2024] [Indexed: 08/19/2024] Open
Abstract
Polygonatum kingianum Collett & Hemsl., is one of the most important traditional Chinese medicines in China. The purpose of this study is to investigate the relationship between herb quality and microbial-soil variables, while also examining the composition and structure of the rhizosphere microbial community in Polygonatum kingianum, the ultimate goal is to provide a scientific approach to enhancing the quality of P. kingianum. Illumina NovaSeq technology unlocks comprehensive genetic variation and biological functionality through high-throughput sequencing. And in this study it was used to analyze the rhizosphere microbial communities in the soils of five P. kingianum planting areas. Conventional techniques were used to measure the organic elements, pH, and organic matter content. The active ingredient content of P. kingianum was identified by High Performance Liquid Chromatography (HPLC) and Colorimetry. A total of 12,715 bacterial and 5487 fungal Operational Taxonomic Units (OTU) were obtained and taxonomically categorized into 81 and 7 different phyla. Proteobacteria, Bacteroidetes, and Acidobacteriae were the dominant bacterial phyla Ascomycota and Basidiomycota were the dominat fungal phyla. The key predictors for bacterial community structure included hydrolysable nitrogen and available potassium, while for altering fungal community structure, soil organic carbon content (OCC), total nitrogen content (TNC), and total potassium content (TPOC) were the main influencing factors. Bryobacter and Candidatus Solibacter may indirectly increase the polysaccharide content of P. kingianum, and can be developed as potential Plant Growth Promoting Rhizobacteria (PGPR). This study has confirmed the differences in the soil and microorganisms of different origins of P. kingianum, and their close association with its active ingredients. And it also broadens the idea of studying the link between plants and microorganisms.
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Affiliation(s)
- Jiahao Liu
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
- Western Yunnan Traditional Chinese Medicine and Ethnic Drug Engineering Center, Dali, 671000, China
| | - Yan Qian
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
- Western Yunnan Traditional Chinese Medicine and Ethnic Drug Engineering Center, Dali, 671000, China
| | - Wanqing Yang
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
- Western Yunnan Traditional Chinese Medicine and Ethnic Drug Engineering Center, Dali, 671000, China
| | - Meihua Yang
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
- Western Yunnan Traditional Chinese Medicine and Ethnic Drug Engineering Center, Dali, 671000, China
| | - Yue Zhang
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
- Western Yunnan Traditional Chinese Medicine and Ethnic Drug Engineering Center, Dali, 671000, China
| | - Baozhong Duan
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
- Western Yunnan Traditional Chinese Medicine and Ethnic Drug Engineering Center, Dali, 671000, China
| | - Yongcheng Yang
- College of Pharmaceutical Science, Dali University, Dali, 671000, China.
- Western Yunnan Traditional Chinese Medicine and Ethnic Drug Engineering Center, Dali, 671000, China.
| | - Aien Tao
- College of Medicine, Lijiang Culture and Tourism College, Lijiang, 674100, China.
| | - Conglong Xia
- College of Pharmaceutical Science, Dali University, Dali, 671000, China.
- Western Yunnan Traditional Chinese Medicine and Ethnic Drug Engineering Center, Dali, 671000, China.
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Qiu Z, He S, Lian CA, Qiao X, Zhang Q, Yao C, Mu R, Wang L, Cao XA, Yan Y, Yu K. Large scale exploration reveals rare taxa crucially shape microbial assembly in alkaline lake sediments. NPJ Biofilms Microbiomes 2024; 10:62. [PMID: 39069527 DOI: 10.1038/s41522-024-00537-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 07/19/2024] [Indexed: 07/30/2024] Open
Abstract
Alkaline lakes are extreme environments inhabited by diverse microbial extremophiles. However, large-scale distribution patterns, environmental adaptations, community assembly, and evolutionary dynamics of microbial communities remain largely underexplored. This study investigated the characteristics of microbial communities on rare and abundant taxa in alkaline lake sediments in west and northwest China. We observed that abundant taxa varied significantly with geographical distance, while rare taxa remained unaffected by regional differences. The assembly process of abundant taxa was influenced by dispersal limitation, whilst rare taxa were predominantly driven by heterogeneous selection. Network analysis indicated that rare taxa as core species for community interactions and community stability. Rare taxa exhibited higher speciation and transition rate than abundant taxa, serving as a genetic reservoir and potential candidates to become abundance taxa, highlighting their crucial role in maintaining microbial diversity. These insights underscore the significant influence of rare taxa on ecosystem biodiversity and stability in alkaline lakes.
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Affiliation(s)
- Zhiguang Qiu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, 518055, China
| | - Shuhang He
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Chun-Ang Lian
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, 518055, China
| | - Xuejiao Qiao
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Qing Zhang
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Ciqin Yao
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Rong Mu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Li Wang
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Xiao-Ai Cao
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Yan Yan
- State Key Laboratory of Isotope Geochemistry, CAS Center for Excellence in Deep Earth Science, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Ke Yu
- Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China.
- AI for Science (AI4S)-Preferred Program, Peking University, Shenzhen, 518055, China.
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3
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Xi M, Wang Y, Yang J, Bi X, Zhong S, Duan T, He Y, Tu T, Qian X. Spatial distribution and community composition of endophytic fungi within Mussaenda pubescens stems. Fungal Biol 2024; 128:1815-1826. [PMID: 38876534 DOI: 10.1016/j.funbio.2024.05.001] [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: 01/09/2024] [Revised: 05/09/2024] [Accepted: 05/11/2024] [Indexed: 06/16/2024]
Abstract
Endophytic fungi, pivotal in facilitating plant co-evolution, significantly enhance plant growth, stress resistance, and environmental adaptability. Despite their importance, the spatial distribution of stem endophytic fungi (SEF) within host plants remains poorly characterized. Here, we employed high-throughput sequencing to conduct a comparative analysis of SEF communities in Mussaenda pubescens on a regional scale. Our findings reveal that whole-SEF communities were overwhelmingly dominated by members of the phylum Ascomycota, accounting for 85.9 %, followed by Basidiomycota at 13.9 %, and that alpha diversity within the whole-SEF community of M. pubescens remains relatively consistent across sampling sites. However, significant variation was observed within conditionally abundant taxa (CAT), conditionally rare or abundant taxa (CRAT), and conditionally rare taxa (CRT). Climatic factors emerged as the primary influence on SEF community distribution, followed by spatial distance and stem chemical properties. Neutral community modeling results suggested that both stochastic and deterministic processes play a role in shaping whole-SEF communities, with deterministic processes having a stronger influence on CRT subcommunities. Furthermore, the CRT co-occurrence network exhibited a more complex structure, characterized by higher values of network betweenness and degree relative to CAT and CRAT subcommunities. These findings enhance our understanding of community assembly and ecological interactions between stem fungal endophytes, presenting opportunities for harnessing fungal resources for the benefit of humanity.
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Affiliation(s)
- Meijuan Xi
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yonglong Wang
- Faculty of Biological Science and Technology, Baotou Teacher's College, Baotou, China
| | - Juanjuan Yang
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaohui Bi
- Shangqiu Institute of Quality Inspection and Technical Research, Shangqiu, China
| | - Shengen Zhong
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tingting Duan
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Yimin He
- Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tieyao Tu
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
| | - Xin Qian
- Fujian Agriculture and Forestry University, Fuzhou, China.
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4
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Zhu X, Hu M, Wang X, Zhang Y, Du D. Biogeography and diversity patterns of abundant and rare bacterial communities in paddy soils along middle and lower Yangtze River. Ecol Evol 2024; 14:e11481. [PMID: 38835524 PMCID: PMC11148396 DOI: 10.1002/ece3.11481] [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: 01/01/2024] [Revised: 04/30/2024] [Accepted: 05/13/2024] [Indexed: 06/06/2024] Open
Abstract
The middle and lower reaches of the Yangtze River serve as principal rice production bases in China, yet the biodiversity and ecological processes of bacterial communities in paddy soils are not well understood. This study explores the diversity, composition, ecological function, and assembly processes of abundant and rare bacterial communities in paddy soils. A total of 129 paddy soil samples from 43 sites along the middle and lower reaches of the Yangtze River were collected and analyzed using NovaSeq sequencing. The results showed that the dominant phylum for both abundant and rare taxa was Proteobacteria, with a greater relative abundance of the abundant taxa. The diversity of the abundant community was lower than that of the rare community. Soil properties and geographic variables explained more of the variation in the abundant community than in the rare community. The rare community exhibited a significant distance-decay relationship. The assembly of the abundant community was more influenced by stochastic processes, although both the abundant and rare communities were governed by stochastic processes. It is concluded that both abundant and rare bacterial communities exhibit differing biogeographic patterns, yet they undergo similar ecological processes in the paddy soils along the middle and lower reaches of the Yangtze River. These observations offer a theoretical framework for a deeper comprehension of the function of both abundant and rare bacteria, as well as the development and preservation of soil bacterial diversity within agricultural ecosystems.
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Affiliation(s)
- Xiancan Zhu
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-Founded by Anhui Province and Ministry of Education Anhui Normal University Wuhu China
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, College of Life Sciences Anhui Normal University Wuhu China
| | - Minghui Hu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, College of Life Sciences Anhui Normal University Wuhu China
| | - Xiaoli Wang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, College of Life Sciences Anhui Normal University Wuhu China
| | - Ya Zhang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, College of Life Sciences Anhui Normal University Wuhu China
| | - Dongsheng Du
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, College of Life Sciences Anhui Normal University Wuhu China
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5
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Stocker MD, Smith JE, Pachepsky YA, Blaustein RA. Fine-scale spatiotemporal variations in bacterial community diversity in agricultural pond water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:170143. [PMID: 38242477 DOI: 10.1016/j.scitotenv.2024.170143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 01/21/2024]
Abstract
Microbial communities in surface waters are affected by environmental conditions and can influence changes in water quality. To explore the hypothesis that the microbiome in agricultural waters associates with spatiotemporal variations in overall water quality and, in turn, has implications for resource monitoring and management, we characterized the relationships between the microbiota and physicochemical properties in a model irrigation pond as a factor of sampling time (i.e., 9:00, 12:00, 15:00) and location within the pond (i.e., bank vs. interior sites and cross-sectional depths at 0, 1, and 2 m). The microbial communities, which were defined by 16S rRNA gene sequencing analysis, significantly varied based on all sampling factors (PERMANOVA P < 0.05 for each). While the relative abundances of dominant phyla (e.g., Proteobacteria and Bacteroidetes) were relatively stable throughout the pond, subtle yet significant increases in α-diversity were observed as the day progressed (ANOVA P < 0.001). Key water quality properties that also increased between the morning and afternoon (i.e., pH, dissolved oxygen, and temperature) positively associated with relative abundances of Cyanobacteria, though were inversely proportional to Verrucomicrobia. These properties, among additional parameters such as bioavailable nutrients (e.g., NH3, NO3, PO4), chlorophyll, phycocyanin, conductivity, and colored dissolved organic matter, exhibited significant relationships with relative abundances of various bacterial genera as well. Further investigation of the microbiota in underlying sediments revealed significant differences between the bank and interior sites of the pond (P < 0.05 for α- and β-diversity). Overall, our findings emphasize the importance of accounting for time of day and water sampling location and depth when surveying the microbiomes of irrigation ponds and other small freshwater sources.
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Affiliation(s)
- M D Stocker
- United States Department of Agriculture, Agricultural Research Services, Environmental Microbial and Food Safety Laboratory, Beltsville, MD 20705, USA.
| | - J E Smith
- United States Department of Agriculture, Agricultural Research Services, Environmental Microbial and Food Safety Laboratory, Beltsville, MD 20705, USA; Oak Ridge Institute of Science and Education, Oak Ridge, TN 37830, USA
| | - Y A Pachepsky
- United States Department of Agriculture, Agricultural Research Services, Environmental Microbial and Food Safety Laboratory, Beltsville, MD 20705, USA
| | - R A Blaustein
- University of Maryland, Department of Nutrition and Food Science, College Park, MD 20742, USA
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Jing M, Yang W, Ding X, Rao L, Zhang Q, Zhu J. Environmental heterogeneity associated with boat activity shapes bacteria and microeukaryotic communities with discrepant response patterns. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166943. [PMID: 37690748 DOI: 10.1016/j.scitotenv.2023.166943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 09/07/2023] [Accepted: 09/07/2023] [Indexed: 09/12/2023]
Abstract
With the development of global tourism, tourist boats, a significant form of anthropogenic disturbance, are having an increasingly serious impact on the structure and function of aquatic ecosystems. In this study, the effects of different intensities of tourist boat activities on the microbial communities of West lake, were investigated by high-throughput sequencing. The results showed significant differences in the composition of bacterioplankton and microeukaryotic communities between the high-intensity boat activity (HIBA) area and low-intensity boat activity (LIBA) area. Variation partitioning analysis showed that environmental factors contributed the most to microbial community variation, and the effect of boat activities on microbial communities mainly occurred through coupling with environmental factors. The contribution of boat activity to microbial community changes occupies the second place, the first being environmental factors. Co-occurrence network analyses showed that microbial communities in the HIBA area had more nodes and edges, higher connectivity and lower modularity than in the LIBA area, suggesting a more complex and stable network. Networks of associations between potential keystone taxa and environmental factors reveal the way in which boat activity affects microbial communities. The bacterial community responded strongly to environmental factors associated with boat activities, whereas the microeukaryotic community was more likely to be regulated by interspecific interactions. This also suggests that when faced with disturbances from the boat activity, microeukaryotes might exert a stronger direct resistance effect compared to bacterioplankton. These findings imply that bacterioplankton and microeukaryotes demonstrate distinct response patterns in the presence of disturbance caused by boat activity. Our research expand our understanding of the effects of boat activities on aquatic ecosystems and provide further insights into the assessment of anthropogenic disturbances in aquatic ecosystems.
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Affiliation(s)
- MingFei Jing
- School of Marine Science, Ningbo University, Ningbo 315800, China
| | - Wen Yang
- School of Marine Science, Ningbo University, Ningbo 315800, China
| | - Xiuying Ding
- Hangzhou West Lake Administration, Hangzhou 310002, China
| | - Lihua Rao
- Hangzhou West Lake Administration, Hangzhou 310002, China
| | - Quanxiang Zhang
- School of Marine Science, Ningbo University, Ningbo 315800, China
| | - Jinyong Zhu
- School of Marine Science, Ningbo University, Ningbo 315800, China.
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7
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Song W, Li H, Zhou Y, Liu X, Li Y, Wang M, Li DD, Tu Q. Discordant patterns between nitrogen-cycling functional traits and taxa in distant coastal sediments reveal important community assembly mechanisms. Front Microbiol 2023; 14:1291242. [PMID: 38053549 PMCID: PMC10694361 DOI: 10.3389/fmicb.2023.1291242] [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: 09/08/2023] [Accepted: 11/01/2023] [Indexed: 12/07/2023] Open
Abstract
A central question in microbial ecology is how immense microbes are assembled in changing natural environments while executing critical ecosystem functions. Over the past decade, effort has been made to unravel the contribution of stochasticity and determinism to the compositional of microbial communities. However, most studies focus on microbial taxa, ignoring the importance of functional traits. By employing shotgun metagenomic sequencing and state-of-the-art bioinformatics approaches, this study comprehensively investigated the microbially mediated nitrogen (N) cycling processes in two geographically distant coastal locations. Both shotgun and 16S rRNA gene amplicon sequencing demonstrated significantly differed taxonomic compositions between the two sites. The relative abundance of major microbial phyla, such as Pseudomonadota, Thaumarchaeota, and Bacteroidota, significantly differed. In contrast, high homogeneity was observed for N-cycling functional traits. Statistical analyses suggested that N-cycling taxonomic groups were more related to geographic distance, whereas microbial functional traits were more influenced by environmental factors. Multiple community assembly models demonstrated that determinism strongly governed the microbial N-cycling functional traits, whereas their carrying taxonomic groups were highly stochastic. Such discordant patterns between N-cycling functional traits and taxa demonstrated an important mechanism in microbial ecology in which essential ecosystem functions are stably maintained despite geographic distance and stochastic community assembly.
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Affiliation(s)
- Wen Song
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Hongjun Li
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, China
| | - Yuqi Zhou
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xia Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Yueyue Li
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Mengqi Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Dan-dan Li
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
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8
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Pernthaler J, Krempaska N, le Moigne A. Small-scale spatial beta diversity of bacteria in the mixed upper layer of a lake. Environ Microbiol 2023; 25:1847-1859. [PMID: 37173811 DOI: 10.1111/1462-2920.16399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/27/2023] [Indexed: 05/15/2023]
Abstract
Bacterial community composition among individual, experimentally generated 'lake snow' particles may be highly variable. Since such aggregates are seasonally abundant in the mixed upper layer of lakes, we hypothesized that particle-attached (PA) bacteria disproportionally contribute to the small-scale spatial beta diversity of pelagic communities. Community composition was analysed in sets of small (10 mL) samples collected from a pre-alpine lake in May, July and October 2018. Bacteria were classified as free-living (FL) or PA depending on their presence in large, 5-μm pre-filtered reference samples. FL exhibited clear seasonal differences in community composition and assembly. They were spatially uniform in May and July, and only a few FL taxa exhibited significant spatial variability. Spatial heterogeneity of FL in October was caused by high alpha and beta diversity of rare taxa, many with a presumably 'tychoplanktic' (alternating attached and free-living) lifestyle. The spatial beta diversity of PA was always high, and only about 10% of their seasonal richness was present in any single sample. Thus, most compositional variability of pelagic bacteria at spatial scales of cm to m either directly or indirectly originated from PA. On a functional level, this genotypic heterogeneity might affect the spatial distribution of rare metabolic traits.
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Affiliation(s)
- Jakob Pernthaler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Natalia Krempaska
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Alizée le Moigne
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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Sadeghi J, Hashemi Shahraki A, Chaganti SR, Heath D. Functional gene transcription variation in bacterial metatranscriptomes in large freshwater Lake Ecosystems: Implications for ecosystem and human health. ENVIRONMENTAL RESEARCH 2023; 231:116298. [PMID: 37268212 DOI: 10.1016/j.envres.2023.116298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 05/12/2023] [Accepted: 05/31/2023] [Indexed: 06/04/2023]
Abstract
Little is known regarding the temporal and spatial functional variation of freshwater bacterial community (BC) under non-bloom conditions, especially in winter. To address this, we used metatranscriptomics to assess bacterial gene transcription variation among three sites across three seasons. Our metatranscriptome data for freshwater BCs at three public beaches (Ontario, Canada) sampled in the winter (no ice), summer and fall (2019) showed relatively little spatial, but a strong temporal variation. Our data showed high transcriptional activity in summer and fall but surprisingly, 89% of the KEGG pathway genes and 60% of the selected candidate genes (52 genes) associated with physiological and ecological activity were still active in freezing temperatures (winter). Our data also supported the possibility of an adaptively flexible gene expression response of the freshwater BC to low temperature conditions (winter). Only 32% of the bacterial genera detected in the samples were active, indicating that the majority of detected taxa were non-active (dormant). We also identified high seasonal variation in the abundance and activity of taxa associated with health risks (i.e., Cyanobacteria and waterborne bacterial pathogens). This study provides a baseline for further characterization of freshwater BCs, health-related microbial activity/dormancy and the main drivers of their functional variation (such as rapid human-induced environmental change and climate change).
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Affiliation(s)
- Javad Sadeghi
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
| | | | - Subba Rao Chaganti
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI, USA.
| | - Daniel Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada; Department of Integrative Biology, University of Windsor, Windsor, ON, Canada.
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Gao P, Wang P, Ding M, Zhang H, Huang G, Nie M, Wang G. A meta-analysis reveals that geographical factors drive the bacterial community variation in Chinese lakes. ENVIRONMENTAL RESEARCH 2023; 224:115561. [PMID: 36828247 DOI: 10.1016/j.envres.2023.115561] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/14/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
The biogeographical distribution of plants and animals has been extensively studied, however, the biogeographical patterns and the factors that influence bacterial communities in lakes over large scales are yet to be fully understood, even though they play critical roles in biogeochemical cycles. Here, bacterial community compositional data, geographic information, and environmental factors were integrated for 326 Chinese lakes based on previously published studies to determine the underlying factors that shape bacterial diversity among Chinese lakes. The composition of bacterial communities significantly varied among the three primary climatic regions of China (Northern China, NC; Southern China, SC; and the Tibetan Plateau, TIP), and across two different lake habitats (waters and sediments). Sediment bacterial communities exhibited significantly higher alpha-diversity and distance-decay relationships compared to water communities. The results indicate that the "scale-dependent patterns" of controlling factors, primarily influenced by geographical factors, become increasingly pronounced as the spatial scale increases. At a national scale, geographical factors exerted a dominant influence on both the water and sediment communities across all lakes, as geographical barriers restrict the dispersal of individuals. At smaller spatial scales, temperature-driven selection effects played a greater role in shaping water bacterial community variation in the NC, SC, and TIP, while geographical factors had a stronger association with sediment bacterial community variation in the lakes of the three regions. This synthesis offers novel insights into the ecological factors that determine the distribution of bacteria in Chinese lakes.
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Affiliation(s)
- Pengfei Gao
- School of Geography and Environment, Jiangxi Normal University, Nanchang, 330022, Jiangxi, China; Key Laboratory of Poyang Lake Wetland and Watershed Research, Ministry of Education, Jiangxi Normal University, Nanchang, 330022, Jiangxi, China
| | - Peng Wang
- School of Geography and Environment, Jiangxi Normal University, Nanchang, 330022, Jiangxi, China; Key Laboratory of Poyang Lake Wetland and Watershed Research, Ministry of Education, Jiangxi Normal University, Nanchang, 330022, Jiangxi, China.
| | - Mingjun Ding
- School of Geography and Environment, Jiangxi Normal University, Nanchang, 330022, Jiangxi, China; Key Laboratory of Poyang Lake Wetland and Watershed Research, Ministry of Education, Jiangxi Normal University, Nanchang, 330022, Jiangxi, China
| | - Hua Zhang
- School of Geography and Environment, Jiangxi Normal University, Nanchang, 330022, Jiangxi, China; Key Laboratory of Poyang Lake Wetland and Watershed Research, Ministry of Education, Jiangxi Normal University, Nanchang, 330022, Jiangxi, China
| | - Gaoxiang Huang
- School of Geography and Environment, Jiangxi Normal University, Nanchang, 330022, Jiangxi, China; Key Laboratory of Poyang Lake Wetland and Watershed Research, Ministry of Education, Jiangxi Normal University, Nanchang, 330022, Jiangxi, China
| | - Minghua Nie
- School of Geography and Environment, Jiangxi Normal University, Nanchang, 330022, Jiangxi, China; Key Laboratory of Poyang Lake Wetland and Watershed Research, Ministry of Education, Jiangxi Normal University, Nanchang, 330022, Jiangxi, China
| | - Guangwei Wang
- Graduate School of Horticulture, Chiba University, Chiba, 648 Matsudo, Matsudo-City, 271-8510, Japan; Guangzhou South Surveying & Mapping Technology Co., Ltd., South Geo-information Industrial Park, No.39 Si Cheng Rd, Guangzhou, China
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11
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Pan WS, Zou Q, Hu M, Li WC, Xiong XR, Qi YT, Wu C. Microbial community composition and cooccurrence patterns driven by co-contamination of arsenic and antimony in antimony-mining area. JOURNAL OF HAZARDOUS MATERIALS 2023; 454:131535. [PMID: 37148793 DOI: 10.1016/j.jhazmat.2023.131535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/08/2023] [Accepted: 04/27/2023] [Indexed: 05/08/2023]
Abstract
In the current study, a typical Sb mine was selected to explore the microbial community composition and assembly driven by the cocontamination of As/Sb with geographic distance. Our results showed that environmental parameters, especially pH, TOC, nitrate, total and bioavailable As/Sb contents largely affected the microbial community diversity and composition. The total and bioavailable As/Sb levels were significantly positively correlated with the relative abundance of Zavarzinella, Thermosporothrix and Holophaga, while the pH presented a significant negative correlation with the three genera, potentially implying they are important taxonomic groups in acid-mining soils. The cooccurrence network analysis indicated the environmental stress dominated by pH and As/Sb co-contamination affected the microbial modularity and interaction. Meanwhile, Homogeneous selection (HoS, 26.4-49.3%), and drift and others (DR, 27.1∼40.2%) were the most important assembly processes for soil bacterial, and the importance of HoS decreased and the DR increased with geographic distance to the contamination source respectively. Soil pH, nutrient availability, total and bioavailable As/Sb contents significantly affected the HoS and DR processes. This study provides theoretical support for microbial remediation in metal(loid)-contaminated soils.
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Affiliation(s)
- Wei-Song Pan
- College of Bioscience and Biotechnology, Hunan Agriculture University, Changsha 410128, China
| | - Qi Zou
- South China Institute of Environmental Sciences, MEE, Guangzhou 510535, China; School of Metallurgy and Environment, Central South University, Changsha 410083, China.
| | - Min Hu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510520, China
| | - Wai-Chin Li
- Department of Science and Environmental Studies, The Education University of Hong Kong, Administrative Region, Hong Kong, China
| | - Xiao-Ran Xiong
- College of Bioscience and Biotechnology, Hunan Agriculture University, Changsha 410128, China
| | - Yan-Ting Qi
- School of Metallurgy and Environment, Central South University, Changsha 410083, China
| | - Chuan Wu
- School of Metallurgy and Environment, Central South University, Changsha 410083, China.
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12
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Bai C, Gao G, Tang X, Shao K, Hu Y, Xia J, Liu J. Contrasting diversity patterns and community assembly mechanisms of bacterioplankton among different aquatic habitats in Lake Taihu, a large eutrophic shallow lake in China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 315:120342. [PMID: 36240961 DOI: 10.1016/j.envpol.2022.120342] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/13/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Eutrophication leads to the degradation of lake habitat types from macrophyte-dominated habitats (MDH) to algae-dominated habitats (ADH), which is a common environmental problem faced by many lakes. However, the variations in diversities and community assembly processes of bacterioplankton in the process of lake eutrophication have not been thoroughly elucidated. Here, we contrasted bacterial diversity patterns and processes of community assembly among ADH, MDH, and other habitats (OH) of Lake Taihu, a large shallow eutrophic lake in China with strong wind-induced disturbances. We found that the bacterial diversity patterns and potential functions between ADH and MDH were significantly different. Moreover, the contributions of purely environmental variables to the bacterial diversity patterns of all habitat types were much higher than those of spatial variables. However, the relative importance of stochasticity in the bacterial community assembly of each habitat type was much higher than that of determinism. Intriguingly, 'undominated' stochastic processes shape the diversity patterns of bacterioplankton in ADH, MDH, and OH of Lake Taihu. These findings demonstrate that the degradation of lake habitats caused by eutrophication can profoundly change the diversity and potential function patterns of the bacterioplankton community in lake ecosystems. Although the distinct diversity patterns of the bacterioplankton among the different aquatic habitats in Lake Taihu can be affected by deterministic processes (local environmental variables), they were dominated by stochastic processes (drift). Our study confirms that strong, disordered, wind-induced disturbances in shallow lakes could lead to strong hydrologic mixing, thus increasing the randomness of bacterial community assembly in each habitat.
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Affiliation(s)
- Chengrong Bai
- Shandong Key Laboratory of Eco-Environmental Science for Yellow River Delta, Binzhou University, Binzhou, 256600, PR China
| | - Guang Gao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China.
| | - Keqiang Shao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China
| | - Yang Hu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, PR China
| | - Jiangbao Xia
- Shandong Key Laboratory of Eco-Environmental Science for Yellow River Delta, Binzhou University, Binzhou, 256600, PR China
| | - Jingtao Liu
- Shandong Key Laboratory of Eco-Environmental Science for Yellow River Delta, Binzhou University, Binzhou, 256600, PR China
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13
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Ren W, Li P, Wang X, Che Y, Long H, Zhang X, Cai X, Huang A, Zeng Y, Xie Z. Cross-habitat distribution pattern of Bacillus communities and their capacities of producing industrial hydrolytic enzymes in Paracel Islands: Habitat-dependent differential contributions of the environment. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 323:116252. [PMID: 36126600 DOI: 10.1016/j.jenvman.2022.116252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 06/15/2023]
Abstract
Bacillus as a predominant genus of enzyme-producing bacteria presents desirable features to fulfill the vast demand of specific industries, whereas the knowledge of the Bacillus communities and their capacities of producing industrial hydrolytic enzymes across the microhabitats of the Paracel Islands is limited. Herein, a total of 193 culturable Bacillus strains belonging to 19 species were isolated across the microhabitats of seawater, sediment, coral and seagrass, covering 39 stations of the Paracel Islands. Each microhabitat displayed its unique species, while the species of Bacillus paramycoides besides being the dominant species with an abundance of 54.94% also was the only species shared by all microhabitats of the Paracel Islands. Of the Bacillus communities, 97.41% of the isolates exhibited the capacity of producing one-or-more types of enzymes with comparatively higher and broader ranges of enzyme activities, including 163 protease-, 27 cellulase-, 118 alginate lyase-, 140 K-carrageenase- and 158 agarose-producing strains. By the correlation analyses of "Bacillus-environmental factors" and "Enzyme-producing Bacillus-environmental factors", the cross-habitat distribution and enzyme-producing capacity pattern of the Bacillus communities were strongly driven by habitat type, and the environmental factors made habitat-dependent differential contributions to that in the Paracel Islands. It's worth noting that the cellulase-producing strain wasn't detected in seagrass due to its survival strategy to prevent cellulose degradation by inhibiting cellulase-producing bacteria, while coral contained more stable microbial metabolic functions to protect against environmental fluctuations. These findings besides providing large quantities of promising enzyme-producing candidates for specific industrial desires, also facilitate the development and utilization of marine microbial resources and the environmental policy- and/or law-making according to environmental features across the microhabitats of the Paracel Islands.
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Affiliation(s)
- Wei Ren
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, 570228, Hainan Province, China; Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, 570228, Hainan Province, China; College of Marine Sciences, Hainan University, Haikou, 570228, Hainan Province, China; Laboratory of Development and Utilization of Marine Microbial Resource, Hainan University, Haikou, 570228, Hainan Province, China
| | - Peiwei Li
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, 570228, Hainan Province, China; College of Marine Sciences, Hainan University, Haikou, 570228, Hainan Province, China
| | - Xinyi Wang
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, 570228, Hainan Province, China; College of Marine Sciences, Hainan University, Haikou, 570228, Hainan Province, China
| | - Yuhan Che
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, 570228, Hainan Province, China; College of Marine Sciences, Hainan University, Haikou, 570228, Hainan Province, China
| | - Hao Long
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, 570228, Hainan Province, China; Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, 570228, Hainan Province, China; College of Marine Sciences, Hainan University, Haikou, 570228, Hainan Province, China; Laboratory of Development and Utilization of Marine Microbial Resource, Hainan University, Haikou, 570228, Hainan Province, China
| | - Xiang Zhang
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, 570228, Hainan Province, China; Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, 570228, Hainan Province, China; College of Marine Sciences, Hainan University, Haikou, 570228, Hainan Province, China; Laboratory of Development and Utilization of Marine Microbial Resource, Hainan University, Haikou, 570228, Hainan Province, China
| | - Xiaoni Cai
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, 570228, Hainan Province, China; Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, 570228, Hainan Province, China; College of Marine Sciences, Hainan University, Haikou, 570228, Hainan Province, China; Laboratory of Development and Utilization of Marine Microbial Resource, Hainan University, Haikou, 570228, Hainan Province, China
| | - Aiyou Huang
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, 570228, Hainan Province, China; Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, 570228, Hainan Province, China; College of Marine Sciences, Hainan University, Haikou, 570228, Hainan Province, China; Laboratory of Development and Utilization of Marine Microbial Resource, Hainan University, Haikou, 570228, Hainan Province, China
| | - Yanhua Zeng
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, 570228, Hainan Province, China; Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, 570228, Hainan Province, China; College of Marine Sciences, Hainan University, Haikou, 570228, Hainan Province, China; Laboratory of Development and Utilization of Marine Microbial Resource, Hainan University, Haikou, 570228, Hainan Province, China
| | - Zhenyu Xie
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, 570228, Hainan Province, China; Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, 570228, Hainan Province, China; College of Marine Sciences, Hainan University, Haikou, 570228, Hainan Province, China; Laboratory of Development and Utilization of Marine Microbial Resource, Hainan University, Haikou, 570228, Hainan Province, China.
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14
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Liu Y, Pan B, Zhu X, Zhao X, Sun H, He H, Jiang W. Patterns of microbial communities and their relationships with water quality in a large-scale water transfer system. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 319:115678. [PMID: 35842990 DOI: 10.1016/j.jenvman.2022.115678] [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: 01/14/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 06/15/2023]
Abstract
Revealing the patterns and their mechanisms of microbial community in water transfer projects, especially in inter-basin water transfer projects, is the premise of biohazard warning, water quality monitoring and sustainable management of water resources. Using a river and impounded lakes from the eastern route of South-to-North Water Transfer project as a model system, we studied the diversity and assembly patterns of bacterial communities in artificially connected ecosystems and their influencing factors. Our results showed that water quality improved during the water transfer period (WTP). Further, the latitudinal pattern of bacterioplankton was reversed, which was mainly due to the change of evenness caused by water transfer and had no significant correlation with water quality parameters. Importantly, the spatial heterogeneity of the bacterial communities decreased during the WTP, and the differences in the communities between the impounded lakes and river was more significant in the non-water transfer period (NWTP) than in the WTP, which was the result of water transfer and water quality. Overall, bacterial community was largely shaped by stochastic processes. The bacterial communities had a higher migration rate during the WTP than during the NWTP. We believe that the water transfer increased the risk of biological homogenization while improving water quality. Combined, our work systematically discusses the microbial community pattern and mechanism in the inter-basin water transfer project, providing theoretical support for inter-basin water transfer project planning management and ecological environment protection.
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Affiliation(s)
- Yaping Liu
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi, PR China
| | - Baozhu Pan
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi, PR China.
| | - Xinzheng Zhu
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi, PR China
| | - Xiaohui Zhao
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, Shaanxi, PR China
| | - He Sun
- College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, PR China
| | - Haoran He
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, Shaanxi, PR China
| | - Wanxiang Jiang
- College of Life Sciences, Zaozhuang University, Zaozhuang 277160, Shandong, PR China
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15
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Cleary DFR, Polónia ARM, Swierts T, Coelho FJRC, de Voogd NJ, Gomes NCM. Spatial and environmental variables structure sponge symbiont communities. Mol Ecol 2022; 31:4932-4948. [PMID: 35881675 PMCID: PMC9804187 DOI: 10.1111/mec.16631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 05/13/2022] [Accepted: 07/08/2022] [Indexed: 01/05/2023]
Abstract
Understanding the maintenance and origin of beta diversity is a central topic in ecology. However, the factors that drive diversity patterns and underlying processes remain unclear, particularly for host-prokaryotic associations. Here, beta diversity patterns were studied in five prokaryotic biotopes, namely, two high microbial abundance (HMA) sponge taxa (Xestospongia spp. and Hyrtios erectus), one low microbial abundance (LMA) sponge taxon (Stylissa carteri), sediment and seawater sampled across thousands of kilometres. Using multiple regression on distance matrices (MRM), spatial (geographic distance) and environmental (sea surface temperature and chlorophyll α concentrations) variables proved significant predictors of beta diversity in all five biotopes and together explained from 54% to 82% of variation in dissimilarity of both HMA species, 27% to 43% of variation in sediment and seawater, but only 20% of variation of the LMA S. carteri. Variance partitioning was subsequently used to partition the variation into purely spatial, purely environmental and spatially-structured environmental components. The amount of variation in dissimilarity explained by the purely spatial component was lowest for S. carteri at 11% and highest for H. erectus at 55%. The purely environmental component, in turn, only explained from 0.15% to 2.83% of variation in all biotopes. In addition to spatial and environmental variables, a matrix of genetic differences between pairs of sponge individuals also proved a significant predictor of variation in prokaryotic dissimilarity of the Xestospongia species complex. We discuss the implications of these results for the HMA-LMA dichotomy and compare the MRM results with results obtained using constrained ordination and zeta diversity.
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Affiliation(s)
- Daniel F. R. Cleary
- CESAM ‐ Centre for Environmental and Marine Studies, Department of BiologyUniversity of AveiroAveiroPortugal
| | - Ana R. M. Polónia
- CESAM ‐ Centre for Environmental and Marine Studies, Department of BiologyUniversity of AveiroAveiroPortugal
| | - Thomas Swierts
- Marine Biodiversity, Naturalis Biodiversity CenterLeidenThe Netherlands,Institute of Environmental Sciences (CML)Leiden UniversityLeidenThe Netherlands
| | - Francisco J. R. C. Coelho
- CESAM ‐ Centre for Environmental and Marine Studies, Department of BiologyUniversity of AveiroAveiroPortugal
| | - Nicole J. de Voogd
- Marine Biodiversity, Naturalis Biodiversity CenterLeidenThe Netherlands,Institute of Environmental Sciences (CML)Leiden UniversityLeidenThe Netherlands
| | - Newton C. M. Gomes
- CESAM ‐ Centre for Environmental and Marine Studies, Department of BiologyUniversity of AveiroAveiroPortugal
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16
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Li Y, Pan J, Zhang R, Wang J, Tian D, Niu S. Environmental factors, bacterial interactions and plant traits jointly regulate epiphytic bacterial community composition of two alpine grassland species. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 836:155665. [PMID: 35513157 DOI: 10.1016/j.scitotenv.2022.155665] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/15/2022] [Accepted: 04/29/2022] [Indexed: 06/14/2023]
Abstract
Epiphytic microbes on the surfaces of leaves and roots can bring substantial benefits or damages to their plant hosts. Although various factors have been proposed for shaping the epiphytic microbial composition, the contributions of environment factors, endogenous microbial taxa interactions, host plant traits, and their interactive effects are poorly understood. Here, we conducted a field investigation along a precipitation gradient and collected leaf and root surface microbes of two alpine plant species for 16S rRNA sequencing. We found that epiphytic bacterial community composition significantly changed along the precipitation gradient through ordination analyses and permutational multivariate analysis of variance. Beneficial bacterial taxa from Caulobacteraceae, Sphingomonadaceae, Comamonadaceae and Rhizobiales were enriched in the high precipitation zones. The stress-tolerant Hymenobacteraceae, Micrococcaceae, and Geodermatophilaceae occurred more frequently in the phyllosphere, and the Thermoleophilia, Thermomicrobiales and Bacillales were enriched in the rhizosphere at the drier sites. Mean annual precipitation was the most important factor regulating the epiphytic bacterial community composition. The direct effect of climate on bacterial community composition was higher in the phyllosphere than in the rhizosphere where joint effects of climate, plant traits and soil properties predominated. Distinct leaf trichome cover and plant height clearly explained the host effect on the phyllosphere bacterial community composition while belowground traits did not explain the host effect well on the rhizosphere bacterial community composition. We detected a significant role of bacterial taxa interactions in shaping microbial communities, where greater negative taxa interactions led to lesser composition changes. Structural equation modeling showed that environmental factors and bacterial interactions substantially contributed to the variation in epiphytic community composition, followed by host plant traits. This study advances our understanding of complex factors affecting alpine epiphytic community assembly and further confirms the role of biotic interactions.
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Affiliation(s)
- Yang Li
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Junxiao Pan
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ruiyang Zhang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Jinsong Wang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Dashuan Tian
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Shuli Niu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, PR China.
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17
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Zhang G, Bai J, Tebbe CC, Huang L, Jia J, Wang W, Wang X, Yu L, Zhao Q. Plant invasion reconstructs soil microbial assembly and functionality in coastal salt marshes. Mol Ecol 2022; 31:4478-4494. [PMID: 35789059 DOI: 10.1111/mec.16600] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 06/25/2022] [Accepted: 06/30/2022] [Indexed: 11/27/2022]
Abstract
Microbiologically driven ecosystem processes can be profoundly altered by alien plant invasions. The understanding of ecological mechanisms orchestrating different microbial constituents and their roles in emerging functional properties under plant invasions is limited. Here, we investigated soil microbial communities and functions using high-throughput amplicon sequencing and GeoChip technology, respectively, along a chronological gradient of smooth cordgrass invasion in salt marshes located in the Yellow River Estuary, China. We found a positive correlation between microbial diversity and the duration age of invasion, and both bacterial and fungal communities exerted orderly changes with invasion. Soil microbial metabolic potential, as indicated by the abundance of microbial functional genes involved in biogeochemical cycling, decreased in response to invasion. As a consequence, declined soil microbial metabolisms by plant invasion facilitated the carbon accumulation in invaded salt marshes. Bacteria and fungi exhibited distinct contributions to assembly processes along the invasion gradient: bacterial communities were mainly driven by selection and dispersal limitation, while fungi were dramatically shaped by stochastic processes. Soil microbial-mediated functions were taxon-specific, as indicated by community-function relationships. This study demonstrates the distinct contributions of microbial constituents to microbial community assembly and functions and sheds light on the implications of plant invasion on microbiologically driven ecosystem processes in coastal wetlands.
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Affiliation(s)
- Guangliang Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, P.R. China
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, P.R. China
| | - Christoph C Tebbe
- Thünen Institute of Biodiversity, Bundesallee 65, Braunschweig, Germany
| | - Laibin Huang
- Department of Land, Air, and Water Resources, University of California-, Davis, USA
| | - Jia Jia
- Henan Key Laboratory of Ecological Environment Protection and Restoration of Yellow River Basin, Yellow River Institute of Hydraulic Research, Zhengzhou, P.R. China
| | - Wei Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, P.R. China
| | - Xin Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, P.R. China
| | - Lu Yu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, P.R. China
| | - Qingqing Zhao
- Qilu University of Technology (Shandong Academy of Sciences), Ji' nan, P.R. China.,Ecology Institute of Shandong Academy of Sciences, Ji' nan, P.R. China
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18
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Osland MJ, Hughes AR, Armitage AR, Scyphers SB, Cebrian J, Swinea SH, Shepard CC, Allen MS, Feher LC, Nelson JA, O'Brien CL, Sanspree CR, Smee DL, Snyder CM, Stetter AP, Stevens PW, Swanson KM, Williams LH, Brush JM, Marchionno J, Bardou R. The impacts of mangrove range expansion on wetland ecosystem services in the southeastern United States: Current understanding, knowledge gaps, and emerging research needs. GLOBAL CHANGE BIOLOGY 2022; 28:3163-3187. [PMID: 35100489 DOI: 10.1111/gcb.16111] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Climate change is transforming ecosystems and affecting ecosystem goods and services. Along the Gulf of Mexico and Atlantic coasts of the southeastern United States, the frequency and intensity of extreme freeze events greatly influence whether coastal wetlands are dominated by freeze-sensitive woody plants (mangrove forests) or freeze-tolerant grass-like plants (salt marshes). In response to warming winters, mangroves have been expanding and displacing salt marshes at varying degrees of severity in parts of north Florida, Louisiana, and Texas. As winter warming accelerates, mangrove range expansion is expected to increasingly modify wetland ecosystem structure and function. Because there are differences in the ecological and societal benefits that salt marshes and mangroves provide, coastal environmental managers are challenged to anticipate the effects of mangrove expansion on critical wetland ecosystem services, including those related to carbon sequestration, wildlife habitat, storm protection, erosion reduction, water purification, fisheries support, and recreation. Mangrove range expansion may also affect wetland stability in the face of extreme climatic events and rising sea levels. Here, we review the current understanding of the effects of mangrove range expansion and displacement of salt marshes on wetland ecosystem services in the southeastern United States. We also identify critical knowledge gaps and emerging research needs regarding the ecological and societal implications of salt marsh displacement by expanding mangrove forests. One consistent theme throughout our review is that there are ecological trade-offs for consideration by coastal managers. Mangrove expansion and marsh displacement can produce beneficial changes in some ecosystem services, while simultaneously producing detrimental changes in other services. Thus, there can be local-scale differences in perceptions of the impacts of mangrove expansion into salt marshes. For very specific local reasons, some individuals may see mangrove expansion as a positive change to be embraced, while others may see mangrove expansion as a negative change to be constrained.
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Affiliation(s)
- Michael J Osland
- Wetland and Aquatic Research Center, U.S. Geological Survey, Lafayette, Louisiana, USA
| | - A Randall Hughes
- Northeastern University Marine Science Center, Nahant, Massachusetts, USA
| | - Anna R Armitage
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, Texas, USA
| | - Steven B Scyphers
- Northeastern University Marine Science Center, Nahant, Massachusetts, USA
| | - Just Cebrian
- Northern Gulf Institute, Mississippi State University, Stennis Space Center, Mississippi, USA
| | - Savannah H Swinea
- Northeastern University Marine Science Center, Nahant, Massachusetts, USA
| | | | | | - Laura C Feher
- Wetland and Aquatic Research Center, U.S. Geological Survey, Lafayette, Louisiana, USA
| | - James A Nelson
- University of Louisiana at Lafayette, Lafayette, Louisiana, USA
| | | | | | | | - Caitlin M Snyder
- Apalachicola National Estuarine Research Reserve, Eastpoint, Florida, USA
| | | | - Philip W Stevens
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, St. Petersburg, Florida, USA
| | - Kathleen M Swanson
- Mission-Aransas National Estuarine Research Reserve, Port Aransas, Texas, USA
| | | | - Janell M Brush
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, Gainesville, Florida, USA
| | - Joseph Marchionno
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, Gainesville, Florida, USA
| | - Rémi Bardou
- Northeastern University Marine Science Center, Nahant, Massachusetts, USA
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19
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Song W, Liu J, Qin W, Huang J, Yu X, Xu M, Stahl D, Jiao N, Zhou J, Tu Q. Functional Traits Resolve Mechanisms Governing the Assembly and Distribution of Nitrogen-Cycling Microbial Communities in the Global Ocean. mBio 2022; 13:e0383221. [PMID: 35285696 PMCID: PMC9040759 DOI: 10.1128/mbio.03832-21] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/02/2022] [Indexed: 12/22/2022] Open
Abstract
Microorganisms drive much of the marine nitrogen (N) cycle, which jointly controls the primary production in the global ocean. However, our understanding of the microbial communities driving the global ocean N cycle remains fragmented. Focusing on "who is doing what, where, and how?", this study draws a clear picture describing the global biogeography of marine N-cycling microbial communities by utilizing the Tara Oceans shotgun metagenomes. The marine N-cycling communities are highly variable taxonomically but relatively even at the functional trait level, showing clear functional redundancy properties. The functional traits and taxonomic groups are shaped by the same set of geo-environmental factors, among which, depth is the major factor impacting marine N-cycling communities, differentiating mesopelagic from epipelagic communities. Latitudinal diversity gradients and distance-decay relationships are observed for taxonomic groups, but rarely or weakly for functional traits. The composition of functional traits is strongly deterministic as revealed by null model analysis, while a higher degree of stochasticity is observed for taxonomic composition. Integrating multiple lines of evidence, in addition to drawing a biogeographic picture of marine N-cycling communities, this study also demonstrated an essential microbial ecological theory-determinism governs the assembly of microbial communities performing essential biogeochemical processes; the environment selects functional traits rather than taxonomic groups; functional redundancy underlies stochastic taxonomic community assembly. IMPORTANCE A critical question in microbial ecology is how the complex microbial communities are formed in natural ecosystems with the existence of thousands different species, thereby performing essential ecosystem functions and maintaining ecosystem stability. Previous studies disentangling the community assembly mechanisms mainly focus on microbial taxa, ignoring the functional traits they carry. By anchoring microbial functional traits and their carrying taxonomic groups involved in nitrogen cycling processes, this study demonstrated an important mechanism associated with the complex microbial community assembly. Evidence shows that the environment selects functional traits rather than taxonomic groups, and functional redundancy underlies stochastic taxonomic community assembly. This study is expected to provide valuable mechanistic insights into the complex microbial community assembly in both natural and artificial ecosystems.
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Affiliation(s)
- Wen Song
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China
| | - Jihua Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China
| | - Wei Qin
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Jun Huang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China
| | - Xiaoli 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
| | - Mengzhao Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China
| | - David Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
| | - Nianzhi Jiao
- Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China
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20
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Liu B, Yao J, Chen Z, Ma B, Li H, Wancheng P, Liu J, Wang D, Duran R. Biogeography, assembly processes and species coexistence patterns of microbial communities in metalloids-laden soils around mining and smelting sites. JOURNAL OF HAZARDOUS MATERIALS 2022; 425:127945. [PMID: 34896705 DOI: 10.1016/j.jhazmat.2021.127945] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 06/14/2023]
Abstract
Microbes are important component in terrestrial ecosystem, which are believed to play vital roles in biogeochemical cycles of metalloids in mining and smelting surroundings. Many studies on microbial diversity and structures have been investigated around mining and smelting sites, whereas the ecological processes and co-occurrence patterns that influence the biogeographic distributions of microbial communities is yet poorly understood. Herein, microbial biogeography, assembly mechanism and co-occurrence pattern around mining and smelting zone were systematically unraveled using 16S rRNA gene sequencing. The 66 microbial phyla co-occurring across all the samples were dominated by Proteobacteria, Chloroflexi, Acidobacteria and Crenarchaeota. Obvious distance-decay (r = 0.3448, p < 0.001) of microbial community was observed across geographic distances. Differences in microbial communities were driven by the joint impacts of soil factors, spatial and metalloids levels. Dispersal limitation dominated the microbial assemblies in whole, SC and GX sites while homogeneous selection governed that in YN site. The changes in pH and Sb level significantly influenced the deterministic and stochastic processes of microbial communities. Network analysis suggested a typical module distribution, which had apparent ecological links among taxa in modules. This study provides first insight of the mechanism to maintain microbial diversity in metalloids-laden biospheres.
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Affiliation(s)
- Bang Liu
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, People's Republic of China
| | - Jun Yao
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, People's Republic of China.
| | - Zhihui Chen
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, People's Republic of China
| | - Bo Ma
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, People's Republic of China
| | - Hao Li
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, People's Republic of China
| | - Pang Wancheng
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, People's Republic of China
| | - Jianli Liu
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, People's Republic of China
| | - Daya Wang
- Huawei National Engineering Research Center of High Efficient Cyclic Utilization of Metallic Mineral Resources Co., Ltd., 666 Xitang Road, Huashan District, Maanshan, Anhui 243000, People's Republic of China; Sinosteel Maanshan Institute of Mining Research Co., Ltd., 666 Xitang Road, Huashan District, Maanshan, Anhui 243000, People's Republic of China
| | - Robert Duran
- School of Water Resource and Environment, Research Center of Environmental Science and Engineering, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, Beijing 100083, People's Republic of China; Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, 64013 Pau Cedex, France
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21
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Tamminen M, Spaak J, Tlili A, Eggen R, Stamm C, Räsänen K. Wastewater constituents impact biofilm microbial community in receiving streams. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:151080. [PMID: 34678363 DOI: 10.1016/j.scitotenv.2021.151080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/01/2021] [Accepted: 10/15/2021] [Indexed: 05/27/2023]
Abstract
Microbial life in natural biofilms is dominated by prokaryotes and microscopic eukaryotes living in dense association. In stream ecosystems, microbial biofilms influence primary production, elemental cycles, food web interactions as well as water quality. Understanding how biofilm communities respond to anthropogenic impacts, such as wastewater treatment plant (WWTP) effluent, is important given the key role of biofilms in stream ecosystem function. Here, we implemented 16S and 18S rRNA gene sequencing of stream biofilms upstream (US) and downstream (DS) of WWTP effluents in four Swiss streams to test how bacterial and eukaryotic communities respond to wastewater constituents. Stream biofilm composition was strongly affected by geographic location - particularly for bacteria. However, the abundance of certain microbial community members was related to micropollutants in the wastewater - among bacteria, micropollutant-associated members were found e.g. in Alphaproteobacteria, and among eukaryotes e.g. in Bacillariophyta (algal diatoms). This study corroborates several previously characterized responses (e.g. as seen in diatoms), but also reveals previously unknown community responses - such as seen in Alphaproteobacteria. This study advances our understanding of the ecological impact of the current wastewater treatment practices and provides information about potential new marker organisms to assess ecological change in stream biofilms.
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Affiliation(s)
- Manu Tamminen
- Department of Biology, University of Turku, Finland.
| | - Jenny Spaak
- Department of Environmental Microbiology, Eawag, Switzerland
| | - Ahmed Tlili
- Department of Environmental Toxicology, Eawag, Switzerland
| | - Rik Eggen
- Department of Environmental Toxicology, Eawag, Switzerland; Department of Environmental Systems Science, ETH Zürich, Switzerland
| | | | - Katja Räsänen
- Department of Aquatic Ecology, Eawag, Switzerland; Dept. of Biology and Environmental Science, University of Jyväskylä, Finland
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22
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Huang J, Zhu J, Liu S, Luo Y, Zhao R, Guo F, Li B. Estuarine salinity gradient governs sedimentary bacterial community but not antibiotic resistance gene profile. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:151390. [PMID: 34740654 DOI: 10.1016/j.scitotenv.2021.151390] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
Antibiotic resistance gene (ARG) pollution in estuarine environment has drawn great attention, and it is not clear if the physical and chemical parameters such as salinity, total organic carbon, total nitrogen, total phosphorus and antibiotics affects the distribution of ARGs. Herein, we deciphered the ARG profiles and microbial community compositions in sediments from Jiulong River Estuary (JRE) and Min River Estuary (MRE) of China using high-throughput sequencing-based metagenomics analysis. Furthermore, we explored the influence of salinity on bacterial community and ARG profiles. The results showed that Proteobacteria, Chloroflexi, and Acidobacteria were the dominant phyla in these two estuaries. The abundance of ARGs ranged from 1.05 × 10-1 to 2.93 × 10-1 copy of ARG per copy of 16S rRNA gene in all the sediment samples and the profiles of ARGs presented similar patterns in two estuaries. Multidrug resistance genes were the dominant ARG types in both estuaries, with an overall abundance of 2.39 × 10-2-1.07 × 10-1 copy of ARG per copy of 16S rRNA gene, followed by genes conferring resistance to bacitracin and macrolide-lincosamide-streptogramin. Salinity was an important influencing factor on the bacterial community but not on the ARG profiles. Instead, stochastic processes exerted the main influence on the distribution of ARGs. The comparison of ARG profiles among estuary sediments, marine sediments, and samples from anthropogenic pollution environments revealed remarkable similarity of ARG profiles between samples from estuary sediments and those from municipal wastewater treatment plants. These results suggested that the complex emission of anthropogenic pollution could cause the stochastic ecological pattern of ARGs.
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Affiliation(s)
- Jin Huang
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China; Shenzhen Environmental Science and New Energy Laboratory, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen 518055, China
| | - Jun Zhu
- School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Xiamen University, Xiamen, China
| | - Siguang Liu
- Fujian Institute of Oceanography, Xiamen, China
| | - Yuanrong Luo
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, China
| | - Renxin Zhao
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Feng Guo
- School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Xiamen University, Xiamen, China; Key Laboratory of Fujian Provincial University for Microorganism Resource, Xiamen, China.
| | - Bing Li
- Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China.
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23
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Xu Q, Ling N, Quaiser A, Guo J, Ruan J, Guo S, Shen Q, Vandenkoornhuyse P. Rare Bacteria Assembly in Soils Is Mainly Driven by Deterministic Processes. MICROBIAL ECOLOGY 2022; 83:137-150. [PMID: 33792742 DOI: 10.1007/s00248-021-01741-8] [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: 12/23/2020] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
Rare species are crucial components of the highly diverse soil microbial pool and over-proportionally contribute to the soil functions. However, much remains unknown about their assembling rules. The biogeographic patterns and species aggregations of the rare bacterial biosphere were assessed using 140 soil samples from a gradient of 2000 km across the main tea-producing areas in China. About 96% OTUs with ~40% sequences were classified as rare taxa. The rare bacterial communities were significantly affected by geographical regions and showed distance-decay effects, indicating that the rare bacteria are not cosmopolitan, they displayed a pattern of limited dispersal and were restricted to certain sites. Variation partitioning analysis (VPA) revealed that environmental variation and spatial factors explained 12.5% and 6.4%, respectively, of the variance in rare bacterial community. The Mantel and partial Mantel tests also showed that the environmental factors had stronger (~3 times) impacts than spatial factors. The null model showed that deterministic processes contributed more than stochastic processes in rare bacterial assembly (75% vs. 25%). There is likely an enrichment in ecological functions within the rare biosphere, considering this high contribution of deterministic processes in the assembly. In addition, the assembly of rare taxa was found to be mainly driven by soil pH. Overall, this study revealed that rare bacteria were not cosmopolitan, and their assembly was more driven by deterministic processes. These findings provided a new comprehensive understanding of rare bacterial biogeographic patterns and assembly rules.
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Affiliation(s)
- Qicheng Xu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Université de Rennes 1, CNRS, UMR 6553 EcoBio, Campus Beaulieu, Avenue du Général Leclerc, 35042, Rennes Cedex, France
| | - Ning Ling
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- Université de Rennes 1, CNRS, UMR 6553 EcoBio, Campus Beaulieu, Avenue du Général Leclerc, 35042, Rennes Cedex, France.
| | - Achim Quaiser
- Université de Rennes 1, CNRS, UMR 6553 EcoBio, Campus Beaulieu, Avenue du Général Leclerc, 35042, Rennes Cedex, France
| | - Junjie Guo
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jianyun Ruan
- Key Laboratory of Tea Plant Biology and Resources Utilization (Ministry of Agriculture), Tea Research Institute, Chinese Academy of Agricultural Sciences, Zhejiang, 310008, Hangzhou, China
| | - Shiwei Guo
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Philippe Vandenkoornhuyse
- Université de Rennes 1, CNRS, UMR 6553 EcoBio, Campus Beaulieu, Avenue du Général Leclerc, 35042, Rennes Cedex, France
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24
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Shahraki AH, Chaganti SR, Heath D. Spatio-temporal dynamics of bacterial communities in the shoreline of Laurentian great Lake Erie and Lake St. Clair's large freshwater ecosystems. BMC Microbiol 2021; 21:253. [PMID: 34548037 PMCID: PMC8454060 DOI: 10.1186/s12866-021-02306-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 09/01/2021] [Indexed: 11/16/2022] Open
Abstract
Background Long-term trends in freshwater bacterial community composition (BCC) and dynamics are not yet well characterized, particularly in large lake ecosystems. We addressed this gap by temporally (15 months) and spatially (6 sampling locations) characterizing BCC variation in lakes Erie and St. Clair; two connected ecosystems in the Laurentian Great Lakes. Results We found a spatial variation of the BCC between the two lakes and among the sampling locations (significant changes in the relative abundance of 16% of the identified OTUs at the sampling location level). We observed five distinct temporal clusters (UPGMA broad-scale temporal variation) corresponding to seasonal variation over the 15 months of sampling. Temporal variation among months was high, with significant variation in the relative abundance of 69% of the OTUs. We identified significant differences in taxonomic composition between summer months of 2016 and 2017, with a corresponding significant reduction in the diversity of BCC in summer 2017. Conclusions As bacteria play a key role in biogeochemical cycling, and hence in healthy ecosystem function our study defines the scope for temporal and spatial variation in large lake ecosystems. Our data also show that freshwater BCC could serve as an effective proxy and monitoring tool to access large lake health. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02306-y.
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Affiliation(s)
| | - Subba Rao Chaganti
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada. .,Present Address: Cooperative Institute for Great Lakes Research, School of Environmental and Sustainability, University of Michigan, Ann Arbor, MI, USA.
| | - Daniel Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada. .,Department of Integrative Biology, University of Windsor, Windsor, Ontario, Canada.
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25
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Zhu C, Liu W, Li X, Xu Y, El-Serehy HA, Al-Farraj SA, Ma H, Stoeck T, Yi Z. High salinity gradients and intermediate spatial scales shaped similar biogeographical and co-occurrence patterns of microeukaryotes in a tropical freshwater-saltwater ecosystem. Environ Microbiol 2021; 23:4778-4796. [PMID: 34258839 DOI: 10.1111/1462-2920.15668] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 06/12/2021] [Accepted: 07/09/2021] [Indexed: 11/26/2022]
Abstract
Microeukaryotes play key ecological roles in the microbial web of aquatic ecosystems. However, large knowledge gaps urgently need to be filled regarding the biogeography with associated shaping mechanisms and co-occurrence patterns of microeukaryotes under freshwater-saltwater gradients, especially true in tropical regions. Here, we investigated microeukaryotes of six mixed freshwater-saltwater regions in the Pearl River Estuary and surrounding coasts in southern China, with salinity ranging 0.1-32.0% and distances spanned up to 500 km, using molecular ecological methods. Results indicate that the biogeography of abundant and rare microeukaryotic communities was similar, both their co-occurrence patterns and biogeographical patterns were driven by deterministic and stochastic processes. The environmental factors with higher selective pressure than dispersal limitation meant that the role of deterministic process in structuring communities was more significant than that of stochastic process, and salinity played important role in structuring both microeukaryotic communities and networks. The abundant communities had stronger influence on entire microeukaryotic communities and seemed to be more sensitive to environmental changes than their rare counterparts, while rare ones had stronger interspecific relationships. Finally, the geographic scale and environmental gradients of study regions should firstly be clarified in future research on the ecological processes of microeukaryotes before conclusions are drawn.
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Affiliation(s)
- Changyu Zhu
- Institute of Evolution & Marine Biodiversity, and College of Fisheries, Ocean University of China, Qingdao, 266003, China.,Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Weiwei Liu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.,Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China
| | - Xinghao Li
- Key Laboratory of Regional Development and Environmental Response, and Hubei Engineering Research Center for Rural Drinking Water Security, Hubei University, Wuhan, 430062, China
| | - Yusen Xu
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Hamed A El-Serehy
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.,Department of Oceanography, College of Science, Port Said University, Port Said, 42511, Egypt
| | - Saleh A Al-Farraj
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Honggang Ma
- Institute of Evolution & Marine Biodiversity, and College of Fisheries, Ocean University of China, Qingdao, 266003, China
| | - Thorsten Stoeck
- Department of Ecology, University of Technology Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Zhenzhen Yi
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
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26
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Teng J, Tian J, Yu G, Kuzyakov Y. Soil properties and root traits jointly shape fine-scale spatial patterns of bacterial community and metabolic functions within a Korean pine forest. PeerJ 2021; 9:e10902. [PMID: 33680578 PMCID: PMC7919533 DOI: 10.7717/peerj.10902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 01/13/2021] [Indexed: 11/20/2022] Open
Abstract
Spatial heterogeneity of soil bacterial community depends on scales. The fine-scale spatial heterogeneity of bacterial community composition and functions remains unknown. We analyzed the main driving factors of fine-scale spatial patterns of soil bacterial community composition and carbon metabolic functions across a 30 m × 40 m plot within a Korean pine forest by combining Illumina 16S rRNA sequencing with Biolog Ecoplates based on 53 soil samples. Clear spatial patterns in bacterial community composition and metabolic functions were observed in the forest soil. The bacterial community composition and metabolic functions both showed distance-decay of similarity within a distance of meters. Structural equation model analysis revealed that environmental variables and geographic distance together explained 37.9% and 63.1% of community and metabolic functions, respectively. Among all environmental factors, soil organic carbon (SOC) and root biomass emerged as the most important drivers of the bacterial community structure. In contrast, soil pH explained the largest variance in metabolic functions. Root biomass explained the second-largest variance in soil bacterial community composition, but root traits made no difference in metabolic functions variance. These results allow us to better understand the mechanisms controlling belowground diversity and plant-microbe interactions in forest ecosystems.
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Affiliation(s)
- Jialing Teng
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Jing Tian
- College of Resources and Environmental Sciences; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Guirui Yu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, University of Göttingen, Göttingen, Germany.,Institute of Environmental Sciences, Kazan Federal University, Kazan, Russia
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27
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Du Y, Yang W, Ding X, Zhang J, Zheng Z, Zhu J. High heterogeneity of bacterioplankton community shaped by spatially structured environmental factors in West Lake, a typical urban lake in eastern China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:42283-42293. [PMID: 32319051 DOI: 10.1007/s11356-020-08818-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 04/07/2020] [Indexed: 06/11/2023]
Abstract
Elucidating the bacterioplankton spatial distribution patterns and its determinants is a central topic in ecological research. However, research on the distribution patterns of bacterioplankton community composition (BCC) within a small-sized, highly dynamic freshwater lake remains unclear. In this study, we collected surface water samples from West Lake to investigate the spatiotemporal variation of BCC by 16S rRNA gene high-throughput sequencing. Clear spatial heterogeneity in BCC was identified both in summer and winter. The relatively high abundant taxa exhibited greater correlations with environmental factors and other abundant species in summer than in winter. Variation partitioning analysis was used to unravel the relative importance of environmental factors and spatial processes and further explore the underlying mechanism of BCC successions. Our results showed the predominant shared effect of environmental and spatial factors on BCC in summer (68.41%) and winter (57.37%), indicating that spatially structured environmental factors were the key determinants of structuring BCC spatial heterogeneity in West Lake in the two seasons. Furthermore, environmental factors alone explained a higher proportion of the variation in summer whereas spatial factors explained a higher proportion in winter. These divergences may be related to seasonal environmental changes and anthropogenic disturbances. Our study provided knowledge on BCC spatial heterogeneity in small freshwater habitats and their underlying determinants in different seasons.
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Affiliation(s)
- Yi Du
- School of Marine Science, Ningbo University, Ningbo, 315800, China
| | - Wen Yang
- School of Marine Science, Ningbo University, Ningbo, 315800, China
| | - Xiuying Ding
- Hangzhou West Lake Administration, Hangzhou, 310002, China
| | - Jinjie Zhang
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315800, China
| | - Zhongming Zheng
- School of Marine Science, Ningbo University, Ningbo, 315800, China
| | - Jinyong Zhu
- School of Marine Science, Ningbo University, Ningbo, 315800, China.
- , Ningbo, China.
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28
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Paruch L, Paruch AM, Eiken HG, Skogen M, Sørheim R. Seasonal dynamics of lotic bacterial communities assessed by 16S rRNA gene amplicon deep sequencing. Sci Rep 2020; 10:16399. [PMID: 33009479 PMCID: PMC7532223 DOI: 10.1038/s41598-020-73293-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 09/15/2020] [Indexed: 12/04/2022] Open
Abstract
Aquatic microbial diversity, composition, and dynamics play vital roles in sustaining water ecosystem functionality. Yet, there is still limited knowledge on bacterial seasonal dynamics in lotic environments. This study explores a temporal pattern of bacterial community structures in lotic freshwater over a 2-year period. The aquatic bacterial communities were assessed using Illumina MiSeq sequencing of 16S rRNA genes. Overall, the communities were dominated by α-, β-, and γ-Proteobacteria, Bacteroidetes, Flavobacteriia, and Sphingobacteriia. The bacterial compositions varied substantially in response to seasonal changes (cold vs. warm), but they were rather stable within the same season. Furthermore, higher diversity was observed in cold seasons compared to warm periods. The combined seasonal-environmental impact of different physico-chemical parameters was assessed statistically, and temperature, suspended solids, and nitrogen were determined to be the primary abiotic factors shaping the temporal bacterial assemblages. This study enriches particular knowledge on the seasonal succession of the lotic freshwater bacteria.
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Affiliation(s)
- Lisa Paruch
- Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research - NIBIO, Oluf Thesens vei 43, 1433, Ås, Norway
| | - Adam M Paruch
- Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research - NIBIO, Oluf Thesens vei 43, 1433, Ås, Norway.
| | - Hans Geir Eiken
- Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research - NIBIO, Oluf Thesens vei 43, 1433, Ås, Norway
| | - Monica Skogen
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research - NIBIO, Høgskoleveien 7, 1433, Ås, Norway
| | - Roald Sørheim
- Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research - NIBIO, Oluf Thesens vei 43, 1433, Ås, Norway
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Grajal-Puche A, Murray CM, Kearley M, Merchant M, Nix C, Warner JK, Walker DM. Microbial Assemblage Dynamics Within the American Alligator Nesting Ecosystem: a Comparative Approach Across Ecological Scales. MICROBIAL ECOLOGY 2020; 80:603-613. [PMID: 32424717 DOI: 10.1007/s00248-020-01522-9] [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: 02/05/2020] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
Understanding the ecological processes that shape species assemblage patterns is central to community ecology. The effects of ecological processes on assemblage patterns are scale-dependent. We used metabarcoding and shotgun sequencing to determine bacterial taxonomic and functional assemblage patterns among varying defined focal scales (micro-, meso-, and macroscale) within the American alligator (Alligator mississippiensis) nesting microbiome. We correlate bacterial assemblage patterns among eight nesting compartments within and proximal to alligator nests (micro-), across 18 nests (meso-), and between 4 geographic sampling sites (macro-), to determine which ecological processes may drive bacterial assemblage patterns within the nesting environment. Among all focal scales, bacterial taxonomic and functional richness (α-diversity) did not statistically differ. In contrast, bacterial assemblage structure (β-diversity) was unique across all focal scales, whereas functional pathways were redundant within nests and across geographic sites. Considering these observed scale-based patterns, taxonomic bacterial composition may be governed by unique environmental filters and dispersal limitations relative to microbial functional attributes within the alligator nesting environment. These results advance pattern-process dynamics within the field of microbial community ecology and describe processes influencing the American alligator nest microbiome.
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Affiliation(s)
| | - Christopher M Murray
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, LA, 70402, USA
- Biology Department, Tennessee Technological University, Cookeville, TN, 38505, USA
| | - Matthew Kearley
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Mark Merchant
- Department of Chemistry, McNeese State University, Lake Charles, LA, 70609, USA
| | - Christopher Nix
- Alabama Wildlife and Freshwater Fisheries Division, Montgomery, AL, 36130, USA
| | | | - Donald M Walker
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA.
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30
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Montenegro D, Astudillo-García C, Hickey T, Lear G. A non-invasive method to monitor marine pollution from bacterial DNA present in fish skin mucus. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 263:114438. [PMID: 32283451 DOI: 10.1016/j.envpol.2020.114438] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 01/28/2020] [Accepted: 03/21/2020] [Indexed: 06/11/2023]
Abstract
Marine coastal contamination caused by human activity is a major issue worldwide. The implementation of effective pollution monitoring programs, especially in coastal areas, is important and urgent. The use of biological, physiological, or biochemical measurements to monitor the impacts of pollution has garnered increasing interest, particularly for the development of new non-invasive tools to assess water pollution. Fish skin mucus is in direct contact with the marine environment, making it a favourable microenvironment for the formation of biofilm bacterial communities. In this study, we developed a non-invasive technique, sampling fish skin mucus to determine and analyse bacterial community composition using next-generation sequencing. We hypothesised that bacterial communities associated with the skin mucus of a common harbour benthic blennioid triplefin fish, Forsterygion capito, would reflect conditions of different marine environments. We detected clear differences in bacterial community alpha-diversity between contaminated and reference sites. Beta-diversity analysis also revealed differences in the bacterial community structure of the skin mucus of fish inhabiting different geographical areas. The relative abundance of different bacterial orders varied among sites, as determined by linear discriminant analysis (LDA) and effect size (LEfSe) analyses. The observed variation in bacterial community compositions correlated more strongly with variation in hydrocarbons than to various metal concentrations. Using advanced DNA sequencing technologies, we have developed a novel non-invasive, low-cost and effective tool to monitor the impacts of pollution through analysis of the bacterial communities associated with fish skin mucus.
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Affiliation(s)
- Diana Montenegro
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand.
| | | | - Tony Hickey
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
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31
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Sala MM, Ruiz-González C, Borrull E, Azúa I, Baña Z, Ayo B, Álvarez-Salgado XA, Gasol JM, Duarte CM. Prokaryotic Capability to Use Organic Substrates Across the Global Tropical and Subtropical Ocean. Front Microbiol 2020; 11:918. [PMID: 32582044 PMCID: PMC7287293 DOI: 10.3389/fmicb.2020.00918] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/17/2020] [Indexed: 12/17/2022] Open
Abstract
Prokaryotes play a fundamental role in decomposing organic matter in the ocean, but little is known about how microbial metabolic capabilities vary at the global ocean scale and what are the drivers causing this variation. We aimed at obtaining the first global exploration of the functional capabilities of prokaryotes in the ocean, with emphasis on the under-sampled meso- and bathypelagic layers. We explored the potential utilization of 95 carbon sources with Biolog GN2 plates® in 441 prokaryotic communities sampled from surface to bathypelagic waters (down to 4,000 m) at 111 stations distributed across the tropical and subtropical Atlantic, Indian, and Pacific oceans. The resulting metabolic profiles were compared with biological and physico-chemical properties such as fluorescent dissolved organic matter (DOM) or temperature. The relative use of the individual substrates was remarkably consistent across oceanic regions and layers, and only the Equatorial Pacific Ocean showed a different metabolic structure. When grouping substrates by categories, we observed some vertical variations, such as an increased relative utilization of polymers in bathypelagic layers or a higher relative use of P-compounds or amino acids in the surface ocean. The increased relative use of polymers with depth, together with the increases in humic DOM, suggest that deep ocean communities have the capability to process complex DOM. Overall, the main identified driver of the metabolic structure of ocean prokaryotic communities was temperature. Our results represent the first global depiction of the potential use of a variety of carbon sources by prokaryotic communities across the tropical and the subtropical ocean and show that acetic acid clearly emerges as one of the most widely potentially used carbon sources in the ocean.
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Affiliation(s)
- Maria Montserrat Sala
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - Clara Ruiz-González
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - Encarna Borrull
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - Iñigo Azúa
- Department of Immunology, Microbiology, and Parasitology, Faculty of Science and Technology, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Zuriñe Baña
- Department of Immunology, Microbiology, and Parasitology, Faculty of Science and Technology, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Begoña Ayo
- Department of Immunology, Microbiology, and Parasitology, Faculty of Science and Technology, University of the Basque Country UPV/EHU, Leioa, Spain.,Research Centre for Experimental Marine Biology and Biotechnology PiE-UPV/EHU, Plentzia, Spain
| | | | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas, Barcelona, Spain.,Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, Joondalup, WA, Australia
| | - Carlos M Duarte
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Department of Global Change Research, Instituto Mediterráneo de Estudios Avanzados-Universitat de les Illes Balears, Consejo Superior de Investigaciones Científicas, Esporles, Spain
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32
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Huang J, Yang J, Jiang H, Wu G, Xie Z, Dong H. Surviving onshore soil microbial communities differ among the Qing-Tibetan lakes with different salinity. FEMS Microbiol Ecol 2020; 95:5582604. [PMID: 31589308 DOI: 10.1093/femsec/fiz156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 10/03/2019] [Indexed: 11/12/2022] Open
Abstract
Little is known about the onshore microbial contribution to the microbial communities in nearby lakes and its response to salinity. In this study, transplanting experiments were established by caging onshore soils with dialysis bags followed by in situ 50-day incubation in nearby lakes with different salinity on the Qinghai-Tibetan Plateau. At the end of the experiment, geochemical and microbial analyses were performed on the original soils, caged soils and lake waters and sediments at the incubation sites. The results showed that the salinity increased significantly (P < 0.05) in the caged soils and such salinity increases showed significant (P < 0.05) positive correlation with the salinity of the studied lakes. The microbial community composition and predicted functions in the caged soils were significantly (P < 0.05) changed in comparison with their corresponding original soils, and such variation could be mainly explained by the succession of members of the Proteobacteria, Bacteroidetes and Actinobacteria from the original soils to their corresponding caged soils. The onshore microbial contribution appeared to be limited (up to 11.2% for sediment and negligible for water, respectively) to nearby lake microbial communities. Nevertheless, the survival of onshore soil microbial communities was mainly limited by the salinity of the receiving lakes.
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Affiliation(s)
- Jianrong Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Geng Wu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Zhanling Xie
- College of Ecology-Environment Engineering, Qinghai University, Xining, 810016, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China.,Department of Geology and Environmental Earth Science, Miami University, Oxford, OH 5056, USA
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33
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Mathieu C, Hermans SM, Lear G, Buckley TR, Lee KC, Buckley HL. A Systematic Review of Sources of Variability and Uncertainty in eDNA Data for Environmental Monitoring. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00135] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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34
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Ding Q, Liu K, Song Z, Sun R, Zhang J, Yin L, Pu Y. Effects of Microcystin-LR on Metabolic Functions and Structure Succession of Sediment Bacterial Community under Anaerobic Conditions. Toxins (Basel) 2020; 12:toxins12030183. [PMID: 32183408 PMCID: PMC7150748 DOI: 10.3390/toxins12030183] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/05/2020] [Accepted: 03/14/2020] [Indexed: 01/02/2023] Open
Abstract
Microcystins (MCs), which are produced by harmful cyanobacteria blooms, pose a serious threat to environmental health. However, the effect of MCs on the bacterial community under anaerobic conditions is still unclear. This study examined the dynamic changes of MC-degrading capacity, metabolic activity, and structure of the bacterial community in lake sediment repeatedly treated with 1 mg/L microcystin-LR (MC-LR) under anaerobic conditions. The results showed that the MC-degrading capacity of the bacterial community was increased nearly three-fold with increased treatment frequency. However, the metabolic profile behaved in exactly opposite trend, in which the overall carbon metabolic activity was inhibited by repeated toxin addition. Microbial diversity was suppressed by the first addition of MC-LR and then gradually recovered. The 16S amplicon sequencing showed that the dominant genera were changed from Exiguobacterium and Acinetobacter to Prosthecobacter, Dechloromonas, and Agrobacterium. Furthermore, the increase in the relative abundance of Dechloromonas, Pseudomonas, Hydrogenophaga, and Agrobacterium was positively correlated with the MC-LR treatment times. This indicates that they might be responsible for MC degradation under anaerobic conditions. Our findings reveal the relationship between MC-LR and the sediment bacterial community under anaerobic conditions and indicate that anaerobic biodegradation is an effective and promising method to remediate MCs pollution.
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Affiliation(s)
- Qin Ding
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing 210009, China; (Q.D.)
| | - Kaiyan Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing 210009, China; (Q.D.)
| | - Zhiquan Song
- Department of Civil and Environmental Engineering, University of California, Irvine, CA 92697, USA
| | - Rongli Sun
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing 210009, China; (Q.D.)
| | - Juan Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing 210009, China; (Q.D.)
| | - Lihong Yin
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing 210009, China; (Q.D.)
| | - Yuepu Pu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China, School of Public Health, Southeast University, Nanjing 210009, China; (Q.D.)
- Correspondence: ; Tel.: +86-25-83272582
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35
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Geographic Patterns of Bacterioplankton among Lakes of the Middle and Lower Reaches of the Yangtze River Basin, China. Appl Environ Microbiol 2020; 86:AEM.02423-19. [PMID: 31924617 DOI: 10.1128/aem.02423-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 12/17/2019] [Indexed: 02/01/2023] Open
Abstract
The revolution of molecular techniques has revealed that the composition of natural bacterial communities normally includes a few abundant taxa and many rare taxa. Unraveling the mechanisms underlying the spatial assembly process of both abundant and rare bacterial taxa has become a central goal in microbial ecology. Here, we used high-throughput sequencing to explore geographic patterns and the relative importance of ecological processes in the assembly of abundant and rare bacterial subcommunities from 25 lakes across the middle and lower reaches of Yangtze River basin (MLYB), located in Southeast China, where most of the lakes are interconnected by river networks. We found similar biogeographic patterns of abundant and rare subcommunities which could significantly distinguish the community compositions of the two lake groups that were far from each other but which could not distinguish the community compositions of the nearby lakes. Both abundant and rare bacteria followed a strong distance-decay relationship. These findings suggest that the interconnectivity between lakes homogenizes the bacterial communities in local areas, and the abundant and rare taxa therein may be affected by the same ecological process. In addition, based on the measured environmental variables, the deterministic processes explain a small fraction of variation within both abundant and rare subcommunities, while both neutral and null models revealed a high stochasticity ratio for the spatial distribution patterns of both abundant and rare taxa. These findings indicate that the stochastic processes exhibited a greater influence on both abundant and rare bacterial subcommunity assemblies among interconnected lakes.IMPORTANCE The middle and lower Yangtze Plain is a typical floodplain in which many lakes connect with each other, especially in the wet season. More importantly, with the frequent change of regional water level in the wet season, there is a mutual hydrodynamic exchange among these lakes. The microbial biogeography among these interconnected lakes is still poorly understood. This study aims to unravel the mechanisms underlying the assembly process of abundant and rare bacteria among the interconnected lakes in the middle and lower Yangtze Plain. Our findings will provide a deeper understanding of the biogeographic patterns of rare and abundant bacterial taxa and their determined processes among interconnected aquatic habitats.
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36
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Wang Y, Lu L, Hong Y, Wu J, Zhu G, Ye F, Li Z. Divergent responses of taxonomic and predicted functional profiles of bacterioplankton to reservoir impoundment. ENVIRONMENTAL RESEARCH 2020; 182:109083. [PMID: 31901627 DOI: 10.1016/j.envres.2019.109083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 06/10/2023]
Abstract
Freshwater ecosystems are undergoing extensive human disturbance of dam construction which form large amounts of reservoirs and lead to dramatic changes in hydraulic conditions. Bacterioplankton are key component of aquatic ecosystems. Investigation on their taxonomic compositions and associated functions responded to reservoir operation is essential to understand the ecological consequence of dam construction. In this study, we use the Three Gorges Reservoir as a model system. High-throughput sequencing is used to investigate the bacterioplankton community composition, and the bioinformatic tool of Tax4Fun is applied to predict the potential metabolic functions responded to reservoir impoundment. Results show that the taxonomic communities of bacterioplankton are significantly impacted by impoundment. The dominant group of Actinobacteria which accounts for 17.0%-58.1% of the retrieved sequences significantly increases after impoundment on phylum level. The influences of impoundment appear to be more apparent on order level that the relative abundances of four groups including Frankiales, Sphingomonadales, Sphingobacteriales and SubsectionI of class Cyanobacteria significantly vary after impoundment. In contrast, the predicted functional communities of bacterioplankton remain relatively stable that most of predicted functional categories including methane and nitrogen metabolisms have no significant variation after impoundment. Besides, significant distance decay patterns appear on the taxonomic communities after impoundment rather than the predicted functional communities. The environmental variables show significant impacts on the taxonomic community rather than predicted functional community, whereas the spatial variables have no effect on both taxonomic and predicted functional communities. In general, the taxonomic and predicted functional communities of bacterioplankton exhibit divergent responses to the impoundment in reservoir.
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Affiliation(s)
- Yu Wang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Lunhui Lu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Fei Ye
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China.
| | - Zhe Li
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China.
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Mayr MJ, Besemer K, Sieczko A, Demeter K, Peduzzi P. Bacterial community composition and function along spatiotemporal connectivity gradients in the Danube floodplain (Vienna, Austria). AQUATIC SCIENCES 2020; 82:28. [PMID: 32165802 PMCID: PMC7045780 DOI: 10.1007/s00027-020-0700-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 01/02/2020] [Indexed: 05/25/2023]
Abstract
It is well recognized that river-floodplain systems contribute significantly to riverine ecosystem metabolism, and that bacteria are key players in the aquatic organic carbon cycle, but surprisingly few studies have linked bacterial community composition (BCC), function and carbon quality in these hydrologically highly dynamic habitats. We investigated aquatic BCC and extracellular enzymatic activity (EEA) related to dissolved organic carbon quality and algae composition, including the impact of a major flood event in one of the last remaining European semi-natural floodplain-systems. We found that surface connectivity of floodplain pools homogenizes BCC and EEA, whereas low connectivity led to increased BCC and EEA heterogeneity, supported by their relationship to electrical conductivity, an excellent indicator for surface connection strength. Hydrogeochemical parameters best explained variation of both BCC and EEA, while the algal community and chromophoric DOM properties explained only minor fractions of BCC variation. We conclude that intermittent surface connectivity and especially permanent isolation of floodplain pools from the main river channel may severely alter BCC and EEA, with potential consequences for nutrient cycling, ecological services and greenhouse gas emissions. Disentangling microbial structure-function coupling is therefore crucial, if we are to understand and predict the consequences of human alterations on these dynamic systems.
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Affiliation(s)
- Magdalena J. Mayr
- Department of Limnology and Oceanography, University of Vienna, Althanstrasse 14, 1090 Wien, Austria
| | - Katharina Besemer
- WasserCluster Lunz, Dr. Carl Kupelwieser Promenade 5, 3293 Lunz Am See, Austria
| | - Anna Sieczko
- Department of Limnology and Oceanography, University of Vienna, Althanstrasse 14, 1090 Wien, Austria
- Department of Thematic Studies–Environmental Change, Linköping University, Tema M, Campus Valla, 581 83 Linköping, Sweden
| | - Katalin Demeter
- Department of Limnology and Oceanography, University of Vienna, Althanstrasse 14, 1090 Wien, Austria
| | - Peter Peduzzi
- Department of Limnology and Oceanography, University of Vienna, Althanstrasse 14, 1090 Wien, Austria
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Zhao W, Wang J, Xu S, Lei Y, Yang R, Shi L, Wang X, Huang Z. Bacterioplankton community variation in Bohai Bay (China) is explained by joint effects of environmental and spatial factors. Microbiologyopen 2020; 9:e997. [PMID: 32022464 PMCID: PMC7142376 DOI: 10.1002/mbo3.997] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/23/2019] [Accepted: 12/31/2019] [Indexed: 02/01/2023] Open
Abstract
Parsing the relative importance of environmental (recent disturbances) and spatial factors (historical processes) in determining community structure is a core issue in ecology. The Bohai Bay is a typical semi‐enclosed bay located in the north of China, surrounding by the metropolitan area with anthropogenic disturbances made it a complex marine coastal system with pollution gradients, where the distributions and determinants of bacterioplankton communities remain unclear. In this study, we collected surface water samples from 19 sites across Bohai Bay at about 100 km scale to investigate the relative roles of local environments and regional spatial factors in shaping bacterioplankton community composition (BCC). The environmental parameters in the sampling region showed gradient change according to the geographic variation. Several abundant OTUs were significantly correlated with the pollution parameters in the studied area, and 16 OTUs of them showed distinct distribution pattern in different polluted regions with obvious geographic segmentation, which indicated the effects of pollution gradient and dispersal limitation on specific taxon. The BCCs did not show obviously clustering effect between different polluted regions, which indicated the complexity for explaining the BCC variation in the studied region. The partial Mantel test revealed stronger spatial effects on beta diversity than those of local environmental factors, which indicated that dispersal limitation accounted more for the beta diversity than environmental heterogeneity. Furthermore, variation partitioning analysis (VPA) conducted by combining the environmental variables, linear trends, and principal coordinates of the variables from neighbor matrices (PCNM) showed that it was the joint effects of environmental and spatial factors contributed to the explained variation of BCC in the studied area. Considering the special human geography characteristics of Bohai Bay, the unmeasured biotic/abiotic factors, stochastic factors, and anthropogenic disturbances may be responsible for the unexplained variation of the BCC.
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Affiliation(s)
- Wei Zhao
- Tianjin Key Laboratory of Industrial Biological Systems and Process Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jingjing Wang
- Tianjin Key Laboratory of Industrial Biological Systems and Process Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Song Xu
- Tianjin Key Laboratory of Industrial Biological Systems and Process Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yu Lei
- Core Facility, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Rong Yang
- Tianjin Key Laboratory of Industrial Biological Systems and Process Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Liuyang Shi
- Tianjin Key Laboratory of Industrial Biological Systems and Process Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xingbiao Wang
- Tianjin Key Laboratory of Industrial Biological Systems and Process Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Zhiyong Huang
- Tianjin Key Laboratory of Industrial Biological Systems and Process Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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Hu A, Wang H, Cao M, Rashid A, Li M, Yu CP. Environmental Filtering Drives the Assembly of Habitat Generalists and Specialists in the Coastal Sand Microbial Communities of Southern China. Microorganisms 2019; 7:microorganisms7120598. [PMID: 31766562 PMCID: PMC6955893 DOI: 10.3390/microorganisms7120598] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/18/2019] [Accepted: 11/20/2019] [Indexed: 11/16/2022] Open
Abstract
Coastal sands harbor diverse microbial assemblages that play a critical role in the biogeochemical cycling of beach ecosystems. However, little is known about the relative importance of the different ecological processes underlying the assembly of communities of sand microbiota. Here, we employed 16S rDNA amplicon sequencing to investigate the sand microbiota of two coastal beaches, in southern China. The results showed that sand microbial assemblages at intertidal and supratidal zones exhibited contrasting compositions that can be attributed to environmental filtering by electric conductivity. A consistent pattern of habitat generalists and specialists of sand microbiota was observed among different beach zones. Null and neutral model analyses indicated that the environmental filtering was mainly responsible for supratidal microbial communities, while the neutral processes could partially influence the assembly of intertidal communities. Moreover, environmental filtering was found to shape the habitat specialists, while random dispersal played a major role in shaping generalists. The neutral model analysis revealed that the habitat generalists exceeding the neutral prediction harbored a relatively higher proportion of microbial taxa than the specialist counterparts. An opposite pattern was observed for taxa falling below the neutral prediction. Collectively, these findings offer a novel insight into the assembly mechanisms of coastal sand microbiota.
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Affiliation(s)
- Anyi Hu
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (H.W.); (M.C.); (A.R.); (C.-P.Y.)
- Correspondence: (A.H.); (M.L.); Tel.: +86-592-6190582 (A.H.); +86-596-2591356 (M.L.)
| | - Hongjie Wang
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (H.W.); (M.C.); (A.R.); (C.-P.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meixian Cao
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (H.W.); (M.C.); (A.R.); (C.-P.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Azhar Rashid
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (H.W.); (M.C.); (A.R.); (C.-P.Y.)
- Nuclear Institute for Food and Agriculture, Tarnab, Peshawar 446, Pakistan
| | - Mingfeng Li
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou 363000, China
- Correspondence: (A.H.); (M.L.); Tel.: +86-592-6190582 (A.H.); +86-596-2591356 (M.L.)
| | - Chang-Ping Yu
- CAS Key Laboratory of Urban pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (H.W.); (M.C.); (A.R.); (C.-P.Y.)
- Graduate Institute of Environmental Engineering, National Taiwan University, Taipei 106, Taiwan
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40
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Liu M, Sui X, Hu Y, Feng F. Microbial community structure and the relationship with soil carbon and nitrogen in an original Korean pine forest of Changbai Mountain, China. BMC Microbiol 2019; 19:218. [PMID: 31519147 PMCID: PMC6743161 DOI: 10.1186/s12866-019-1584-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 08/28/2019] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND The broad-leaved Korean pine mixed forest is an important and typical component of a global temperate forest. Soil microbes are the main driver of biogeochemical cycling in this forest ecosystem and have complex interactions with carbon (C) and nitrogen (N) components in the soil. RESULTS We investigated the vertical soil microbial community structure in a primary Korean pine-broadleaved mixed forest in Changbai Mountain (from 699 to 1177 m) and analyzed the relationship between the microbial community and both C and N components in the soil. The results showed that the total phospholipid fatty acid (PLFA) of soil microbes and Gram-negative bacteria (G-), Gram-positive bacteria (G+), fungi (F), arbuscular mycorrhizal fungi (AMF), and Actinomycetes varied significantly (p < 0.05) at different sites (elevations). The ratio of fungal PLFAs to bacterial PLFAs (F/B) was higher at site H1, and H2. The relationship between microbial community composition and geographic distance did not show a distance-decay pattern. The coefficients of variation for bacteria were maximum among different sites (elevations). Total soil organic carbon (TOC), total nitrogen (TN), soil water content (W), and the ratio of breast-height basal area of coniferous trees to that of broad-leaved tree species (RBA) were the main contributors to the variation observed in each subgroup of microbial PLFAs. The structure equation model showed that TOC had a significant direct effect on bacterial biomass and an indirect effect upon bacterial and fungal biomass via soil readily oxidized organic carbon (ROC). No significant relationship was observed between soil N fraction and the biomass of fungi and bacteria. CONCLUSION The total PLFAs (tPLFA) and PLFAs of soil microbes, including G-, G+, F, AMF, and Actinomycetes, were significantly affected by elevation. Bacteria were more sensitive to changes in elevation than other microbes. Environmental heterogeneity was the main factor affecting the geographical distribution pattern of microbial community structure. TOC, TN, W and RBA were the main driving factors for the change in soil microbial biomass. C fraction was the main factor affecting the biomass of fungi and bacteria and ROC was one of the main sources of the microbial-derived C pool.
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Affiliation(s)
- Minghui Liu
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Xin Sui
- College of Life Science, Heilongjiang University, Harbin, 150080, China
| | - Yanbo Hu
- Northeast Forestry University, Harbin, 150040, China
| | - Fujuan Feng
- College of Life Science, Northeast Forestry University, Harbin, 150040, China.
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41
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Zhang JH, Yu N, Xu XX, Liu ZW. Community structure, dispersal ability and functional profiling of microbiome existing in fat body and ovary of the brown planthopper, Nilaparvata lugens. INSECT SCIENCE 2019; 26:683-694. [PMID: 29425401 DOI: 10.1111/1744-7917.12575] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/15/2018] [Accepted: 02/04/2018] [Indexed: 06/08/2023]
Abstract
The endosymbionts play vital roles in growth, development and reproduction in insects. Yeast-like endosymbionts (YLSs) have been well studied in Nilaparvata lugens (N. lugens), but little is known about the tissue-specific bacterial microbiomes, especially on the microbial intersection among internal tissues. Here, the correlation of microbial composition, structure, dispersal ability and functional profiling were illuminated in two tissues, the fat body and ovary in N. lugens. A total of 11 phyla and 105 genera were captured from all samples; Firmicutes and Proteobacteria were the most predominant and accounted for more than 99% in all samples. However, the relative abundance of Firmicutes and Proteobacteria was significantly different in ovary and fat body through Fisher's Least Significant Difference test. Microbial diversity but not the richness index in the two tissues exhibited significant difference. Furthermore, the microbial community structure of the ovary and fat body were primarily determined by tissue quality. Firmicutes showed strong dispersal ability between ovary and fat body based on the quantitative null model assessing, indicating the frequent interaction of these microbiomes in the two tissues. In addition, the Kyoto Encyclopedia of Genes and Genomes pathways of microbial participation were delineated. The ten most abundant pathways counted for over 46% of the annotation and were shared between the two tissues, mainly containing Energy Metabolism and Amino Acid Metabolism/Biosynthesis. The results will provide insights into the correlation of microbial community structure between ovary and fat body of N. lugens.
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Affiliation(s)
- Jian-Hua Zhang
- Key laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Na Yu
- Key laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Xi-Xia Xu
- Key laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ze-Wen Liu
- Key laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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42
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Kavazos CRJ, Huggett MJ, Mueller U, Horwitz P. Bacterial and ciliate biofilm community structure at different spatial levels of a salt lake meta-community. FEMS Microbiol Ecol 2019; 94:5066167. [PMID: 30124812 DOI: 10.1093/femsec/fiy148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 08/01/2018] [Indexed: 11/14/2022] Open
Abstract
Meta-communities are assembled along an ecological scale that determines local and regional diversity. Spatial patterns have been detected in planktonic bacterial communities at distances <20 m, but little is known about the occurrence of similar variation for other microbial groups and changes in microbial meta-community assembly at different levels of a meta-community. To examine this variation, the biofilm of eight saline ponds were used to investigate processes shaping diversity within ponds (β) and between ponds (δ). Bacterial and ciliate communities were assessed using ARISA and T-RFLP respectively, while diversity partitioning methods were used to examine the importance of taxonomic turnover and variation partitioning was used to distinguish spatial from environmental determinants. The results show that turnover is important for determining β- and δ-diversity of biofilms. Spatial factors are important drivers of bacterial β-diversity but were unimportant for ciliate β-diversity. Environmental variation was a strong determinant of bacterial and ciliate δ-diversity, suggesting sorting processes are important for assembling pond communities. Determinants of diversity in bacteria are not universal for ciliates, suggesting higher functional redundancy of bacteria or the greater niche breadth of ciliates may be important in discriminating assembly processes between the two organisms.
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Affiliation(s)
- Christopher R J Kavazos
- Centre for Ecosystem Management, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - Megan J Huggett
- Centre for Ecosystem Management, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia.,Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia.,School of Environmental and Life Sciences, The University of Newcastle, 10 Chittaway Dr, Ourimbah, NSW 2258, Australia
| | - Ute Mueller
- Centre for Ecosystem Management, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia.,Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - Pierre Horwitz
- Centre for Ecosystem Management, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
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43
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Fiddler crab bioturbation determines consistent changes in bacterial communities across contrasting environmental conditions. Sci Rep 2019; 9:3749. [PMID: 30842580 PMCID: PMC6403291 DOI: 10.1038/s41598-019-40315-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/08/2019] [Indexed: 11/25/2022] Open
Abstract
Ecosystem functions are regulated by compositional and functional traits of bacterial communities, shaped by stochastic and deterministic processes. Biogeographical studies have revealed microbial community taxonomy in a given ecosystem to change alongside varying environmental characteristics. Considering that stable functional traits are essential for community stability, we hypothesize that contrasting environmental conditions affect microbial taxonomy rather than function in a model system, testing this in three geographically distinct mangrove forests subjected to intense animal bioturbation (a shared deterministic force). Using a metabarcoding approach combined with sediment microprofiling and biochemistry, we examined vertical and radial sediment profiles of burrows belonging to the pantropical fiddler crab (subfamily Gelasiminae) in three contrasting mangrove environments across a broad latitudinal range (total samples = 432). Each mangrove was environmentally distinct, reflected in taxonomically different bacterial communities, but communities consistently displayed the same spatial stratification (a halo effect) around the burrow which invariably determined the retention of similar inferred functional community traits independent of the local environment.
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44
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Habtom H, Pasternak Z, Matan O, Azulay C, Gafny R, Jurkevitch E. Applying microbial biogeography in soil forensics. Forensic Sci Int Genet 2018; 38:195-203. [PMID: 30447564 DOI: 10.1016/j.fsigen.2018.11.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 10/10/2018] [Accepted: 11/07/2018] [Indexed: 11/28/2022]
Abstract
The ubiquity, heterogeneity and transferability of soil makes it useful as evidence in criminal investigations, especially using new methods that survey the microbial DNA it contains. However, to be used effectively and reliably, more needs to be learned about the natural distribution patterns of microbial communities in soil. In this study we examine these patterns in detail, at local to regional scales (2 m-260 km), across an environmental gradient in three different soil types. Geographic location was found to be more important than soil type in determining the microbial community composition: communities from the same site but different soil types, although significantly different from each other, were still much more similar to each other than were communities from the same soil type but from different sites. At a local scale (25-1000 m), distance-decay relationships were observed in all soil types: the farther apart two soil communities were located, even in the same soil type, the more they differed. At regional-scale distances (1-260 km), differences between communities did not increase with increased geographic distance between them, and the dominant factor determining the community profile was the physico-chemical environment, most notably annual precipitation (R2 = 0.69), soil sodium (R2 = 0.49) and soil ammonium (R2 = 0.47) levels. We introduce a likelihood-ratio framework for quantitative evaluation of soil microbial DNA profile evidence in casework. In conclusion, these profiles, along with detailed knowledge of natural soil microbial biogeography, provide valuable forensic information on soil sample comparison and allow the determination of approximate source location on large (hundreds of km) spatial scales. Moreover, at small spatial scales it may enable pinpointing the source location of a sample to within at least 25 m, regardless of soil type and environmental conditions.
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Affiliation(s)
- Habteab Habtom
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Zohar Pasternak
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Ofra Matan
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Chen Azulay
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ron Gafny
- Forensic Biology Laboratory, Division of Identification and Forensic Science, Israel Police, National Headquarters, Haim Bar-Lev Road, Jerusalem, Israel
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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Hu A, Li S, Zhang L, Wang H, Yang J, Luo Z, Rashid A, Chen S, Huang W, Yu CP. Prokaryotic footprints in urban water ecosystems: A case study of urban landscape ponds in a coastal city, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 242:1729-1739. [PMID: 30064876 DOI: 10.1016/j.envpol.2018.07.097] [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: 01/30/2018] [Revised: 07/19/2018] [Accepted: 07/22/2018] [Indexed: 06/08/2023]
Abstract
The urban water ecosystems, such as the landscape ponds are commonly considered under the influence of anthropogenic disturbances, which can lead to the deterioration of the water quality. The prokaryotic communities are considered as one of the best indicators of the water quality. However, there are significant gaps in understanding the ecological processes that shape the composition and function of prokaryotic communities in the urban water ecosystems. Here, we investigated the biogeographic distribution of prokaryotic assemblages in water environments including landscape ponds, drinking water reservoirs, influents (IFs) and effluents (EFs) of wastewater treatment plants of a coastal city (Xiamen), China, by using 16S rDNA amplicon sequencing. Our results indicated that the ponds had higher α-diversity of prokaryotic communities than those in the reservoirs, while there were significant variations in the community compositions among ponds, reservoirs, IFs and EFs. Moreover, ponds harbored a significantly higher proportion of sewage- and fecal-indicator taxa than those in the reservoirs, suggesting the occurrence of exogenous pollution in the urban ponds. Null model analysis revealed that dispersal limitation was the main ecological processes resulting in the divergence of prokaryotic community compositions between ponds and other environments, while dispersal limitation and variable selection played an essential role in the formation of unique prokaryotic assemblages in the reservoirs. Function predication analysis demonstrated that the ponds shared more similar functional profiles with IFs or EFs (e.g., chemoheterotrophy, fermentation, chlorate reducers, nitrate reduction and respiration) than the reservoirs, whereas dominance of photoautotrophy was observed in the reservoirs. Overall, this study provides a profound insight of the ecological mechanisms underlying the responses of prokaryotic communities in the urban landscape ponds to the anthropogenic disturbances.
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Affiliation(s)
- Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| | - Shuang Li
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lanping Zhang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongjie Wang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Zhuanxi Luo
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Azhar Rashid
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Nuclear Institute for Food and Agriculture, Tarnab, Peshawar, Pakistan
| | - Shaoqing Chen
- Village Planning and Construction Management Station of Jimei District, Xiamen 361022, China
| | - Weixiong Huang
- Xinglin Construction and Development Co. LTD., Xiamen 361022, China
| | - Chang-Ping Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Graduate Institute of Environmental Engineering, National Taiwan University, Taipei 106, Taiwan
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46
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Hernando-Morales V, Varela MM, Needham DM, Cram J, Fuhrman JA, Teira E. Vertical and Seasonal Patterns Control Bacterioplankton Communities at Two Horizontally Coherent Coastal Upwelling Sites off Galicia (NW Spain). MICROBIAL ECOLOGY 2018; 76:866-884. [PMID: 29675703 DOI: 10.1007/s00248-018-1179-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 03/14/2018] [Indexed: 06/08/2023]
Abstract
Analysis of seasonal patterns of marine bacterial community structure along horizontal and vertical spatial scales can help to predict long-term responses to climate change. Several recent studies have shown predictable seasonal reoccurrence of bacterial assemblages. However, only a few have assessed temporal variability over both horizontal and vertical spatial scales. Here, we simultaneously studied the bacterial community structure at two different locations and depths in shelf waters of a coastal upwelling system during an annual cycle. The most noticeable biogeographic patterns observed were seasonality, horizontal homogeneity, and spatial synchrony in bacterial diversity and community structure related with regional upwelling-downwelling dynamics. Water column mixing eventually disrupted bacterial community structure vertical heterogeneity. Our results are consistent with previous temporal studies of marine bacterioplankton in other temperate regions and also suggest a marked influence of regional factors on the bacterial communities inhabiting this coastal upwelling system. Bacterial-mediated carbon fluxes in this productive region appear to be mainly controlled by community structure dynamics in surface waters, and local environmental factors at the base of the euphotic zone.
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Affiliation(s)
- Víctor Hernando-Morales
- Grupo de Oceanografía Biolóxica, Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, 36310, Vigo, Spain.
- Estación de Ciencias Mariñas de Toralla (ECIMAT), Universidade de Vigo, Illa de Toralla, 36331, Vigo, Spain.
| | - Marta M Varela
- IEO, Instituto Español de Oceanografía, Centro Oceanográfico de A Coruña, Apdo 130, 15080, A Coruña, Spain
| | - David M Needham
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-0371, USA
| | - Jacob Cram
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-0371, USA
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-0371, USA
| | - Eva Teira
- Grupo de Oceanografía Biolóxica, Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, 36310, Vigo, Spain
- Estación de Ciencias Mariñas de Toralla (ECIMAT), Universidade de Vigo, Illa de Toralla, 36331, Vigo, Spain
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47
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Kong Z, Kou W, Ma Y, Yu H, Ge G, Wu L. Seasonal dynamics of the bacterioplankton community in a large, shallow, highly dynamic freshwater lake. Can J Microbiol 2018; 64:786-797. [DOI: 10.1139/cjm-2018-0126] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The spatiotemporal shifts of the bacterioplankton community can mirror their transition of functional traits in an aquatic ecosystem. However, the spatiotemporal variation of the bacterioplankton community composition structure (BCCS) within a large, shallow, highly dynamic freshwater lake is still poorly understood. Here, we examined the seasonal and spatial variability of the BCCs within Poyang Lake by sequencing the 16S rRNA gene amplicon to explore how hydrological changes affect the BCCs. Principal coordinate analysis showed that the BCCs varied significantly among four sampling seasons, but not spatially. The seasonal changes of the BCCs were mainly attributed to the differences between autumn and spring–winter. Higher α diversity indices were observed in autumn. Redundancy analysis indicated that the BCCs co-variated with water level, pH, temperature, total phosphorus, ammoniacal nitrogen, electrical conductivity, total nitrogen, and turbidity. Among them, water level was the key determinant separating autumn BCCs from the BCCs in other seasons. A significantly lower relative abundance of Burkholderiales (betI and betVII) and a higher relative abundance of Actinomycetales (acI, acTH1, and acTH2) were found in autumn than in other seasons. Overall, our results suggest that water level changes associated with pH, temperature, and nutrient status shaped the seasonal patterns of the BCCs within Poyang Lake.
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Affiliation(s)
- Zhaoyu Kong
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330031, China
- Key Laboratory of Aquatic Resources and Utilization of Jiangxi, Nanchang University, Nanchang 330022, China
| | - Wenbo Kou
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330031, China
| | - Yantian Ma
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330031, China
| | - Haotian Yu
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330031, China
| | - Gang Ge
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330031, China
| | - Lan Wu
- School of Life Science, Key Laboratory of Poyang Lake Environment and Resource Utilization, Ministry of Education, Nanchang University, Nanchang 330031, China
- Key Laboratory of Aquatic Resources and Utilization of Jiangxi, Nanchang University, Nanchang 330022, China
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48
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Obertegger U, Bertilsson S, Pindo M, Larger S, Flaim G. Temporal variability of bacterioplankton is habitat driven. Mol Ecol 2018; 27:4322-4335. [PMID: 30176079 DOI: 10.1111/mec.14855] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 08/24/2018] [Accepted: 08/29/2018] [Indexed: 11/27/2022]
Abstract
Temporal dynamics of bacterioplankton are rarely investigated for multiple habitats and years within individual lakes, limiting our understanding of the variability of bacterioplankton community (BC) composition with respect to environmental factors. We assessed the BC composition of a littoral and two pelagic habitats (euphotic zone and hypolimnion) of Lake Tovel monthly from April 2014 to May 2017 by high-throughput sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. The three habitats differed in temperature, light, oxygen and hydrology. In particular, the littoral was the most hydrologically unstable because it receives most of the lake inflow, the hypolimnion was the most stable because of its hydrologically sheltered position, and the pelagic euphotic habitat was intermediate. Consequently, we hypothesized different temporal patterns of BC composition for all three habitats according to their environmental differences. We applied PERMANOVA, nonmetric multidimensional scaling and source-sink analysis to characterize BC composition. Overall, BCs were different among habitats with the littoral showing the highest variability and the hypolimnion the highest stability. The BC of rainy 2014 was distinct from the BCs of other years irrespective of the habitats considered. Seasonal differences in BCs were limited to spring, probably linked to meltwater inflow and mixing. Thus, temporal effects related to year and season were linked to the hydrological gradient of habitats. We suggest that despite potential within-lake dispersal of bacterioplankton by water flow and mixing, local environmental conditions played a major role in Lake Tovel, fostering distinct BCs in the three habitats.
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Affiliation(s)
- Ulrike Obertegger
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Stefan Bertilsson
- Limnology and Science for Life Laboratory, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Massimo Pindo
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Simone Larger
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Giovanna Flaim
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
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49
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Orland C, Emilson EJS, Basiliko N, Mykytczuk NCS, Gunn JM, Tanentzap AJ. Microbiome functioning depends on individual and interactive effects of the environment and community structure. ISME JOURNAL 2018; 13:1-11. [PMID: 30042502 DOI: 10.1038/s41396-018-0230-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/15/2018] [Accepted: 06/20/2018] [Indexed: 01/16/2023]
Abstract
How ecosystem functioning changes with microbial communities remains an open question in natural ecosystems. Both present-day environmental conditions and historical events, such as past differences in dispersal, can have a greater influence over ecosystem function than the diversity or abundance of both taxa and genes. Here, we estimated how individual and interactive effects of microbial community structure defined by diversity and abundance, present-day environmental conditions, and an indicator of historical legacies influenced ecosystem functioning in lake sediments. We studied sediments because they have strong gradients in all three of these ecosystem properties and deliver important functions worldwide. By characterizing bacterial community composition and functional traits at eight sites fed by discrete and contrasting catchments, we found that taxonomic diversity and the normalized abundance of oxidase-encoding genes explained as much variation in CO2 production as present-day gradients of pH and organic matter quantity and quality. Functional gene diversity was not linked to CO2 production rates. Surprisingly, the effects of taxonomic diversity and normalized oxidase abundance in the model predicting CO2 production were attributable to site-level differences in bacterial communities unrelated to the present-day environment, suggesting that colonization history rather than habitat-based filtering indirectly influenced ecosystem functioning. Our findings add to limited evidence that biodiversity and gene abundance explain patterns of microbiome functioning in nature. Yet we highlight among the first time how these relationships depend directly on present-day environmental conditions and indirectly on historical legacies, and so need to be contextualized with these other ecosystem properties.
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Affiliation(s)
- Chloé Orland
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Downing Street, CB2 3EA, Cambridge, UK.
| | - Erik J S Emilson
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Downing Street, CB2 3EA, Cambridge, UK.,Natural Resources Canada, Great Lakes Forestry Centre, 1219 Queen St. E., Sault. Ste. Marie, ON, P6A 2E5, Canada
| | - Nathan Basiliko
- Vale Living with Lakes Centre, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, Canada, P3E 2C6
| | - Nadia C S Mykytczuk
- Vale Living with Lakes Centre, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, Canada, P3E 2C6
| | - John M Gunn
- Vale Living with Lakes Centre, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, Canada, P3E 2C6
| | - Andrew J Tanentzap
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Downing Street, CB2 3EA, Cambridge, UK
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Souffreau C, Busschaert P, Denis C, Van Wichelen J, Lievens B, Vyverman W, De Meester L. A comparative hierarchical analysis of bacterioplankton and biofilm metacommunity structure in an interconnected pond system. Environ Microbiol 2018; 20:1271-1282. [PMID: 29441664 DOI: 10.1111/1462-2920.14073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 02/11/2018] [Indexed: 11/30/2022]
Abstract
It is unknown whether bacterioplankton and biofilm communities are structured by the same ecological processes, and whether they influence each other through continuous dispersal (known as mass effects). Using a hierarchical sampling approach we compared the relative importance of ecological processes structuring the dominant fraction (relative abundance ≥0.1%) of bacterioplankton and biofilm communities from three microhabitats (open water, Nuphar and Phragmites sites) at within- and among-pond scale in a set of 14 interconnected shallow ponds. Our results demonstrate that while bacterioplankton and biofilm communities are highly distinct, a similar hierarchy of ecological processes is acting on them. For both community types, most variation in community composition was determined by pond identity and environmental variables, with no effect of space. The highest β-diversity within each community type was observed among ponds, while microhabitat type (Nuphar, Phragmites, open water) significantly influenced biofilm communities but not bacterioplankton. Mass effects among bacterioplankton and biofilm communities were not detected, as suggested by the absence of within-site covariation of biofilm and bacterioplankton communities. Both biofilm and plankton communities were thus highly structured by environmental factors (i.e., species sorting), with among-lake variation being more important than within-lake variation, whereas dispersal limitation and mass effects were not observed.
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Affiliation(s)
- Caroline Souffreau
- Laboratory of Aquatic Ecology Evolution & Conservation, KU Leuven, Leuven, Belgium
| | - Pieter Busschaert
- Laboratory for Process Microbial Ecology and Bioinspirational Management, KU Leuven, Campus De Nayer, St.-Katelijne-Waver, Belgium
| | - Carla Denis
- Laboratory of Aquatic Ecology Evolution & Conservation, KU Leuven, Leuven, Belgium
| | - Jeroen Van Wichelen
- Laboratory of Protistology and Aquatic Ecology, Ghent University, Gent, Belgium.,Research Institute for Nature and Forest (INBO), Brussels, Belgium
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management, KU Leuven, Campus De Nayer, St.-Katelijne-Waver, Belgium
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Ghent University, Gent, Belgium
| | - Luc De Meester
- Laboratory of Aquatic Ecology Evolution & Conservation, KU Leuven, Leuven, Belgium
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