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El-Malah SS, Rasool K, Jabbar KA, Sohail MU, Baalousha HM, Mahmoud KA. Marine Bacterial Community Structures of Selected Coastal Seawater and Sediment Sites in Qatar. Microorganisms 2023; 11:2827. [PMID: 38137970 PMCID: PMC10745943 DOI: 10.3390/microorganisms11122827] [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: 10/15/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 12/24/2023] Open
Abstract
Severe environmental conditions can have a diverse impact on marine microorganisms, including bacteria. This can have an inevitable impact on the biofouling of membrane-based desalination plants. In this work, we have utilized indicator bacteria such as total coliform, fecal coliform, and Pseudomonas aeruginosa, as well as 16S rRNA sequencing, to investigate the impact of environmental conditions and spatial variations on the diversity of bacterial communities in the coastal waters and sediments from selected sites in Qatar. The concentration levels of indicator bacteria were affected by increasing temperatures and pH, and by decreasing salinity of seawater samples. Diversity indices and the molecular phylogeny demonstrated that Proteobacteria, Bacteroidetes, and Cyanobacteria were the dominant phyla in all locations. The most abundant operational taxonomic units (OTUs) at the family level were from Flavobacteriaceae (27.07%, 4.31%) and Rhodobacteraceae (22.51%, 9.86%) in seawater and sediment, respectively. Alphaproteobacteria (33.87%, 16.82%), Flavobacteria (30.68%, 5.84%), and Gammaproteobacteria (20.35%, 12.45%) were abundant at the species level in both seawater and sediment, while Clostridia (13.72%) was abundant in sediment only. The results suggest that sediment can act as a reservoir for indicator bacteria, with higher diversity and lower abundance compared to seawater.
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Affiliation(s)
- Shimaa S. El-Malah
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, Doha P.O. Box 34110, Qatar; (S.S.E.-M.); (K.R.); (K.A.J.)
| | - Kashif Rasool
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, Doha P.O. Box 34110, Qatar; (S.S.E.-M.); (K.R.); (K.A.J.)
| | - Khadeeja Abdul Jabbar
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, Doha P.O. Box 34110, Qatar; (S.S.E.-M.); (K.R.); (K.A.J.)
| | | | - Husam Musa Baalousha
- Department of Geosciences, College of Petroleum Engineering and Geosciences, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia;
| | - Khaled A. Mahmoud
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, Doha P.O. Box 34110, Qatar; (S.S.E.-M.); (K.R.); (K.A.J.)
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2
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Doane MP, Ostrowski M, Brown M, Bramucci A, Bodrossy L, van de Kamp J, Bissett A, Steinberg P, Doblin MA, Seymour J. Defining marine bacterioplankton community assembly rules by contrasting the importance of environmental determinants and biotic interactions. Environ Microbiol 2023. [PMID: 36700447 DOI: 10.1111/1462-2920.16341] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/17/2023] [Indexed: 01/27/2023]
Abstract
Bacterioplankton communities govern marine productivity and biogeochemical cycling, yet drivers of bacterioplankton assembly remain unclear. Here, we contrast the relative contribution of deterministic processes (environmental factors and biotic interactions) in driving temporal dynamics of bacterioplankton diversity at three different oceanographic time series locations, spanning 15° of latitude, which are each characterized by different environmental conditions and varying degrees of seasonality. Monthly surface samples (5.5 years) were analysed using 16S rRNA amplicon sequencing. The high- and mid-latitude sites of Maria Island and Port Hacking were characterized by high and intermediate levels of environmental heterogeneity, respectively, with both alpha diversity (72%; 24% of total variation) and beta diversity (32%; 30%) patterns within bacterioplankton assemblages explained by day length, ammonium, and mixed layer depth. In contrast, North Stradbroke Island, a sub-tropical location where environmental conditions are less variable, interspecific interactions were of increased importance in structuring bacterioplankton diversity (alpha: 33%; beta: 26%) with environment only contributing 11% and 13% to predicting diversity, respectively. Our results demonstrate that bacterioplankton diversity is the result of both deterministic environmental and biotic processes and that the importance of these different deterministic processes varies, potential in response to environmental heterogeneity.
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Affiliation(s)
- Michael P Doane
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Martin Ostrowski
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia.,Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Mark Brown
- School of Environmental and Life Sciences, University of Newcastle Australia, Callaghan, New South Wales, Australia
| | - Anna Bramucci
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia
| | | | | | | | - Peter Steinberg
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia.,Centre for Marine Science and Innovation, University of New South Wales, Sydney, New South Wales, Australia
| | - Martina A Doblin
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia.,Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Justin Seymour
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia
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3
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Bouchali R, Mandon C, Marti R, Michalon J, Aigle A, Marjolet L, Vareilles S, Kouyi GL, Polomé P, Toussaint JY, Cournoyer B. Bacterial assemblages of urban microbiomes mobilized by runoff waters match land use typologies and harbor core species involved in pollutant degradation and opportunistic human infections. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:152662. [PMID: 34963611 DOI: 10.1016/j.scitotenv.2021.152662] [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: 09/02/2021] [Revised: 11/23/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
Cities are patchworks of urban catchments divided into functional units according to their commercial, residential and industrial activities, and socio-urbanistic patterns. The hypothesis of city surface microbiomes being structured by socio-urbanistic variables leading to an emergence of synurbic taxa was tested. According to the r/K microbial ecology theory, a gradient of well-adapted synurbic K-strategists and of opportunistic -r-strategists should occur over city surfaces. K-strategists would be core components while r-ones would be transiently detected. To resolve these patterns, sub-catchments (n = 21) of an area of high commercial and industrial activities were investigated over three time periods covering one year. The sub-catchments' land use patterns and associated human behaviors were converted into socio-urbanistic variables and groupings. Bacterial cells mobilized by runoffs per sub-catchment were recovered, and analyzed by classical approaches, microbial source tracking DNA assays and DNA meta-barcoding approaches. Relationships between these datasets, the runoff physico-chemical properties, and descriptors of the socio-urbanistic groupings were investigated. 16S rRNA meta-barcoding analyses showed evidence of the occurrence of K- and r-like strategists. Twenty-eight core genera were identified, and correlation networks revealed large bacterial modules organized around actinobacterial taxa involved in hydrocarbon degradation processes. Other bacterial networks were related to the occurrences of hygienic wastes, and involved bacteria originating from fecal contaminations. Several r-strategists like Sulfurospirillum were recorded and found associated to point source pollutions. The tpm-metabarcoding approach deciphered these r / K strategists at the species level among more than ten genera. Nine core K-like Pseudomomas species were identified. The P. aeruginosa human opportunistic pathogen and P. syringae phytopathogens were part of these K-strategists. Other tpm-harboring bacterial pathogens showed r-like opportunistic distribution patterns. Correlation network analyses indicated a strong incidence of hygienic wastes and hydrocarbon-pollutions on tpm-harboring bacteria. These analyses demonstrated the occurrence of core synurbic bacterial K-strategists over city surfaces.
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Affiliation(s)
- Rayan Bouchali
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne, CNRS 5557, INRAE 1418, 69280 Marcy L'Etoile, France
| | - Claire Mandon
- Université de Lyon, INSA Lyon, UMR Environnement, Ville, Société, CNRS 5600, 18 rue Chevreul, 69362 Lyon, France
| | - Romain Marti
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne, CNRS 5557, INRAE 1418, 69280 Marcy L'Etoile, France
| | - Jérôme Michalon
- Université de Lyon, UMR Triangle, CNRS 5206 Université Jean Monnet Saint Etienne, 6 rue Basse des Rives, 42023 Saint-Etienne, France
| | - Axel Aigle
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne, CNRS 5557, INRAE 1418, 69280 Marcy L'Etoile, France
| | - Laurence Marjolet
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne, CNRS 5557, INRAE 1418, 69280 Marcy L'Etoile, France
| | - Sophie Vareilles
- Université de Lyon, INSA Lyon, UMR Environnement, Ville, Société, CNRS 5600, 18 rue Chevreul, 69362 Lyon, France
| | - Gislain Lipeme Kouyi
- Université de Lyon, INSA Lyon, DEEP, EA7429, 11 rue de la physique, 69621 Villeurbanne, France
| | - Philippe Polomé
- Université de Lyon, UMR GATE, CNRS 5824, Université Lumière Lyon 2, 93 chemin des Mouilles, 69131 Ecully, France
| | - Jean-Yves Toussaint
- Université de Lyon, INSA Lyon, UMR Environnement, Ville, Société, CNRS 5600, 18 rue Chevreul, 69362 Lyon, France
| | - Benoit Cournoyer
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne, CNRS 5557, INRAE 1418, 69280 Marcy L'Etoile, France.
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4
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Hou Y, Li B, Xu G, Li D, Zhang C, Jia R, Li Q, Zhu J. Dynamic and Assembly of Benthic Bacterial Community in an Industrial-Scale In-Pond Raceway Recirculating Culture System. Front Microbiol 2022; 12:797817. [PMID: 35003028 PMCID: PMC8733461 DOI: 10.3389/fmicb.2021.797817] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
To reduce water utilization, limit environmental pollution, and guarantee aquatic production and quality, the in-pond raceway recirculating culture system (IPRS) has been developed and is widely used. The effectiveness and sustainability of IPRSs rely on a good understanding of the ecological processes related to bacterial communities in the purification area. In this study, we investigated the dynamics and assembly mechanisms of benthic bacterial communities in the purification area of an industrial-scale IRPS. We found significant temporal and spatial variations in the sediment characteristics and benthic bacterial communities of the IPRS, although correlation analyses revealed a very limited relationship between them. Among the different culture stages, we identified numerous benthic bacteria with different abundances. Abundances of the phyla Bacteroidota and Desulfobacterota decreased whereas those of Myxococcota and Gemmatimonadota increased as the culture cycle progressed. Co-occurrence networks revealed that the bacterial community was less complex but more stable in the IPRS at the final stage compared with the initial stage. The neutral community model (NCM) showed that stochastic processes were the dominant ecological processes shaping the assembly of the benthic bacterial community. The null model suggested that homogenizing dispersal was more powerful than dispersal limitation and drift in regulating the assembly of the community. These findings indicate that the benthic microbial communities in purification areas of the IPRS may not be affected by the deposited wastes, and a more stable benthic microbial communities were formed and mainly driven by stochastic processes. However, the benthic microbial communities in the purification area at the end of the culturing stage was characterized by potentially inhibited organic matter degradation and carbon and sulfur cycling abilities, which was not corresponding to the purification area’s function. From this point on, the IPRS, especially the purification area was needed to be further optimized and improved.
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Affiliation(s)
- Yiran Hou
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Bing Li
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Gangchun Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Da Li
- Ocean and Fishery Research Institute of Rizhao, Rizhao, China
| | - Chengfeng Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Rui Jia
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Quanjie Li
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Jian Zhu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
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5
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Covington BC, Xu F, Seyedsayamdost MR. A Natural Product Chemist's Guide to Unlocking Silent Biosynthetic Gene Clusters. Annu Rev Biochem 2021; 90:763-788. [PMID: 33848426 PMCID: PMC9148385 DOI: 10.1146/annurev-biochem-081420-102432] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microbial natural products have provided an important source of therapeutic leads and motivated research and innovation in diverse scientific disciplines. In recent years, it has become evident that bacteria harbor a large, hidden reservoir of potential natural products in the form of silent or cryptic biosynthetic gene clusters (BGCs). These can be readily identified in microbial genome sequences but do not give rise to detectable levels of a natural product. Herein, we provide a useful organizational framework for the various methods that have been implemented for interrogating silent BGCs. We divide all available approaches into four categories. The first three are endogenous strategies that utilize the native host in conjunction with classical genetics, chemical genetics, or different culture modalities. The last category comprises expression of the entire BGC in a heterologous host. For each category, we describe the rationale, recent applications, and associated advantages and limitations.
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Affiliation(s)
- Brett C Covington
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA; ,
| | - Fei Xu
- Institute of Pharmaceutical Biotechnology and Department of Gastroenterology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China;
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA; ,
- Department of Molecular Biology, Princeton University, New Jersey 08544, USA
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6
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Wu X, Wang Y, Zhu Y, Tian H, Qin X, Cui C, Zhao L, Simonet P, Zhang X. Variability in the Response of Bacterial Community Assembly to Environmental Selection and Biotic Factors Depends on the Immigrated Bacteria, as Revealed by a Soil Microcosm Experiment. mSystems 2019; 4:e00496-19. [PMID: 31796565 PMCID: PMC6890929 DOI: 10.1128/msystems.00496-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 11/13/2019] [Indexed: 11/28/2022] Open
Abstract
Exploring the assembly mechanism of microbiota is critical for understanding soil ecosystem functions. However, the relative importance of different biotic and abiotic factors in determining the bacterial community has not been properly clarified. In this study, the effects of inocula and recipients on the assembly of the soil community were investigated to evaluate their importance by inoculation experiments with sterile soil. Two distinct soils, conventional nitrogen-fertilized soil and aromatic-compound-contaminated soil, were sterilized, cross inoculated, and incubated for 2 months under different inoculation doses and oxygen conditions. The results showed that the greatest variation in community structure emerged in the samples inoculated with distinct inocula rather than in the samples of different soil recipients. The phylogenies in the two inocula were diverse and dissimilar, although there were many ecologically equivalent bacteria. When the inocula with dissimilar ecologically equivalent species were used, the assembled communities were primarily determined by the inocula as indicated by the beta diversity and variation partitioning analyses. In contrast, environmental selection dominated the process when ecologically equivalent species in the inocula were similar, as when only one type of inoculum was used, where the soil habitat selected the most adaptive bacteria from the defined inoculum pool. These results indicate that inoculated bacteria are dominant over environmental selection if they are sufficiently dissimilar, although the effect of environmental selection is more obvious when similar bacteria are inoculated in the soil for community assembly. Our findings suggest that the immigration of exotic bacteria could be a primary factor impacting community assembly.IMPORTANCE The soil microbiota conducts important biological ecosystem functions, but the mechanism underlying community-environment interactions for soil microbiota remains unclear. By using two distinct soils for cross inoculation, we successfully simulated the assembly of the bacterial community in sterile soil. Thus, the reasons why inoculum and recipient have dominated community assembly in previous investigations are investigated in this study. We found that inoculated bacteria presided over environmental selection for community assembly due to the varied difference of ecological equivalent bacteria, either divergent or convergent. The significance of neutrality for the ecologically equivalent bacterial species that immigrated into the recipients should be emphasized in exploring the mechanisms of community assembly. Our finding is helpful for understanding the community-environment interaction, a basic question in ecology, and it would shed light on this issue that has perplexed scientists for many years.
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Affiliation(s)
- Xiaogang Wu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yun Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Zhu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Tian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xianchao Qin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Changzheng Cui
- School of Resource and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Liping Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Pascal Simonet
- Environmental Microbial Genomics Group, Laboratoire AMPERE, CNRS, Ecole Centrale de Lyon, Université de Lyon, Ecully, France
| | - Xiaojun Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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7
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Langenheder S, Lindström ES. Factors influencing aquatic and terrestrial bacterial community assembly. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:306-315. [PMID: 30618071 DOI: 10.1111/1758-2229.12731] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 12/26/2018] [Indexed: 05/12/2023]
Abstract
During recent years, many studies have shown that different processes including drift, environmental selection and dispersal can be important for the assembly of bacterial communities in aquatic and terrestrial ecosystems. However, we lack a conceptual overview about the ecological context and factors that influence the relative importance of the different assembly mechanisms and determine their dynamics in time and space. Focusing on free-living, i.e., nonhost associated, bacterial communities, this minireview, therefore, summarizes and conceptualizes findings from empirical studies about how (i) environmental factors, such as environmental heterogeneity, disturbances, productivity and trophic interactions; (ii) connectivity and dispersal rates (iii) spatial scale, (iv) community properties and traits and (v) the use of taxonomic/phylogenetic or functional metrics influence the relative importance of different community assembly processes. We find that there is to-date little consistency among studies and suggest that future studies should now address how (i)-(v) differ between habitats and organisms and how this, in turn, influences the temporal and spatial-scale dependency of community assembly processes in microorganisms.
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Affiliation(s)
- Silke Langenheder
- Department of Ecology and Genetics/Limnology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Eva S Lindström
- Department of Ecology and Genetics/Limnology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
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8
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Zhang FG, Bell T, Zhang QG. Experimental Testing of Dispersal Limitation in Soil Bacterial Communities with a Propagule Addition Approach. MICROBIAL ECOLOGY 2019; 77:905-912. [PMID: 30417222 DOI: 10.1007/s00248-018-1284-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 10/29/2018] [Indexed: 06/09/2023]
Abstract
The role of dispersal in the assembly of microbial communities remains contentious. This study tested the importance of dispersal limitation for the structuring of local soil bacterial communities using an experimental approach of propagule addition. Microbes extracted from soil pooled from samples collected at 20 localities across ~ 400 km in a temperate steppe were added to microcosms of local soils at three sites; the microcosms were then incubated in situ for 3 months. We then assessed the composition and diversity of bacterial taxa in the soils using 16S rRNA gene amplicon sequencing. The addition of the regional microbial pool did not cause significant changes in the overall composition or diversity of the total bacterial community, although a very small number of individual taxa may have been affected by the addition treatment. Our results suggest a negligible role of dispersal limitation in structuring soil bacterial communities in our study area.
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Affiliation(s)
- Fen-Guo Zhang
- College of Life Sciences, Shanxi Normal University, Linfen, 041004, Shanxi, China
| | - Thomas Bell
- Department of Life Sciences, Imperial College London, Ascot, Berkshire, SL5 7PY, UK
| | - Quan-Guo Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
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9
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Albright MBN, Chase AB, Martiny JBH. Experimental Evidence that Stochasticity Contributes to Bacterial Composition and Functioning in a Decomposer Community. mBio 2019; 10:e00568-19. [PMID: 30992354 PMCID: PMC6469972 DOI: 10.1128/mbio.00568-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 03/14/2019] [Indexed: 11/20/2022] Open
Abstract
Stochasticity emerging from random differences in replication, death, mutation, and dispersal is thought to alter the composition of ecological communities. However, the importance of stochastic effects remains somewhat speculative because stochasticity is not directly measured but is instead inferred from unexplained variations in beta-diversity. Here, we performed a field experiment to more directly disentangle the role of stochastic processes, environmental selection, and dispersal in the composition and functioning of a natural bacterial decomposer community in the field. To increase our ability to detect these effects, we reduced initial biological and environmental heterogeneity using replicate nylon litterbags in the field. We then applied two treatments: ambient/added precipitation and bacterial and fungal dispersal using "open" litterbags (made from 18.0-μm-pore-size mesh) ("open bacterial dispersal") versus bacterial and fungal dispersal using "closed" litterbags (made from 22.0-μm-pore-size mesh) ("closed bacterial dispersal"). After 5 months, we assayed composition and functioning by the use of three subsamples from each litterbag to disentangle stochastic effects from residual variation. Our results indicate that stochasticity via ecological drift can contribute to beta-diversity in bacterial communities. However, residual variation, which had previously been included in stochasticity estimates, accounted for more than four times as much variability. At the same time, stochastic effects on beta-diversity were not attenuated at the functional level, as measured by genetic functional potential and extracellular enzyme activity. Finally, dispersal was found to interact with precipitation availability to influence the degree to which stochasticity contributed to functional variation. Together, our results demonstrate that the ability to quantify stochastic processes is key to understanding microbial diversity and its role in ecosystem functioning.IMPORTANCE Randomness can alter the diversity and composition of ecological communities. Such stochasticity may therefore obscure the relationship between the environment and community composition and hinder our ability to predict the relationship between biodiversity and ecosystem functioning. This study investigated the role of stochastic processes, environmental selection, and dispersal in microbial composition and its functioning on an intact field community. To do this, we used a controlled and replicated experiment that was similar to that used to study population genetics in the laboratory. Our study showed that, while the stochastic effects on taxonomic composition are smaller than expected, the degree to which stochasticity contributes to variability in ecosystem processes may be much higher than previously assumed.
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Affiliation(s)
- Michaeline B N Albright
- Dept. of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California, USA
| | - Alexander B Chase
- Dept. of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California, USA
| | - Jennifer B H Martiny
- Dept. of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California, USA
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10
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Ul-Hasan S, Bowers RM, Figueroa-Montiel A, Licea-Navarro AF, Beman JM, Woyke T, Nobile CJ. Community ecology across bacteria, archaea and microbial eukaryotes in the sediment and seawater of coastal Puerto Nuevo, Baja California. PLoS One 2019; 14:e0212355. [PMID: 30763377 PMCID: PMC6375613 DOI: 10.1371/journal.pone.0212355] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 01/31/2019] [Indexed: 11/19/2022] Open
Abstract
Microbial communities control numerous biogeochemical processes critical for ecosystem function and health. Most analyses of coastal microbial communities focus on the characterization of bacteria present in either sediment or seawater, with fewer studies characterizing both sediment and seawater together at a given site, and even fewer studies including information about non-bacterial microbial communities. As a result, knowledge about the ecological patterns of microbial biodiversity across domains and habitats in coastal communities is limited-despite the fact that archaea, bacteria, and microbial eukaryotes are present and known to interact in coastal habitats. To better understand microbial biodiversity patterns in coastal ecosystems, we characterized sediment and seawater microbial communities for three sites along the coastline of Puerto Nuevo, Baja California, Mexico using both 16S and 18S rRNA gene amplicon sequencing. We found that sediment hosted approximately 500-fold more operational taxonomic units (OTUs) for bacteria, archaea, and microbial eukaryotes than seawater (p < 0.001). Distinct phyla were found in sediment versus seawater samples. Of the top ten most abundant classes, Cytophagia (bacterial) and Chromadorea (eukaryal) were specific to the sediment environment, whereas Cyanobacteria and Bacteroidia (bacterial) and Chlorophyceae (eukaryal) were specific to the seawater environment. A total of 47 unique genera were observed to comprise the core taxa community across environment types and sites. No archaeal taxa were observed as part of either the abundant or core taxa. No significant differences were observed for sediment community composition across domains or between sites. For seawater, the bacterial and archaeal community composition was statistically different for the Major Outlet site (p < 0.05), the site closest to a residential area, and the eukaryal community composition was statistically different between all sites (p < 0.05). Our findings highlight the distinct patterns and spatial heterogeneity in microbial communities of a coastal region in Baja California, Mexico.
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Affiliation(s)
- Sabah Ul-Hasan
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA, United States of America
- Quantitative and Systems Biology Graduate Program, University of California Merced, Merced, CA, United States of America
| | - Robert M. Bowers
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States of America
| | - Andrea Figueroa-Montiel
- Department of Biomedical Innovation, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Baja California, México
| | - Alexei F. Licea-Navarro
- Department of Biomedical Innovation, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Baja California, México
| | - J. Michael Beman
- Department of Life and Environmental Sciences, School of Natural Sciences, University of California Merced, Merced, CA, United States of America
| | - Tanja Woyke
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA, United States of America
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States of America
| | - Clarissa J. Nobile
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA, United States of America
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Hu Y, Bai C, Cai J, Shao K, Tang X, Gao G. Low recovery of bacterial community after an extreme salinization-desalinization cycle. BMC Microbiol 2018; 18:195. [PMID: 30470189 PMCID: PMC6251166 DOI: 10.1186/s12866-018-1333-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/31/2018] [Indexed: 11/10/2022] Open
Abstract
Background Understanding the recovery of bacterial communities after extreme environmental disturbances offers key opportunities to investigate ecosystem resilience. However, it is not yet clear whether bacterial communities can rebound to their pre-disturbance levels. To shed light on this issue, we tracked the responses of bacterial communities during an extreme salinization-desalinization cycle. Results Our results showed that salinization-up process induced an ecological succession, shifting from a community dominated by Betaproteobacteria to Gammaproteobacteria. Within the desalinization-down process, taxon-specific recovery trajectories varied profoundly, with only Gammaproteobacteria returning to their initial levels, of which Alphaproteobacteria was the most prominent member. The α-diversity indices gradually increased at oligosaline environment (0.03‰ to 3‰) and subsequently decreased profoundly at hypersaline condition (10‰ to 90‰). However, the indices did not return to pre-disturbance level along the previous trajectory observed during the desalinization. Approximately half of the original OTUs were not detected during desalinization, suggesting that the seed bank may be damaged by the hypersaline environment. Moreover, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) implied that the osmosensors’ capacity of bacterial communities was also impaired by the hypersaline condition. Conclusions These results suggested that the bacterial communities showed a low recovery after the extreme salinization-desalinization cycle. Electronic supplementary material The online version of this article (10.1186/s12866-018-1333-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yang Hu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China.,University of Chinese Academy of Sciences, Beijing, 100000, China
| | - Chengrong Bai
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China.,University of Chinese Academy of Sciences, Beijing, 100000, China
| | - Jian Cai
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China.,University of Chinese Academy of Sciences, Beijing, 100000, China
| | - Keqiang Shao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China
| | - Guang Gao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, 73 East Beijing Road, Nanjing, 210008, China.
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Amycomicin is a potent and specific antibiotic discovered with a targeted interaction screen. Proc Natl Acad Sci U S A 2018; 115:10124-10129. [PMID: 30228116 DOI: 10.1073/pnas.1807613115] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The rapid emergence of antibiotic-resistant pathogenic bacteria has accelerated the search for new antibiotics. Many clinically used antibacterials were discovered through culturing a single microbial species under nutrient-rich conditions, but in the environment, bacteria constantly encounter poor nutrient conditions and interact with neighboring microbial species. In an effort to recapitulate this environment, we generated a nine-strain actinomycete community and used 16S rDNA sequencing to deconvolute the stochastic production of antimicrobial activity that was not observed from any of the axenic cultures. We subsequently simplified the community to just two strains and identified Amycolatopsis sp. AA4 as the producing strain and Streptomyces coelicolor M145 as an inducing strain. Bioassay-guided isolation identified amycomicin (AMY), a highly modified fatty acid containing an epoxide isonitrile warhead as a potent and specific inhibitor of Staphylococcus aureus Amycomicin targets an essential enzyme (FabH) in fatty acid biosynthesis and reduces S. aureus infection in a mouse skin-infection model. The discovery of AMY demonstrates the utility of screening complex communities against specific targets to discover small-molecule antibiotics.
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