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Gu M, Zhang D, Li C, Ren Y, Song G, Chen L, Li S, Zheng X. In-depth metaproteomics analysis reveals the protein profile and metabolism characteristics in pork during refrigerated storage. Food Chem 2024; 459:140149. [PMID: 39002337 DOI: 10.1016/j.foodchem.2024.140149] [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: 01/16/2024] [Revised: 05/28/2024] [Accepted: 06/15/2024] [Indexed: 07/15/2024]
Abstract
Alterations in microbiotas and endogenous enzymes have been implicated in meat deterioration. However, the factors that mediate the interactions between meat quality and microbiome profile were inadequately investigated. In this study, we collected pork samples throughout the refrigeration period and employed metaproteomics to characterize both the pork and microbial proteins. Our findings demonstrated that pork proteins associated with the catabolic process are upregulated during storage compared to the initial stage. Pseudomonas, Clostridium, Goodfellowiella, and Gonapodya contribute to the spoilage process. Notably, we observed an elevated abundance of microbial proteins related to glycolytic enzymes in refrigerated pork, identifying numerous proteins linked to biogenic amine production, thus highlighting their essential role in microbial decay. Further, we reveal that many of these microbial proteins from Pseudomonas are ribosomal proteins, promoting enzyme synthesis by enhancing transcription and translation. This study provides intrinsic insights into the underlying mechanisms by which microorganisms contribute to meat spoilage.
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Affiliation(s)
- Minghui Gu
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Dequan Zhang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Cheng Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Yuqing Ren
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Guangchun Song
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Li Chen
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Shaobo Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Xiaochun Zheng
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs, Beijing 100193, China.
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2
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Hinthong W, Srisook T, Tanyong W, Kongngoen T, Mahikul W, Santajit S, Sookrung N, Indrawattana N. Investigation of the marine bacterial community along the coastline of the Gulf of Thailand. Heliyon 2024; 10:e31896. [PMID: 38868067 PMCID: PMC11167348 DOI: 10.1016/j.heliyon.2024.e31896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/20/2024] [Accepted: 05/23/2024] [Indexed: 06/14/2024] Open
Abstract
The Gulf of Thailand provides many services to the Thai population, and human activities may influence the diversity of microorganisms in the seawater. Information of the microorganisms' profile which inhabit the coastline can be used to monitor the water quality. This study aimed to investigate the bacterial community in the waters along the coastline provinces, including Rayong, Chonburi, Prachuap Kiri Khan, and Nakhon Sri Thammarat. Seawater samples were collected at each site, and the conductivity, pH, salinity, temperature, and turbidity were measured. The samples were subjected to whole DNA extraction, 16S rRNA amplification, next-generation sequencing, and statistical analysis to identify the bacterial diversity and analyse the effects of water parameters on the bacterial community. The dominant bacterial phyla found were Proteobacteria, Bacteroidota, and Cyanobacteria. Spearman rank correlation analysis revealed a high correlation of Pseudoalteromonas, the NS5 marine group, Lachnospiraceae, Marinobacterium, Mariviven, and Vibrio with the seawater parameters. The predatory bacteria Peredibacter and Halobacteriovorax were reported among these bacterial communities for the first time in the Gulf of Thailand. Interestingly, Akkermansia, a novel candidate for next-generation probiotics to improve human health, was also found in the sample from Nakhon Sri Thammarat Province. Although the rich-ness and diversity of the bacterial communities differed among sampling sites, it is a possible source of many valuable bacteria for future use.
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Affiliation(s)
- Woranich Hinthong
- Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, 10210, Thailand
| | - Thassanee Srisook
- Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, 10210, Thailand
| | - Witawat Tanyong
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Thida Kongngoen
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Wiriya Mahikul
- Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, 10210, Thailand
| | - Sirijan Santajit
- Department of Medical Technology, School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, 80160, Thailand
| | - Nitat Sookrung
- Siriraj Center of Research Excellence in Allergy and Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Nitaya Indrawattana
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
- Siriraj Center of Research Excellence in Allergy and Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
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3
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Zhang L, Guo L, Cui Z, Ju F. Exploiting predatory bacteria as biocontrol agents across ecosystems. Trends Microbiol 2024; 32:398-409. [PMID: 37951768 DOI: 10.1016/j.tim.2023.10.005] [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: 06/30/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 11/14/2023]
Abstract
Predatory bacteria have been increasingly known for their ubiquity in environments and great functional potentials in controlling unwanted microorganisms. Fundamental understanding of the predation mechanisms, population dynamics, and interaction patterns underlying bacterial predation is required for wise exploitation of predatory bacteria for enhancing ecoenvironmental, animal, and human health. Here, we review the recent achievements on applying predatory bacteria in different systems as biocontrol agents and living antibiotics as well as new findings in their phylogenetic diversity and predation mechanisms. We finally propose critical issues that deserve priority research and highlight the necessity to combine classic culture-based and advanced culture-independent approaches to push research frontiers of bacterial predation across ecosystems for promising biocontrol and therapy strategies towards a sustainable ecoenvironment and health.
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Affiliation(s)
- Lu Zhang
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang Province, China; Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China; Center of Synthetic Biology and Integrated Bioengineering, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Lingyun Guo
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang Province, China; Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China; Center of Synthetic Biology and Integrated Bioengineering, Westlake University, Hangzhou, Zhejiang Province, China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Feng Ju
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang Province, China; Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China; Center of Synthetic Biology and Integrated Bioengineering, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China.
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4
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Zhao H, Yang S, Qin X, Huang J, Huang H, Li W, Jiang G, Tang J, Dong K, Li N. Disentangling the Ecological Processes and Driving Forces Shaping the Seasonal Pattern of Halobacteriovorax Communities in a Subtropical Estuary. MICROBIAL ECOLOGY 2023; 86:1881-1892. [PMID: 36799977 DOI: 10.1007/s00248-023-02195-w] [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: 10/25/2022] [Accepted: 02/11/2023] [Indexed: 06/18/2023]
Abstract
Halobacteriovorax are predatory bacteria that have a significant ecological role in marine environments. However, understanding of dynamics of populations, driving forces, and community composition of Halobacteriovorax groups in natural marine environments is still limited. Here, we used high-throughput sequencing to study the underlying mechanisms governing the diversity and assembly of the Halobacteriovorax community at spatiotemporal scales in a subtropical estuary. Phylogenetic analysis showed that 10 of 15 known Halobacteriovorax clusters were found in the studied estuary. Halobacteriovorax α-diversity and β-diversity exhibited significant seasonal variation. Variation partitioning analysis showed that the effect of nutrients was greater than that of other measured water properties on Halobacteriovorax community distribution. The results of Spearman's and Mantel's tests indicated that the trophic pollutants dissolved inorganic phosphorus (DIP) and NH4+-N in the estuary were the key factors that significantly affected Halobacteriovorax species and community diversity. In addition, this work indicated that the biological stoichiometry (especially N/P) of nutrients exerted a significant influence on the Halobacteriovorax community. Furthermore, we found that both deterministic and stochastic processes contributed to the turnover of Halobacteriovorax communities, and environmental filtering dominated the assembly of estuarine Halobacteriovorax communities. Overall, we provide new insights into the mechanisms in the generation and maintenance of the Halobacteriovorax community in marine environments.
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Affiliation(s)
- Huaxian Zhao
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, 530001, China
| | - Shu Yang
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, 530001, China
| | - Xinyi Qin
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, 530001, China
| | - Jiongqing Huang
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, 530001, China
| | - Haifeng Huang
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, 530001, China
| | - Wenjing Li
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, 530001, China
| | - Gonglingxia Jiang
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, 530001, China
| | - Jinli Tang
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, 530001, China
| | - Ke Dong
- Department of Biological Sciences, Kyonggi University, 154-42, Gwanggyosan-ro, Yeongtong-gu Gyeonggi-do, Suwon-si, 16227, South Korea
| | - Nan Li
- Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, 530001, China.
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Pereira PHF, Fernandes L, Jesus HE, Costa PG, Lacerda CHF, Mies M, Bianchini A, Santos HF. The Impact of Highly Weathered Oil from the Most Extensive Oil Spill in Tropical Oceans (Brazil) on the Microbiome of the Coral Mussismilia harttii. Microorganisms 2023; 11:1935. [PMID: 37630495 PMCID: PMC10458584 DOI: 10.3390/microorganisms11081935] [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: 06/05/2023] [Revised: 06/30/2023] [Accepted: 07/06/2023] [Indexed: 08/27/2023] Open
Abstract
In 2019, the largest oil spill ever recorded in tropical oceans in terms of extent occurred in Brazil. The oil from the spill was collected directly from the environment and used in an exposure experiment with the endangered reef-building coral Mussismilia harttii. The treatments of the experiment were control (without oil), 1% oil, 2.5% oil, and direct contact of coral with oil. The most abundant hydrocarbon in the seawater of the experiment was phenatrene, which is toxic to corals. However, overall, the concentration of PAHs was not very high. The analysis of the maximum photosynthetic capacity of Symbiodiniaceae dinoflagellates showed a small impact of oil on corals, mainly on the contact treatment. However, coral microbiomes were affected in all oil treatments, with the contact treatment showing the most pronounced impact. A greater number and abundance of stress-indicating and potentially pathogenic bacteria were found in all oil treatments. Finally, this highly weathered oil that had lain in the ocean for a long time was carrying potentially coral-pathogenic bacteria within the Vibrionaceae family and was able to transmit some of these bacteria to corals. Bacteria within Vibrionaceae are the main causes of disease in different species of corals and other marine organisms.
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Affiliation(s)
- Pedro Henrique F. Pereira
- Department of Marine Biology, Fluminense Federal University—UFF, St. Professor Marcos Waldemar de Freitas Reis, Niterói 24210-201, RJ, Brazil; (P.H.F.P.); (L.F.); (H.E.J.)
| | - Luanny Fernandes
- Department of Marine Biology, Fluminense Federal University—UFF, St. Professor Marcos Waldemar de Freitas Reis, Niterói 24210-201, RJ, Brazil; (P.H.F.P.); (L.F.); (H.E.J.)
| | - Hugo E. Jesus
- Department of Marine Biology, Fluminense Federal University—UFF, St. Professor Marcos Waldemar de Freitas Reis, Niterói 24210-201, RJ, Brazil; (P.H.F.P.); (L.F.); (H.E.J.)
| | - Patricia G. Costa
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande—FURG, Av. Itália, s/n, Carreiros, Rio Grande 96203-900, RS, Brazil; (P.G.C.); (A.B.)
| | - Carlos H. F. Lacerda
- Instituto Coral Vivo, Rua dos Coqueiros, 87, Santa Cruz Cabrália 45807-000, BA, Brazil; (C.H.F.L.); (M.M.)
| | - Miguel Mies
- Instituto Coral Vivo, Rua dos Coqueiros, 87, Santa Cruz Cabrália 45807-000, BA, Brazil; (C.H.F.L.); (M.M.)
- Instituto Oceanográfico, Universidade de São Paulo, Praça do Oceanográfico, 191, São Paulo 05508-120, SP, Brazil
| | - Adalto Bianchini
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande—FURG, Av. Itália, s/n, Carreiros, Rio Grande 96203-900, RS, Brazil; (P.G.C.); (A.B.)
- Instituto Coral Vivo, Rua dos Coqueiros, 87, Santa Cruz Cabrália 45807-000, BA, Brazil; (C.H.F.L.); (M.M.)
| | - Henrique F. Santos
- Department of Marine Biology, Fluminense Federal University—UFF, St. Professor Marcos Waldemar de Freitas Reis, Niterói 24210-201, RJ, Brazil; (P.H.F.P.); (L.F.); (H.E.J.)
- Instituto Coral Vivo, Rua dos Coqueiros, 87, Santa Cruz Cabrália 45807-000, BA, Brazil; (C.H.F.L.); (M.M.)
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6
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Luo K, Liu Y, Qin G, Wang S, Wei C, Pan M, Guo Z, Liu Q, Tian X. A comparative study on effects of dietary three strains of lactic acid bacteria on the growth performance, immune responses, disease resistance and intestinal microbiota of Pacific white shrimp, Penaeus vannamei. FISH & SHELLFISH IMMUNOLOGY 2023; 136:108707. [PMID: 36966896 DOI: 10.1016/j.fsi.2023.108707] [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: 12/28/2022] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 06/18/2023]
Abstract
The present study evaluated the growth performance, immune responses, disease resistance and intestinal microbiota in Penaeus vannamei fed diets supplemented with three strains of lactic acid bacteria (LAB). The basal diet (control, CO) supplemented with Lactobacillus plantarum W2 (LA), Pediococcus acidilactici Nj (PE), Enterococcus faecium LYB (EN) and florfenicol (FL), respectively, formed three LAB diets (1 × 1010 cfu kg-1) and a florfenicol diet (15 mg kg-1, positive control), were fed to shrimp for 42 days. Results indicated that specific growth rate, feed efficiency rate, and disease resistance of shrimp against Vibrio parahaemolyticus in the treatment groups were significantly improved versus the control (P < 0.05). Compared with the control, acid phosphatase, alkaline phosphatase, phenonoloxidase, total nitric oxide synthase, peroxidase, superoxide dismutase activities, total antioxidant capacity, and lysozyme content in the serum and the relative expression levels of SOD, LZM, proPO, LGBP, HSP70, Imd, Toll, Relish, TOR, 4E-BP, eIF4E1α and eIF4E2 genes in the hepatopancreas of LAB groups were enhanced to various extents. Intestinal microbiota analysis showed that the LA and EN groups significantly improved microbial diversity and richness, and LAB groups significantly altered intestinal microbial structure of shrimp. At the phylum level, the Verrucomicrobiota in the LA and PE groups, the Firmicutes in the EN group, and the Actinobacteriota in the PE and EN groups were enriched. Moreover, the CO group increased the proportion of potential pathogens (Vibrionaceae and Flavobacteriaceae). The potential pathogen (Vibrio) was reduced, and potential beneficial bacteria (Tenacibaculum, Ruegeria and Bdellovibrio) were enriched in response to dietary three strains of LAB. When the intestinal microbiota homeostasis of shrimp is considered, L. plantarum and E. faecium showed better effects than P. acidilactici. However, due to the concerns on the possible potential risks of E. faecium strains to human health, L. plantarum W2 is more suitable for application in aquaculture than E. faecium LYB. Considering collectively the above, Lactobacillus plantarum W2 could be applied as better probiotic to improve the growth performance, non-specific immunity, disease resistance and promote intestinal health of P. vannamei.
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Affiliation(s)
- Kai Luo
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Yang Liu
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Guangcai Qin
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Shishuang Wang
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Cong Wei
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Miaojun Pan
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | - Zeyang Guo
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China
| | | | - Xiangli Tian
- The Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266003, China.
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7
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Zhong KX, Wirth JF, Chan AM, Suttle CA. Mortality by ribosomal sequencing (MoRS) provides a window into taxon-specific cell lysis. THE ISME JOURNAL 2023; 17:105-116. [PMID: 36209336 PMCID: PMC9751121 DOI: 10.1038/s41396-022-01327-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/05/2022]
Abstract
Microbes are by far the dominant biomass in the world's oceans and drive biogeochemical cycles that are critical to life on Earth. The composition of marine microbial communities is highly dynamic, spatially and temporally, with consequent effects on their functional roles. In part, these changes in composition result from viral lysis, which is taxon-specific and estimated to account for about half of marine microbial mortality. Here, we show that extracellular ribosomal RNA (rRNAext) is produced by viral lysis, and that specific lysed populations can be identified by sequencing rRNAext recovered from seawater samples. In ten seawater samples collected at five depths between the surface and 265 m during and following a phytoplankton bloom, lysis was detected in about 15% of 16,946 prokaryotic taxa, identified from amplicon sequence variants (ASVs), with lysis occurring in up to 34% of taxa within a water sample. The ratio of rRNAext to cellular rRNA (rRNAcell) was used as an index of taxon-specific lysis, and revealed that higher relative lysis was most commonly associated with copiotrophic bacteria that were in relatively low abundance, such as those in the genera Escherichia and Shigella spp., as well as members of the Bacteriodetes; whereas, relatively low lysis was more common in taxa that are often relatively abundant, such as members of the Pelagibacterales (i.e., SAR11 clade), cyanobacteria in the genus Synechococcus, and members of the phylum Thaumarchaeota (synonym, Nitrososphaerota) that comprised about 13-15% of the 16 S rRNA gene sequences below 30 m. These results provide an explanation for the long-standing conundrum of why highly productive bacteria that are readily isolated from seawater are often in very low abundance. The ability to estimate taxon-specific cell lysis will help explore the distribution and abundance of microbial populations in nature.
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Affiliation(s)
- Kevin Xu Zhong
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada.
| | - Jennifer F Wirth
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA
| | - Amy M Chan
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Curtis A Suttle
- Department of Earth, Ocean, and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada.
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC, Canada.
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8
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Summers JK, Kreft JU. The role of mathematical modelling in understanding prokaryotic predation. Front Microbiol 2022; 13:1037407. [PMID: 36643414 PMCID: PMC9835096 DOI: 10.3389/fmicb.2022.1037407] [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: 09/05/2022] [Accepted: 11/23/2022] [Indexed: 12/30/2022] Open
Abstract
With increasing levels of antimicrobial resistance impacting both human and animal health, novel means of treating resistant infections are urgently needed. Bacteriophages and predatory bacteria such as Bdellovibrio bacteriovorus have been proposed as suitable candidates for this role. Microbes also play a key environmental role as producers or recyclers of nutrients such as carbon and nitrogen, and predators have the capacity to be keystone species within microbial communities. To date, many studies have looked at the mechanisms of action of prokaryotic predators, their safety in in vivo models and their role and effectiveness under specific conditions. Mathematical models however allow researchers to investigate a wider range of scenarios, including aspects of predation that would be difficult, expensive, or time-consuming to investigate experimentally. We review here a history of modelling in prokaryote predation, from simple Lotka-Volterra models, through increasing levels of complexity, including multiple prey and predator species, and environmental and spatial factors. We consider how models have helped address questions around the mechanisms of action of predators and have allowed researchers to make predictions of the dynamics of predator-prey systems. We examine what models can tell us about qualitative and quantitative commonalities or differences between bacterial predators and bacteriophage or protists. We also highlight how models can address real-world situations such as the likely effectiveness of predators in removing prey species and their potential effects in shaping ecosystems. Finally, we look at research questions that are still to be addressed where models could be of benefit.
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Affiliation(s)
- J. Kimberley Summers
- Wellington Lab, School of Life Sciences, University of Warwick, Coventry, United Kingdom,Kreft Lab, Institute of Microbiology and Infection and Centre for Computational Biology and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom,*Correspondence: J. Kimberley Summers,
| | - Jan-Ulrich Kreft
- Kreft Lab, Institute of Microbiology and Infection and Centre for Computational Biology and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom,Jan-Ulrich Kreft,
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9
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Liu J, Xue CX, Wang J, Crombie AT, Carrión O, Johnston AWB, Murrell JC, Liu J, Zheng Y, Zhang XH, Todd JD. Oceanospirillales containing the DMSP lyase DddD are key utilisers of carbon from DMSP in coastal seawater. MICROBIOME 2022; 10:110. [PMID: 35883169 PMCID: PMC9327192 DOI: 10.1186/s40168-022-01304-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Ubiquitous and diverse marine microorganisms utilise the abundant organosulfur molecule dimethylsulfoniopropionate (DMSP), the main precursor of the climate-active gas dimethylsulfide (DMS), as a source of carbon, sulfur and/or signalling molecules. However, it is currently difficult to discern which microbes actively catabolise DMSP in the environment, why they do so and the pathways used. RESULTS Here, a novel DNA-stable isotope probing (SIP) approach, where only the propionate and not the DMS moiety of DMSP was 13C-labelled, was strategically applied to identify key microorganisms actively using DMSP and also likely DMS as a carbon source, and their catabolic enzymes, in North Sea water. Metagenomic analysis of natural seawater suggested that Rhodobacterales (Roseobacter group) and SAR11 bacteria were the major microorganisms degrading DMSP via demethylation and, to a lesser extent, DddP-driven DMSP lysis pathways. However, neither Rhodobacterales and SAR11 bacteria nor their DMSP catabolic genes were prominently labelled in DNA-SIP experiments, suggesting they use DMSP as a sulfur source and/or in signalling pathways, and not primarily for carbon requirements. Instead, DNA-SIP identified gammaproteobacterial Oceanospirillales, e.g. Amphritea, and their DMSP lyase DddD as the dominant microorganisms/enzymes using DMSP as a carbon source. Supporting this, most gammaproteobacterial (with DddD) but few alphaproteobacterial seawater isolates grew on DMSP as sole carbon source and produced DMS. Furthermore, our DNA-SIP strategy also identified Methylophaga and other Piscirickettsiaceae as key bacteria likely using the DMS, generated from DMSP lysis, as a carbon source. CONCLUSIONS This is the first study to use DNA-SIP with 13C-labelled DMSP and, in a novel way, it identifies the dominant microbes utilising DMSP and DMS as carbon sources. It highlights that whilst metagenomic analyses of marine environments can predict microorganisms/genes that degrade DMSP and DMS based on their abundance, it cannot disentangle those using these important organosulfur compounds for their carbon requirements. Note, the most abundant DMSP degraders, e.g. Rhodobacterales with DmdA, are not always the key microorganisms using DMSP for carbon and releasing DMS, which in this coastal system were Oceanospirillales containing DddD. Video abstract.
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Affiliation(s)
- Jingli Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences , Ocean University of China, Qingdao, China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Chun-Xu Xue
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences , Ocean University of China, Qingdao, China
| | - Jinyan Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences , Ocean University of China, Qingdao, China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andrew T Crombie
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Ornella Carrión
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andrew W B Johnston
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Ji Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences , Ocean University of China, Qingdao, China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yanfen Zheng
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences , Ocean University of China, Qingdao, China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences , Ocean University of China, Qingdao, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
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10
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Dawood A, Zuberi A, Shi W. Plant-based β-mannanase supplemented diet modulates the gut microbiota and up-regulates the expression of immunity and digestion-related genes in Cyprinus carpio. JOURNAL OF APPLIED ANIMAL RESEARCH 2022. [DOI: 10.1080/09712119.2021.2018327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Aneesa Dawood
- Department of Microbiology, Quaid-I-Azam University, Islamabad, Pakistan
- Department of Zoology, Quaid-I-Azam University, Islamabad, Pakistan
| | - Amina Zuberi
- Department of Zoology, Quaid-I-Azam University, Islamabad, Pakistan
| | - Weibin Shi
- Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA
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11
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Alexander LT, Lepore R, Kryshtafovych A, Adamopoulos A, Alahuhta M, Arvin AM, Bomble YJ, Böttcher B, Breyton C, Chiarini V, Chinnam NB, Chiu W, Fidelis K, Grinter R, Gupta GD, Hartmann MD, Hayes CS, Heidebrecht T, Ilari A, Joachimiak A, Kim Y, Linares R, Lovering AL, Lunin VV, Lupas AN, Makbul C, Michalska K, Moult J, Mukherjee PK, Nutt W(S, Oliver SL, Perrakis A, Stols L, Tainer JA, Topf M, Tsutakawa SE, Valdivia‐Delgado M, Schwede T. Target highlights in CASP14: Analysis of models by structure providers. Proteins 2021; 89:1647-1672. [PMID: 34561912 PMCID: PMC8616854 DOI: 10.1002/prot.26247] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 12/11/2022]
Abstract
The biological and functional significance of selected Critical Assessment of Techniques for Protein Structure Prediction 14 (CASP14) targets are described by the authors of the structures. The authors highlight the most relevant features of the target proteins and discuss how well these features were reproduced in the respective submitted predictions. The overall ability to predict three-dimensional structures of proteins has improved remarkably in CASP14, and many difficult targets were modeled with impressive accuracy. For the first time in the history of CASP, the experimentalists not only highlighted that computational models can accurately reproduce the most critical structural features observed in their targets, but also envisaged that models could serve as a guidance for further studies of biologically-relevant properties of proteins.
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Affiliation(s)
- Leila T. Alexander
- Biozentrum, University of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
| | | | | | - Athanassios Adamopoulos
- Oncode Institute and Division of BiochemistryNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Markus Alahuhta
- Bioscience Center, National Renewable Energy LaboratoryGoldenColoradoUSA
| | - Ann M. Arvin
- Department of PediatricsStanford University School of MedicineStanfordCaliforniaUSA
- Microbiology and ImmunologyStanford University School of MedicineStanfordCaliforniaUSA
| | - Yannick J. Bomble
- Bioscience Center, National Renewable Energy LaboratoryGoldenColoradoUSA
| | - Bettina Böttcher
- Biocenter and Rudolf Virchow Center, Julius‐Maximilians Universität WürzburgWürzburgGermany
| | - Cécile Breyton
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural BiologyGrenobleFrance
| | - Valerio Chiarini
- Program in Structural Biology and BiophysicsInstitute of Biotechnology, University of HelsinkiHelsinkiFinland
| | - Naga babu Chinnam
- Department of Molecular and Cellular OncologyThe University of Texas M.D. Anderson Cancer CenterHoustonTexasUSA
| | - Wah Chiu
- Microbiology and ImmunologyStanford University School of MedicineStanfordCaliforniaUSA
- BioengineeringStanford University School of MedicineStanfordCaliforniaUSA
- Division of Cryo‐EM and Bioimaging SSRLSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | | | - Rhys Grinter
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of MicrobiologyMonash UniversityClaytonAustralia
| | - Gagan D. Gupta
- Radiation Biology & Health Sciences DivisionBhabha Atomic Research CentreMumbaiIndia
| | - Marcus D. Hartmann
- Department of Protein EvolutionMax Planck Institute for Developmental BiologyTübingenGermany
| | - Christopher S. Hayes
- Department of Molecular, Cellular and Developmental BiologyUniversity of California, Santa BarbaraSanta BarbaraCaliforniaUSA
- Biomolecular Science and Engineering ProgramUniversity of California, Santa BarbaraSanta BarbaraCaliforniaUSA
| | - Tatjana Heidebrecht
- Oncode Institute and Division of BiochemistryNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Andrea Ilari
- Institute of Molecular Biology and Pathology of the National Research Council of Italy (CNR)RomeItaly
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of ChicagoChicagoIllinoisUSA
- X‐ray Science DivisionArgonne National Laboratory, Structural Biology CenterArgonneIllinoisUSA
- Department of Biochemistry and Molecular BiologyUniversity of ChicagoChicagoIllinoisUSA
| | - Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of ChicagoChicagoIllinoisUSA
- X‐ray Science DivisionArgonne National Laboratory, Structural Biology CenterArgonneIllinoisUSA
| | - Romain Linares
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural BiologyGrenobleFrance
| | | | - Vladimir V. Lunin
- Bioscience Center, National Renewable Energy LaboratoryGoldenColoradoUSA
| | - Andrei N. Lupas
- Department of Protein EvolutionMax Planck Institute for Developmental BiologyTübingenGermany
| | - Cihan Makbul
- Biocenter and Rudolf Virchow Center, Julius‐Maximilians Universität WürzburgWürzburgGermany
| | - Karolina Michalska
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of ChicagoChicagoIllinoisUSA
- X‐ray Science DivisionArgonne National Laboratory, Structural Biology CenterArgonneIllinoisUSA
| | - John Moult
- Department of Cell Biology and Molecular GeneticsInstitute for Bioscience and Biotechnology Research, University of MarylandRockvilleMarylandUSA
| | - Prasun K. Mukherjee
- Nuclear Agriculture & Biotechnology DivisionBhabha Atomic Research CentreMumbaiIndia
| | - William (Sam) Nutt
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of ChicagoChicagoIllinoisUSA
- X‐ray Science DivisionArgonne National Laboratory, Structural Biology CenterArgonneIllinoisUSA
| | - Stefan L. Oliver
- Department of PediatricsStanford University School of MedicineStanfordCaliforniaUSA
| | - Anastassis Perrakis
- Oncode Institute and Division of BiochemistryNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Lucy Stols
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of ChicagoChicagoIllinoisUSA
- X‐ray Science DivisionArgonne National Laboratory, Structural Biology CenterArgonneIllinoisUSA
| | - John A. Tainer
- Department of Molecular and Cellular OncologyThe University of Texas M.D. Anderson Cancer CenterHoustonTexasUSA
- Department of Cancer BiologyUniversity of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Maya Topf
- Institute of Structural and Molecular Biology, Birkbeck, University College LondonLondonUK
- Centre for Structural Systems Biology, Leibniz‐Institut für Experimentelle VirologieHamburgGermany
| | - Susan E. Tsutakawa
- Molecular Biophysics and Integrated BioimagingLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | | | - Torsten Schwede
- Biozentrum, University of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
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12
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Ooi MC, Goulden EF, Smith GG, Bridle AR. Predatory bacteria in the haemolymph of the cultured spiny lobster Panulirus ornatus. MICROBIOLOGY (READING, ENGLAND) 2021; 167. [PMID: 34846286 PMCID: PMC8743626 DOI: 10.1099/mic.0.001113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bdellovibrio and like organisms (BALOs) are Gram-negative obligate predators of other bacteria in a range of environments. The recent discovery of BALOs in the circulatory system of cultured spiny lobster P. ornatus warrants more investigation. We used a combination of co-culture agar and broth assays and transmission electron microscopy to show a Halobacteriovorax sp. strain Hbv preyed upon the model prey bacterium Vibrio sp. strain Vib. The haemolymph microbiome of juvenile P. ornatus was characterised following injection of phosphate buffered saline (control) or prey and/or predator bacteria for 3 d. The predator Hbv had no effect on survival compared to the control after 3 d. However, when compared to the prey only treatment group, lobsters injected with both prey and predator showed significantly lower abundance of genus Vibrio in the haemolymph bacterial community composition. This study indicates that predatory bacteria are not pathogenic and may assist in controlling microbial population growth in the haemolymph of lobsters.
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Affiliation(s)
- Mei C. Ooi
- Institute for Marine and Antarctic Studies, University of Tasmania, TAS, Australia
- *Correspondence: Mei C. Ooi,
| | - Evan F. Goulden
- Institute for Marine and Antarctic Studies, University of Tasmania, TAS, Australia
- Bribie Island Research Centre, Department of Agriculture and Fisheries, QLD, Australia
| | - Gregory G. Smith
- Institute for Marine and Antarctic Studies, University of Tasmania, TAS, Australia
| | - Andrew R. Bridle
- Institute for Marine and Antarctic Studies, University of Tasmania, TAS, Australia
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13
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Mookherjee A, Jurkevitch E. Interactions between Bdellovibrio and like organisms and bacteria in biofilms: beyond predator-prey dynamics. Environ Microbiol 2021; 24:998-1011. [PMID: 34816563 DOI: 10.1111/1462-2920.15844] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/03/2021] [Accepted: 11/08/2021] [Indexed: 12/19/2022]
Abstract
Bdellovibrio and like organisms (BALOs) prey on Gram-negative bacteria in the planktonic phase as well as in biofilms, with the ability to reduce prey populations by orders of magnitude. During the last few years, evidence has mounted for a significant ecological role for BALOs, with important implications for our understanding of microbial community dynamics as well as for applications against pathogens, including drug-resistant pathogens, in medicine, agriculture and aquaculture, and in industrial settings for various uses. However, our understanding of biofilm predation by BALOs is still very fragmentary, including gaps in their effect on biofilm structure, on prey resistance, and on evolutionary outcomes of both predators and prey. Furthermore, their impact on biofilms has been shown to reach beyond predation, as they are reported to reduce biofilm structures of non-prey cells (including Gram-positive bacteria). Here, we review the available literature on BALOs in biofilms, extending known aspects to potential mechanisms employed by the predators to grow in biofilms. Within that context, we discuss the potential ecological significance and potential future utilization of the predatory and enzymatic possibilities offered by BALOs in medical, agricultural and environmental applications.
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Affiliation(s)
- Abhirup Mookherjee
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
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14
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Predation strategies of the bacterium Bdellovibrio bacteriovorus result in overexploitation and bottlenecks. Appl Environ Microbiol 2021; 88:e0108221. [PMID: 34669451 DOI: 10.1128/aem.01082-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
With increasing antimicrobial resistance, alternatives for treating infections or removing resistant bacteria are urgently needed, such as the bacterial predator Bdellovibrio bacteriovorus or bacteriophage. Therefore, we need to better understand microbial predator-prey dynamics. We developed mass-action mathematical models of predation for chemostats, which capture the low substrate concentration and slow growth typical for intended application areas of the predators such as wastewater treatment, aquaculture or the gut. Our model predicted that predator survival required a minimal prey cell size, explaining why Bdellovibrio is much smaller than its prey. A too good predator (attack rate too high, mortality too low) overexploited its prey leading to extinction (tragedy of the commons). Surprisingly, a predator taking longer to produce more offspring outcompeted a predator producing fewer offspring more rapidly (rate versus yield trade-off). Predation was only efficient in a narrow region around optimal parameters. Moreover, extreme oscillations under a wide range of conditions led to severe bottlenecks. These could be avoided when two prey species became available in alternating seasons. A bacteriophage outcompeted Bdellovibrio due to its higher burst size and faster life cycle. Together, results suggest that Bdellovibrio would struggle to survive on a single prey, explaining why it must be a generalist predator and suggesting it is better suited than phage to environments with multiple prey. Importance The discovery of antibiotics led to a dramatic drop in deaths due to infectious disease. Increasing levels of antimicrobial resistance, however, threaten to reverse this progress. There is thus a need for alternatives, such as therapies based on phage and predatory bacteria that kill bacteria regardless of whether they are pathogens or resistant to antibiotics. To best exploit them, we need to better understand what determines their effectiveness. By using a mathematical model to study bacterial predation in realistic slow growth conditions, we found that the generalist predator Bdellovibrio is most effective within a narrow range of conditions for each prey. For example, a minimum prey cell size is required, and the predator should not be too good as this would result in over-exploitation risking extinction. Together these findings give insights into the ecology of microbial predation and help explain why Bdellovibrio needs to be a generalist predator.
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15
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Predatory Bacteria Select for Sustained Prey Diversity. Microorganisms 2021; 9:microorganisms9102079. [PMID: 34683400 PMCID: PMC8540638 DOI: 10.3390/microorganisms9102079] [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: 07/17/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 11/17/2022] Open
Abstract
Predator impacts on prey diversity are often studied among higher organisms over short periods, but microbial predator-prey systems allow examination of prey-diversity dynamics over evolutionary timescales. We previously showed that Escherichia coli commonly evolved minority mucoid phenotypes in response to predation by the bacterial predator Myxococcus xanthus by one time point of a coevolution experiment now named MyxoEE-6. Here we examine mucoid frequencies across several MyxoEE-6 timepoints to discriminate between the hypotheses that mucoids were increasing to fixation, stabilizing around equilibrium frequencies, or heading to loss toward the end of MyxoEE-6. In four focal coevolved prey populations, mucoids rose rapidly early in the experiment and then fluctuated within detectable minority frequency ranges through the end of MyxoEE-6, generating frequency dynamics suggestive of negative frequency-dependent selection. However, a competition experiment between mucoid and non-mucoid clones found a predation-specific advantage of the mucoid clone that was insensitive to frequency over the examined range, leaving the mechanism that maintains minority mucoidy unresolved. The advantage of mucoidy under predation was found to be associated with reduced population size after growth (productivity) in the absence of predators, suggesting a tradeoff between productivity and resistance to predation that we hypothesize may reverse mucoid vs non-mucoid fitness ranks within each MyxoEE-6 cycle. We also found that mucoidy was associated with diverse colony phenotypes and diverse candidate mutations primarily localized in the exopolysaccharide operon yjbEFGH. Collectively, our results show that selection from predatory bacteria can generate apparently stable sympatric phenotypic polymorphisms within coevolving prey populations and also allopatric diversity across populations by selecting for diverse mutations and colony phenotypes associated with mucoidy. More broadly, our results suggest that myxobacterial predation increases long-term diversity within natural microbial communities.
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16
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Ezzedine JA, Desdevises Y, Jacquet S. Bdellovibrio and like organisms: current understanding and knowledge gaps of the smallest cellular hunters of the microbial world. Crit Rev Microbiol 2021; 48:428-449. [PMID: 34595998 DOI: 10.1080/1040841x.2021.1979464] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Almost sixty years ago, Bdellovibrio and like organisms (BALOs) were discovered as the first obligate bacterial predators of other bacteria known to science. Since then, they were shown to be diverse and ubiquitous in the environment, and to bear astonishing ecological, physiological, and metabolic capabilities. The last decade has seen important strides made in understanding the mechanistic basis of their life cycle, the dynamics of their interactions with prey, along with significant developments towards their use in medicine, agriculture, and industry. This review details these achievements, identify current understanding and knowledge gaps to encourage and guide future BALO research.
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Affiliation(s)
- Jade A Ezzedine
- Université Savoie Mont-Blanc, INRAE, CARRTEL, Thonon-les-Bains, France.,Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, IRIG, Université Grenoble Alpes, Grenoble, France
| | - Yves Desdevises
- CNRS, Biologie Intégrative des Organismes Marins, Observatoire Océanologique, Sorbonne Université, Banyuls-sur-Mer, France
| | - Stéphan Jacquet
- Université Savoie Mont-Blanc, INRAE, CARRTEL, Thonon-les-Bains, France
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17
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Liang J, Liu J, Zhan Y, Zhou S, Xue CX, Sun C, Lin Y, Luo C, Wang X, Zhang XH. Succession of marine bacteria in response to Ulva prolifera-derived dissolved organic matter. ENVIRONMENT INTERNATIONAL 2021; 155:106687. [PMID: 34144477 DOI: 10.1016/j.envint.2021.106687] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 05/21/2021] [Accepted: 05/30/2021] [Indexed: 06/12/2023]
Abstract
Increasing macroalgal blooms as a consequence of climate warming and coastal eutrophication have profound effects on the marine environment. The outbreaks of Ulva prolifera in the Yellow Sea of China occurring every summer since 2007 to present have formed the world's largest green tide. The green tide releases huge amounts of dissolved organic matter (DOM) to the seawater, causing an organic overload. However, how marine bacteria respond to this issue and the potential impact on the marine environment are still unclear. Here, we monitored the highly temporally resolved dynamics of marine bacterial community that occur in response to Ulva prolifera-derived DOM by performing a 168-h microcosm incubation experiment. DOM inputs significantly increased bacterial abundances within 6 h, decreased bacterial diversity and triggered clear community successions during the whole period of incubation. Vibrio of Gammaproteobacteria robustly and rapidly grew over short timescales (6-24 h), with its relative abundance accounting for up to 52.5% of active bacteria. From 24 to 48 h, some genera of Flavobacteriia grew rapidly, which was more conspicuous at a higher DOM concentration than at a lower concentration. The genus Donghicola of Alphaproteobacteria was predominant at later time points (>48 h). This bacterial community succession was accompanied by significant variations in the activity of 12 different extracellular enzymes, resulting in a rapid reduction of dissolved organic carbon by 74.5% within the first 36 h. In summary, our study demonstrates rapid successions of bacterial community and extracellular enzyme activity after DOM inputs, suggesting that the bacterial response to Ulva prolifera-derived organic matter may contribute to environmental restoration and may pose a health threat due to the bloom of potential pathogenic Vibrio.
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Affiliation(s)
- Jinchang Liang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
| | - Jiwen Liu
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yuanchao Zhan
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Shun Zhou
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
| | - Chun-Xu Xue
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
| | - Chuang Sun
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
| | - Yu Lin
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
| | - Chunle Luo
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Qingdao 266100, China
| | - Xuchen Wang
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Qingdao 266100, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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18
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Cohen Y, Pasternak Z, Müller S, Hübschmann T, Schattenberg F, Sivakala KK, Abed-Rabbo A, Chatzinotas A, Jurkevitch E. Community and single cell analyses reveal complex predatory interactions between bacteria in high diversity systems. Nat Commun 2021; 12:5481. [PMID: 34531395 PMCID: PMC8446003 DOI: 10.1038/s41467-021-25824-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/25/2021] [Indexed: 02/08/2023] Open
Abstract
A fundamental question in community ecology is the role of predator-prey interactions in food-web stability and species coexistence. Although microbial microcosms offer powerful systems to investigate it, interrogating the environment is much more arduous. Here, we show in a 1-year survey that the obligate predators Bdellovibrio and like organisms (BALOs) can regulate prey populations, possibly in a density-dependent manner, in the naturally complex, species-rich environments of wastewater treatment plants. Abundant as well as rarer prey populations are affected, leading to an oscillating predatory landscape shifting at various temporal scales in which the total population remains stable. Shifts, along with differential prey range, explain co-existence of the numerous predators through niche partitioning. We validate these sequence-based findings using single-cell sorting combined with fluorescent hybridization and community sequencing. Our approach should be applicable for deciphering community interactions in other systems.
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Affiliation(s)
- Yossi Cohen
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Zohar Pasternak
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
- Division of Identification and Forensic Science, Israel Police, National Headquarters, Jerusalem, Israel
| | - Susann Müller
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Thomas Hübschmann
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Florian Schattenberg
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Kunjukrishnan Kamalakshi Sivakala
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | | | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany
- Institute of Biology, Leipzig University, Talstrasse 33, 04103, Leipzig, Germany
- Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel.
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19
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Ferguson RMW, O'Gorman EJ, McElroy DJ, McKew BA, Coleman RA, Emmerson MC, Dumbrell AJ. The ecological impacts of multiple environmental stressors on coastal biofilm bacteria. GLOBAL CHANGE BIOLOGY 2021; 27:3166-3178. [PMID: 33797829 DOI: 10.1111/gcb.15626] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/04/2021] [Indexed: 06/12/2023]
Abstract
Ecological communities are increasingly exposed to multiple interacting stressors. For example, warming directly affects the physiology of organisms, eutrophication stimulates the base of the food web, and harvesting larger organisms for human consumption dampens top-down control. These stressors often combine in the natural environment with unpredictable results. Bacterial communities in coastal ecosystems underpin marine food webs and provide many important ecosystem services (e.g. nutrient cycling and carbon fixation). Yet, how microbial communities will respond to a changing climate remains uncertain. Thus, we used marine mesocosms to examine the impacts of warming, nutrient enrichment, and altered top-predator population size structure (common shore crab) on coastal microbial biofilm communities in a crossed experimental design. Warming increased bacterial α-diversity (18% increase in species richness and 67% increase in evenness), but this was countered by a decrease in α-diversity with nutrient enrichment (14% and 21% decrease for species richness and evenness, respectively). Thus, we show some effects of these stressors could cancel each other out under climate change scenarios. Warming and top-predator population size structure both affected bacterial biofilm community composition, with warming increasing the abundance of bacteria capable of increased mineralization of dissolved and particulate organic matter, such as Flavobacteriia, Sphingobacteriia, and Cytophagia. However, the community shifts observed with warming depended on top-predator population size structure, with Sphingobacteriia increasing with smaller crabs and Cytophagia increasing with larger crabs. These changes could alter the balance between mineralization and carbon sequestration in coastal ecosystems, leading to a positive feedback loop between warming and CO2 production. Our results highlight the potential for warming to disrupt microbial communities and biogeochemical cycling in coastal ecosystems, and the importance of studying these effects in combination with other environmental stressors.
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Affiliation(s)
| | - Eoin J O'Gorman
- School of Life Sciences, University of Essex, Colchester, UK
| | - David J McElroy
- Coastal & Marine Ecosystems Group, School of Biological Sciences, University of Sydney, Sydney, NSW, Australia
- Marine Stewardship Council, London, UK
| | - Boyd A McKew
- School of Life Sciences, University of Essex, Colchester, UK
| | - Ross A Coleman
- Coastal & Marine Ecosystems Group, School of Biological Sciences, University of Sydney, Sydney, NSW, Australia
| | - Mark C Emmerson
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Alex J Dumbrell
- School of Life Sciences, University of Essex, Colchester, UK
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20
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Hungate BA, Marks JC, Power ME, Schwartz E, van Groenigen KJ, Blazewicz SJ, Chuckran P, Dijkstra P, Finley BK, Firestone MK, Foley M, Greenlon A, Hayer M, Hofmockel KS, Koch BJ, Mack MC, Mau RL, Miller SN, Morrissey EM, Propster JR, Purcell AM, Sieradzki E, Starr EP, Stone BWG, Terrer C, Pett-Ridge J. The Functional Significance of Bacterial Predators. mBio 2021; 12:e00466-21. [PMID: 33906922 PMCID: PMC8092244 DOI: 10.1128/mbio.00466-21] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 03/02/2021] [Indexed: 02/07/2023] Open
Abstract
Predation structures food webs, influences energy flow, and alters rates and pathways of nutrient cycling through ecosystems, effects that are well documented for macroscopic predators. In the microbial world, predatory bacteria are common, yet little is known about their rates of growth and roles in energy flows through microbial food webs, in part because these are difficult to quantify. Here, we show that growth and carbon uptake were higher in predatory bacteria compared to nonpredatory bacteria, a finding across 15 sites, synthesizing 82 experiments and over 100,000 taxon-specific measurements of element flow into newly synthesized bacterial DNA. Obligate predatory bacteria grew 36% faster and assimilated carbon at rates 211% higher than nonpredatory bacteria. These differences were less pronounced for facultative predators (6% higher growth rates, 17% higher carbon assimilation rates), though high growth and carbon assimilation rates were observed for some facultative predators, such as members of the genera Lysobacter and Cytophaga, both capable of gliding motility and wolf-pack hunting behavior. Added carbon substrates disproportionately stimulated growth of obligate predators, with responses 63% higher than those of nonpredators for the Bdellovibrionales and 81% higher for the Vampirovibrionales, whereas responses of facultative predators to substrate addition were no different from those of nonpredators. This finding supports the ecological theory that higher productivity increases predator control of lower trophic levels. These findings also indicate that the functional significance of bacterial predators increases with energy flow and that predatory bacteria influence element flow through microbial food webs.IMPORTANCE The word "predator" may conjure images of leopards killing and eating impala on the African savannah or of great white sharks attacking elephant seals off the coast of California. But microorganisms are also predators, including bacteria that kill and eat other bacteria. While predatory bacteria have been found in many environments, it has been challenging to document their importance in nature. This study quantified the growth of predatory and nonpredatory bacteria in soils (and one stream) by tracking isotopically labeled substrates into newly synthesized DNA. Predatory bacteria were more active than nonpredators, and obligate predators, such as Bdellovibrionales and Vampirovibrionales, increased in growth rate in response to added substrates at the base of the food chain, strong evidence of trophic control. This work provides quantitative measures of predator activity and suggests that predatory bacteria-along with protists, nematodes, and phages-are active and important in microbial food webs.
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Affiliation(s)
- Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jane C Marks
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Mary E Power
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Kees Jan van Groenigen
- Department of Geography, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Steven J Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Peter Chuckran
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Brianna K Finley
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Mary K Firestone
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
| | - Megan Foley
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Alex Greenlon
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
| | - Kirsten S Hofmockel
- Pacific Northwest National Laboratory, Richland, Washington, USA
- Department of Agronomy, Iowa State University, Ames, Iowa, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Michelle C Mack
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Samantha N Miller
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
| | - Ember M Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, USA
| | - Jeffrey R Propster
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Alicia M Purcell
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Ella Sieradzki
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
| | - Evan P Starr
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Bram W G Stone
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
| | - César Terrer
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
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21
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Sathyamoorthy R, Huppert A, Kadouri DE, Jurkevitch E. Effects of the prey landscape on the fitness of the bacterial predators Bdellovibrio and like organisms. FEMS Microbiol Ecol 2021; 97:6178867. [PMID: 33739375 DOI: 10.1093/femsec/fiab047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 03/17/2021] [Indexed: 11/12/2022] Open
Abstract
Bdellovibrio and like organisms (BALOs) are obligate predatory bacteria commonly encountered in the environment. In dual predator-prey cultures, prey accessibility ensures optimal feeding and replication and rapid BALO population growth. However, the environmental prey landscape is complex, as it also incorporates non-prey cells and other particles. These may act as decoys, generating unproductive encounters which in turn may affect both predator and prey population dynamics. In this study, we hypothesized that increasing decoy:prey ratios would bring about increasing costs on the predator's reproductive fitness. We also tested the hypothesis that different BALOs and decoys would have different effects. To this end, we constructed prey landscapes including periplasmic or epibiotic predators including two types of decoy under a large range of initial decoy:prey ratio, and mixed cultures containing multiple predators and prey. We show that as decoy:prey ratios increase, the maximal predator population sizes is reduced and the time to reach it significantly increases. We found that BALOs spent less time handling non-prey (including superinfection-immune invaded prey) than prey cells, and did not differentiate between efficient and less efficient prey. This may explain why in multiple predator and prey cultures, less preferred prey appear to act as decoy.
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Affiliation(s)
- Rajesh Sathyamoorthy
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Amit Huppert
- Bio-statistical Unit, The Gertner Institute for Epidemiology and Health Policy Research, Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Daniel E Kadouri
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, USA
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel
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22
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Li QM, Zhou YL, Wei ZF, Wang Y. Phylogenomic Insights into Distribution and Adaptation of Bdellovibrionota in Marine Waters. Microorganisms 2021; 9:757. [PMID: 33916768 PMCID: PMC8067016 DOI: 10.3390/microorganisms9040757] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/26/2021] [Accepted: 04/01/2021] [Indexed: 11/23/2022] Open
Abstract
Bdellovibrionota is composed of obligate predators that can consume some Gram-negative bacteria inhabiting various environments. However, whether genomic traits influence their distribution and marine adaptation remains to be answered. In this study, we performed phylogenomics and comparative genomics studies using 132 Bdellovibrionota genomes along with five metagenome-assembled genomes (MAGs) from deep sea zones. Four phylogenetic groups, Oligoflexia, Bdello-group1, Bdello-group2 and Bacteriovoracia, were revealed by constructing a phylogenetic tree, of which 53.84% of Bdello-group2 and 48.94% of Bacteriovoracia were derived from the ocean. Bacteriovoracia was more prevalent in deep sea zones, whereas Bdello-group2 was largely distributed in the epipelagic zone. Metabolic reconstruction indicated that genes involved in chemotaxis, flagellar (mobility), type II secretion system, ATP-binding cassette (ABC) transporters and penicillin-binding protein were necessary for the predatory lifestyle of Bdellovibrionota. Genes involved in glycerol metabolism, hydrogen peroxide (H2O2) degradation, cell wall recycling and peptide utilization were ubiquitously present in Bdellovibrionota genomes. Comparative genomics between marine and non-marine Bdellovibrionota demonstrated that betaine as an osmoprotectant is probably widely used by marine Bdellovibrionota, and all the marine genomes have a number of genes for adaptation to marine environments. The genes encoding chitinase and chitin-binding protein were identified for the first time in Oligoflexia, which implied that Oligoflexia may prey on a wider spectrum of microbes. This study expands our knowledge on adaption strategies of Bdellovibrionota inhabiting deep seas and the potential usage of Oligoflexia for biological control.
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Affiliation(s)
- Qing-Mei Li
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Q.-M.L.); (Y.-L.Z.); (Z.-F.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying-Li Zhou
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Q.-M.L.); (Y.-L.Z.); (Z.-F.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhan-Fei Wei
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Q.-M.L.); (Y.-L.Z.); (Z.-F.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Wang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Q.-M.L.); (Y.-L.Z.); (Z.-F.W.)
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23
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Ottaviani D, Pieralisi S, Chierichetti S, Rocchegiani E, Hattab J, Mosca F, Tiscar PG, Leoni F, Angelico G. Vibrio parahaemolyticus control in mussels by a Halobacteriovorax isolated from the Adriatic sea, Italy. Food Microbiol 2020; 92:103600. [PMID: 32950141 DOI: 10.1016/j.fm.2020.103600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 07/03/2020] [Accepted: 07/21/2020] [Indexed: 02/08/2023]
Abstract
This study evaluated the application of a Halobacteriovorax isolated from water of the Adriatic Sea (Italy) in controlling V. parahaemolyticus in mussels (Mytilus galloprovincialis). Two 72 h laboratory-scale V. parahaemolyticus decontamination experiments of mussels were performed. The test microcosm of experiment 1 was prepared using predator/prey free mussels experimentally contaminated with Halobacteriovorax/V. parahaemolyticus at a ratio of 103 PFU/105 CFU per ml, while that of experiment 2 using mussels naturally harbouring Halobacteriovorax that were experimentally contaminated with 105 CFU per ml of V. parahaemolyticus. For experiment 1, was also tested a control microcosm only contaminated with 105 CFU per ml of V. parahaemolyticus.. Double layer agar plating and pour plate techniques were used to enumerate Halobacteriovorax and V. parahaemolyticus, respectively. 16 S rRNA analysis was used to identify Halobacteriovorax. For both experiments in the test microcosm the concentration of prey remained at the same level as that experimentally added, i.e. 5 log for the entire analysis period. In experiment 1, V. parahaemolyticus counts in mussels were significantly lower in the test microcosm than the control with the maximum difference of 2.2 log at 24 h. Results demonstrate that Halobacteriovorax can modulate V. parahaemolyticus level in the mussels. The public impact of V. parahaemolyticus in bivalves is relevant and current decontamination processes are not always effective. Halobacteriovorax is a suitable candidate in the development of a biological approach to the purification of V. parahaemolyticus in mussels.
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Affiliation(s)
- Donatella Ottaviani
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Laboratorio Controllo Alimenti, via Cupa di Posatora 3, 60126, Ancona, Italy.
| | - Silvia Pieralisi
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Laboratorio Controllo Alimenti, via Cupa di Posatora 3, 60126, Ancona, Italy
| | - Serena Chierichetti
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Laboratorio Controllo Alimenti, via Cupa di Posatora 3, 60126, Ancona, Italy
| | - Elena Rocchegiani
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Laboratorio Controllo Alimenti, via Cupa di Posatora 3, 60126, Ancona, Italy
| | - Jasmine Hattab
- Università degli Studi di Teramo, Facoltà di Medicina Veterinaria, Località Piano d'Accio, 64100, Teramo, Italy
| | - Francesco Mosca
- Università degli Studi di Teramo, Facoltà di Medicina Veterinaria, Località Piano d'Accio, 64100, Teramo, Italy
| | - Pietro Giorgio Tiscar
- Università degli Studi di Teramo, Facoltà di Medicina Veterinaria, Località Piano d'Accio, 64100, Teramo, Italy
| | - Francesca Leoni
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Laboratorio Controllo Alimenti, via Cupa di Posatora 3, 60126, Ancona, Italy
| | - Gabriele Angelico
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Laboratorio Controllo Alimenti, via Cupa di Posatora 3, 60126, Ancona, Italy
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24
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Mu DS, Wang S, Liang QY, Du ZZ, Tian R, Ouyang Y, Wang XP, Zhou A, Gong Y, Chen GJ, Van Nostrand J, Yang Y, Zhou J, Du ZJ. Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments. MICROBIOME 2020; 8:126. [PMID: 32867860 PMCID: PMC7460792 DOI: 10.1186/s40168-020-00902-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 07/27/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Bacterial predation is an important selective force in microbial community structure and dynamics. However, only a limited number of predatory bacteria have been reported, and their predatory strategies and evolutionary adaptations remain elusive. We recently isolated a novel group of bacterial predators, Bradymonabacteria, representative of the novel order Bradymonadales in δ-Proteobacteria. Compared with those of other bacterial predators (e.g., Myxococcales and Bdellovibrionales), the predatory and living strategies of Bradymonadales are still largely unknown. RESULTS Based on individual coculture of Bradymonabacteria with 281 prey bacteria, Bradymonabacteria preyed on diverse bacteria but had a high preference for Bacteroidetes. Genomic analysis of 13 recently sequenced Bradymonabacteria indicated that these bacteria had conspicuous metabolic deficiencies, but they could synthesize many polymers, such as polyphosphate and polyhydroxyalkanoates. Dual transcriptome analysis of cocultures of Bradymonabacteria and prey suggested a potential contact-dependent predation mechanism. Comparative genomic analysis with 24 other bacterial predators indicated that Bradymonabacteria had different predatory and living strategies. Furthermore, we identified Bradymonadales from 1552 publicly available 16S rRNA amplicon sequencing samples, indicating that Bradymonadales was widely distributed and highly abundant in saline environments. Phylogenetic analysis showed that there may be six subgroups in this order; each subgroup occupied a different habitat. CONCLUSIONS Bradymonabacteria have unique living strategies that are transitional between the "obligate" and the so-called facultative predators. Thus, we propose a framework to categorize the current bacterial predators into 3 groups: (i) obligate predators (completely prey-dependent), (ii) facultative predators (facultatively prey-dependent), and (iii) opportunistic predators (prey-independent). Our findings provide an ecological and evolutionary framework for Bradymonadales and highlight their potential ecological roles in saline environments. Video abstract.
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Affiliation(s)
- Da-Shuai Mu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72, Jimo Binhai Road, Jimo, Qingdao, 266237, China
- Marine College, Shandong University, Weihai, 264209, China
| | - Shuo Wang
- Marine College, Shandong University, Weihai, 264209, China
| | - Qi-Yun Liang
- Marine College, Shandong University, Weihai, 264209, China
| | - Zhao-Zhong Du
- Marine College, Shandong University, Weihai, 264209, China
| | - Renmao Tian
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Yang Ouyang
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Xin-Peng Wang
- Marine College, Shandong University, Weihai, 264209, China
| | - Aifen Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Ya Gong
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72, Jimo Binhai Road, Jimo, Qingdao, 266237, China
- Marine College, Shandong University, Weihai, 264209, China
| | - Guan-Jun Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72, Jimo Binhai Road, Jimo, Qingdao, 266237, China
- Marine College, Shandong University, Weihai, 264209, China
| | - Joy Van Nostrand
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, 73019, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Zong-Jun Du
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72, Jimo Binhai Road, Jimo, Qingdao, 266237, China.
- Marine College, Shandong University, Weihai, 264209, China.
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25
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Ottaviani D, Pieralisi S, Rocchegiani E, Latini M, Leoni F, Mosca F, Pallavicini A, Tiscar PG, Angelico G. Vibrio parahaemolyticus-specific Halobacteriovorax From Seawater of a Mussel Harvesting Area in the Adriatic Sea: Abundance, Diversity, Efficiency and Relationship With the Prey Natural Level. Front Microbiol 2020; 11:1575. [PMID: 32733427 PMCID: PMC7360731 DOI: 10.3389/fmicb.2020.01575] [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: 01/03/2020] [Accepted: 06/17/2020] [Indexed: 11/13/2022] Open
Abstract
This research aimed to study the abundance and molecular diversity of Vibrio parahaemolyticus-specific Halobacteriovorax strains isolated from seawater of the Adriatic Sea and the relationship between predator and prey abundances. Moreover, predator efficiency of the Halobacteriovorax isolates toward V. parahaemolyticus and Vibrio cholerae non-O1/O139 strains was tested. V. parahaemolyticus NCTC 10885 was used as primary host for the isolation of Halobacteriovorax from seawater by the plaque assay. Molecular identification was performed by PCR detection of a fragment of the 16S rRNA gene of the Halobacteriovoraceae family members. Moreover, 700 bp PCR products were sequenced and compared between them and to clones described for other sampling sites. Vibrio counts were performed on TCBS agar from 100 ml of filtered water samples and presumptive colonies were confirmed by standard methods. Predatory efficiency of Halobacteriovorax isolates was tested by monitoring abilities of 3-day enrichments to form clear lytic halos on a lawn of Vibrio preys, by the plaque assay. Out of 12 seawater samples monthly collected from June 2017 to May 2018, 10 were positive for V. parahaemolyticus specific Halobacteriovorax with counts ranging from 4 to 1.4 × 103 PFU per 7.5 ml. No significant relationship was found between Halobacteriovorax and Vibrio abundances. The 16SrRNA sequences of our Halobacteriovorax strains, one for each positive sample, were divided into three lineages. Within the lineages, some sequences had 100% similarity. Sequence similarity between lineages was always <94.5% suggesting that they may therefore well belong to three different species. All Halobacteriovorax isolates had the ability to prey all tested Vibrio strains. Additional research is necessary to assess whether stable strains of Halobacteriovorax are present in the Adriatic Sea and to understand the mechanisms by which Halobacteriovorax may modulate the abundance of V. parahaemolyticus and other vibrios in a complex marine ecosystem.
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Affiliation(s)
- Donatella Ottaviani
- Laboratorio Controllo Alimenti, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Ancona, Italy
| | - Silvia Pieralisi
- Laboratorio Controllo Alimenti, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Ancona, Italy
| | - Elena Rocchegiani
- Laboratorio Controllo Alimenti, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Ancona, Italy
| | - Mario Latini
- Laboratorio Controllo Alimenti, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Ancona, Italy
| | - Francesca Leoni
- Laboratorio Controllo Alimenti, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Ancona, Italy
| | - Francesco Mosca
- Facoltà di Medicina Veterinaria, Università degli Studi di Teramo, Teramo, Italy
| | - Alberto Pallavicini
- Facoltà di Biologia, Università degli Studi di Trieste, Trieste, Italy.,Istituto Nazionale di Oceanografia e di Geofisica Sperimentale, Trieste, Italy
| | | | - Gabriele Angelico
- Laboratorio Controllo Alimenti, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Ancona, Italy
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26
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Ezzedine JA, Chardon C, Jacquet S. New 16S rRNA primers to uncover Bdellovibrio and like organisms diversity and abundance. J Microbiol Methods 2020; 175:105996. [PMID: 32598974 DOI: 10.1016/j.mimet.2020.105996] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/24/2020] [Accepted: 06/24/2020] [Indexed: 11/29/2022]
Abstract
Appropriate use and specific primers are important in assessing the diversity and abundance of microbial groups of interest. Bdellovibrio and like organisms (BALOs), that refer to obligate Gram-negative bacterial predators of other Gram-negative bacteria, evolved in terms of taxonomy and classification over the past two decades. Hence, some former primers have become inadequate while others are yet to be designed, for both PCR (especially with the advent of NGS) and qPCR approaches. Thus, to study BALOs' abundance and diversity in a variety of aquatic ecosystems, we designed in silico specific primer sets for each BALO genera and tested them in vitro on a variety of cultures and environmental samples. Also, we performed Sanger and Nano Miseq sequencing to reveal the exact degree of specificity of the most promising primers set. Here we report our success in designing specific primers for some BALOs genera, i.e. Bdellovibrio (PCR), Bacteriovorax (qPCR), Peredibacter (PCR).
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Affiliation(s)
- Jade A Ezzedine
- Université Savoie Mont-Blanc, INRAE, UMR CARRTEL, Thonon-les-Bains, France
| | - Cécile Chardon
- Université Savoie Mont-Blanc, INRAE, UMR CARRTEL, Thonon-les-Bains, France
| | - Stéphan Jacquet
- Université Savoie Mont-Blanc, INRAE, UMR CARRTEL, Thonon-les-Bains, France.
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Jain A, Krishnan KP, Begum N, Singh A, Thomas FA, Gopinath A. Response of bacterial communities from Kongsfjorden (Svalbard, Arctic Ocean) to macroalgal polysaccharide amendments. MARINE ENVIRONMENTAL RESEARCH 2020; 155:104874. [PMID: 31975691 DOI: 10.1016/j.marenvres.2020.104874] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 06/10/2023]
Abstract
Macroalgae are abundant in coastal Arctic habitats and contain a large amount of polysaccharides. Increased macroalgal productivity due to warmer temperatures and reduced sea-ice cover contribute a significant amount of polysaccharide-rich detritus in the region. To study bacterial degradation of macroalgal polysaccharides and their potential impact on biogeochemical processes we studied the response of bacterial communities from Kongsfjorden, Svalbard (Arctic Ocean) to alginate (AL) and agarose (AG) amendments, using an ex-situ microcosm experiment. Our results show that bacterial communities responded to the increased availability of macroalgal polysaccharides and community shift was congruent with a significant decline in nutrient concentrations. Initially-rare bacterial taxa affiliated with Gammaproteobacteria and Bacteroidia responded to the polysaccharide addition. Each polysaccharide addition incited the growth of certain distinct bacteria taxa. Compared to the un-amended control microcosms (CM), Polaribacter, Colwellia, Pseudoalteromonas, and unclassified Gammaproteobacteria responded to AL addition, whereas Paraglaciecola, Lentimonas, Colwellia, unclassified Gammaproteobacteria, unclassified Alteromonadales, and unclassified Alteromonadaceae responded to the AG addition. These results suggest that polysaccharides shift bacterial community composition towards copiotrophic bacterial taxa, with implications for carbon and nutrient cycling in coastal Svalbard.
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Affiliation(s)
- Anand Jain
- Cryobiology Laboratory, National Centre for Polar and Ocean Research, Vasco da Gama, Goa, India.
| | | | - Nazira Begum
- Cryobiology Laboratory, National Centre for Polar and Ocean Research, Vasco da Gama, Goa, India
| | - Archana Singh
- Cryobiology Laboratory, National Centre for Polar and Ocean Research, Vasco da Gama, Goa, India
| | - Femi Anna Thomas
- Cryobiology Laboratory, National Centre for Polar and Ocean Research, Vasco da Gama, Goa, India
| | - Anu Gopinath
- Department of Aquatic Environment Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
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Ezzedine JA, Jacas L, Desdevises Y, Jacquet S. Bdellovibrio and Like Organisms in Lake Geneva: An Unseen Elephant in the Room? Front Microbiol 2020; 11:98. [PMID: 32117128 PMCID: PMC7034301 DOI: 10.3389/fmicb.2020.00098] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/17/2020] [Indexed: 01/21/2023] Open
Abstract
When considering microbial biotic interactions, viruses as well as eukaryotic grazers are known to be important components of aquatic microbial food webs. It might be the same for bacterivorous bacteria but these groups have been comparatively less studied. This is typically the case of the Bdellovibrio and like organisms (BALOs), which are obligate bacterial predators of other bacteria. Recently, the abundance and distribution of three families of this functional group were investigated in perialpine lakes, revealing their presence and quantitative importance. Here, a more in-depth analysis is provided for Lake Geneva regarding the diversity of these bacterial predators at different seasons, sites and depths. We reveal a seasonal and spatial (vertical) pattern for BALOs. They were also found to be relatively diverse (especially Bdellovibrionaceae) and assigned to both known and unknown phylogenetic clusters. At last we found that most BALOs were positively correlated to other bacterial groups, mainly Gram-negative, in particular Myxococcales (among which many are predators of other microbes). This study is the first shedding light on this potentially important bacterial killing group in a large and deep lake.
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Affiliation(s)
- Jade A Ezzedine
- Université Savoie Mont-Blanc, INRAE, CARRTEL, Thonon-les-Bains, France
| | - Louis Jacas
- Université Savoie Mont-Blanc, INRAE, CARRTEL, Thonon-les-Bains, France
| | - Yves Desdevises
- CNRS, Biologie Intégrative des Organismes Marins, Observatoire Océanologique, Sorbonne Université, Banyuls-sur-Mer, France
| | - Stéphan Jacquet
- Université Savoie Mont-Blanc, INRAE, CARRTEL, Thonon-les-Bains, France
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Tang BL, Yang J, Chen XL, Wang P, Zhao HL, Su HN, Li CY, Yu Y, Zhong S, Wang L, Lidbury I, Ding H, Wang M, McMinn A, Zhang XY, Chen Y, Zhang YZ. A predator-prey interaction between a marine Pseudoalteromonas sp. and Gram-positive bacteria. Nat Commun 2020; 11:285. [PMID: 31941905 PMCID: PMC6962226 DOI: 10.1038/s41467-019-14133-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/13/2019] [Indexed: 12/23/2022] Open
Abstract
Predator-prey interactions play important roles in the cycling of marine organic matter. Here we show that a Gram-negative bacterium isolated from marine sediments (Pseudoalteromonas sp. strain CF6-2) can kill Gram-positive bacteria of diverse peptidoglycan (PG) chemotypes by secreting the metalloprotease pseudoalterin. Secretion of the enzyme requires a Type II secretion system. Pseudoalterin binds to the glycan strands of Gram positive bacterial PG and degrades the PG peptide chains, leading to cell death. The released nutrients, including PG-derived D-amino acids, can then be utilized by strain CF6-2 for growth. Pseudoalterin synthesis is induced by PG degradation products such as glycine and glycine-rich oligopeptides. Genes encoding putative pseudoalterin-like proteins are found in many other marine bacteria. This study reveals a new microbial interaction in the ocean. Predator-prey interactions play important roles in the cycling of marine organic matter. Here the authors show that a Gram-negative bacterium isolated from marine sediments can kill and feed on Gram-positive bacteria by secreting a peptidoglycan-degrading enzyme.
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Affiliation(s)
- Bai-Lu Tang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Jie Yang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Peng Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China.,College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China
| | - Hui-Lin Zhao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Hai-Nan Su
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Chun-Yang Li
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266373, China
| | - Yang Yu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Shuai Zhong
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Lei Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Ian Lidbury
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Haitao Ding
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, 200136, China
| | - Min Wang
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China
| | - Andrew McMinn
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Yin Chen
- College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China.,School of Life Sciences, University of Warwick, Coventry, UK
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China. .,College of Marine Life Sciences, Institute for Advanced Ocean Study, Ocean University of China, Qingdao, 266003, China. .,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266373, China.
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30
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Bera G, Doyle S, Passow U, Kamalanathan M, Wade TL, Sylvan JB, Sericano JL, Gold G, Quigg A, Knap AH. Biological response to dissolved versus dispersed oil. MARINE POLLUTION BULLETIN 2020; 150:110713. [PMID: 31757392 DOI: 10.1016/j.marpolbul.2019.110713] [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: 05/23/2019] [Revised: 10/21/2019] [Accepted: 10/31/2019] [Indexed: 06/10/2023]
Abstract
The water-soluble compounds of oil (e.g. low molecular weight PAHs) dissolve as a function of their physicochemical properties and environmental conditions, while the non-soluble compounds exist as dispersed droplets. Both the chemical and physical form of oil will affect the biological response. We present data from a mesocosm study comparing the microbial response to the water-soluble fraction (WSF), versus a water-accommodated fraction of oil (WAF), which contains both dispersed and dissolved oil components. WAF and WSF contained similar concentrations of low molecular weight PAHs, but concentrations of 4- and 5-ring PAHs were higher in WAF compared to WSF. Microbial communities were significantly different between WSF and WAF treatments, primary productivity was reduced more in WSF than in WAF, and concentrations of transparent exopolymeric particles were highest in WSF and lowest in the controls. These differences highlight the importance of dosing strategy for mesocosm and toxicity tests.
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Affiliation(s)
- Gopal Bera
- Texas A & M University, College Station, TX, USA.
| | - Shawn Doyle
- Texas A & M University, College Station, TX, USA
| | | | | | - Terry L Wade
- Texas A & M University, College Station, TX, USA
| | | | | | - Gerardo Gold
- Texas A & M University, College Station, TX, USA
| | - Antonietta Quigg
- Texas A & M University, College Station, TX, USA; Texas A & M University at Galveston, Galveston, TX, USA
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Diversity, Dynamics, and Distribution of Bdellovibrio and Like Organisms in Perialpine Lakes. Appl Environ Microbiol 2019; 85:AEM.02494-18. [PMID: 30635378 DOI: 10.1128/aem.02494-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/30/2018] [Indexed: 11/20/2022] Open
Abstract
Microbes drive a variety of ecosystem processes and services, but many of them remain largely unexplored because of a lack of knowledge on both the diversity and functionality of some potentially crucial microbiological compartments. This is the case with and within the group of bacterial predators collectively known as Bdellovibrio and like organisms (BALOs). Here, we report the abundance, distribution, and diversity of three families of these obligate predatory Gram-negative bacteria in three perialpine lakes (Lakes Annecy, Bourget, and Geneva). The study was conducted at different depths (near-surface versus 45 or 50 m) from August 2015 to January 2016. Using PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and cloning-sequencing approaches, we show that the diversity of BALOs is relatively low and very specific to freshwaters or even the lakes themselves. While the Peredibacteraceae family was represented mainly by a single species (Peredibacter starrii), it could represent up to 7% of the total bacterial cell abundances. Comparatively, the abundances of the two other families (Bdellovibrionaceae and Bacteriovoracaceae) were significantly lower. In addition, the distributions in the water column were very different between the three groups, suggesting various life strategies/niches, as follows: Peredibacteraceae dominated near the surface, while Bdellovibrionaceae and Bacteriovoracaceae were more abundant at greater depths. Statistical analyses revealed that BALOs seem mainly to be driven by depth and temperature. Finally, this original study was also the opportunity to design new quantitative PCR (qPCR) primers for Peredibacteraceae quantification.IMPORTANCE This study highlights the abundance, distribution, and diversity of a poorly known microbial compartment in natural aquatic ecosystems, the Bdellovibrio and like organisms (BALOs). These obligate bacterial predators of other bacteria may have an important functional role. This study shows the relative quantitative importance of the three main families of this group, with the design of a new primer pair, and their diversity. While both the diversity and the abundances of these BALOs were globally low, it is noteworthy that the abundance of the Peredibacteraceae could reach important values.
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32
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Interactions in self-assembled microbial communities saturate with diversity. ISME JOURNAL 2019; 13:1602-1617. [PMID: 30809013 PMCID: PMC6775987 DOI: 10.1038/s41396-019-0356-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 12/04/2018] [Accepted: 12/13/2018] [Indexed: 12/14/2022]
Abstract
How the diversity of organisms competing for or sharing resources influences community function is an important question in ecology but has rarely been explored in natural microbial communities. These generally contain large numbers of species making it difficult to disentangle how the effects of different interactions scale with diversity. Here, we show that changing diversity affects measures of community function in relatively simple communities but that increasing richness beyond a threshold has little detectable effect. We generated self-assembled communities with a wide range of diversity by growth of cells from serially diluted seawater on brown algal leachate. We subsequently isolated the most abundant taxa from these communities via dilution-to-extinction in order to compare productivity functions of the entire community to those of individual taxa. To parse the effect of different types of organismal interactions, we defined relative total function (RTF) as an index for positive or negative effects of diversity on community function. Our analysis identified three overall regimes with increasing diversity. At low richness (<12 taxa), positive and negative effects of interactions were both weak, while at moderate richness (12–26 taxa), community resource uptake increased but the carbon use efficiency decreased. Finally, beyond 26 taxa, the effect of interactions on community function saturated and further diversity increases did not affect community function. Although more diverse communities had overall greater access to resources, on average individual taxa within these communities had lower resource availability and reduced carbon use efficiency. Our results thus suggest competition and complementation simultaneously increase with diversity but both saturate at a threshold.
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Mu DS, Liang QY, Wang XM, Lu DC, Shi MJ, Chen GJ, Du ZJ. Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing. MICROBIOME 2018; 6:230. [PMID: 30587241 PMCID: PMC6307301 DOI: 10.1186/s40168-018-0613-2] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 12/04/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND The pure culture of prokaryotes remains essential to elucidating the role of these organisms. Scientists have reasoned that hard to cultivate microorganisms might grow in pure culture if provided with the chemical components of their natural environment. However, most microbial species in the biosphere that would otherwise be "culturable" may fail to grow because of their growth state in nature, such as dormancy. That means even if scientist would provide microorganisms with the natural environment, such dormant microorganisms probably still remain in a dormant state. RESULTS We constructed an enrichment culture system for high-efficiency isolation of uncultured strains from marine sediment. Degree of enrichment analysis, dormant and active taxa calculation, viable but non-culturable bacteria resuscitation analysis, combined with metatranscriptomic and comparative genomic analyses of the interactions between microbial communications during enrichment culture showed that the so-called enrichment method could culture the "uncultured" not only through enriching the abundance of "uncultured," but also through the resuscitation mechanism. In addition, the enrichment culture was a complicated mixed culture system, which contains the competition, cooperation, or coordination among bacterial communities, compared with pure cultures. CONCLUSIONS Considering that cultivation techniques must evolve further-from axenic to mixed cultures-for us to fully understand the microbial world, we should redevelop an understanding of the classic enrichment culture method. Enrichment culture methods can be developed and used to construct a model for analyzing mixed cultures and exploring microbial dark matter. This study provides a new train of thought to mining marine microbial dark matter based on mixed cultures.
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Affiliation(s)
- Da-Shuai Mu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
- College of Marine Science, Shandong University, Weihai, 264209, People's Republic of China
| | - Qi-Yun Liang
- College of Marine Science, Shandong University, Weihai, 264209, People's Republic of China
| | - Xiao-Man Wang
- College of Marine Science, Shandong University, Weihai, 264209, People's Republic of China
| | - De-Chen Lu
- College of Marine Science, Shandong University, Weihai, 264209, People's Republic of China
| | - Ming-Jing Shi
- College of Marine Science, Shandong University, Weihai, 264209, People's Republic of China
| | - Guan-Jun Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
- College of Marine Science, Shandong University, Weihai, 264209, People's Republic of China
| | - Zong-Jun Du
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China.
- College of Marine Science, Shandong University, Weihai, 264209, People's Republic of China.
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Said N, Chatzinotas A, Schmidt M. Have an Ion on It: The Life-Cycle of Bdellovibrio bacteriovorus Viewed by Helium-Ion Microscopy. ACTA ACUST UNITED AC 2018; 3:e1800250. [PMID: 32627346 DOI: 10.1002/adbi.201800250] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/11/2018] [Indexed: 11/12/2022]
Abstract
Helium-ion microscopy (HIM) has so far rarely been employed to image microbial interactions. Here, the visualization of the life-cycle of the bacterial predator Bdellovibrio bacteriovorus HD100 with Escherichia coli and Pseudomonas putida, respectively, as prey is presented. The predator is brought in contact with prey and samples are taken at selected times. The system is monitored by phase-contrast microscopy and HIM. For HIM imaging, a sample preparation protocol is established that preserves the structure of Bdellovibrio, prey, and bdelloplasts. The micrographs show the attachment of the predator to its prey, the evolution of bdelloplasts, their lysis, and the release of predator progeny. The combination of HIM with two more approaches allows for investigating predator-prey interactions from different angles: First, phase-contrast micrographs provide quantitative information for the numbers of predator, prey, and bdelloplasts. Second, a numerical model solving the retarded differential equations that describe the system's time-evolution is developed and fits the experimentally determined cell numbers. In conclusion, the high resolution, the large depth of focus, and surface sensitivity of HIM hold promise to expand future studies on so far neglected ecological interactions within the microbial food web, in particular in samples with pronounced topography such as bacterial biofilms.
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Affiliation(s)
- Nedal Said
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
| | - Matthias Schmidt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany
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Duan Y, Wang Y, Dong H, Ding X, Liu Q, Li H, Zhang J, Xiong D. Changes in the Intestine Microbial, Digestive, and Immune-Related Genes of Litopenaeus vannamei in Response to Dietary Probiotic Clostridium butyricum Supplementation. Front Microbiol 2018; 9:2191. [PMID: 30283419 PMCID: PMC6156435 DOI: 10.3389/fmicb.2018.02191] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 08/27/2018] [Indexed: 01/12/2023] Open
Abstract
The intestine barrier serves as the front-line defense in shrimp. Clostridium butyricum (CB) can produce butyric acid that provides energy for the intestine epithelial cells of the host. However, the effects of dietary CB on the intestine microbiome and the digestion and immunity of the host is not clear. In this study, we therefore investigated the composition and metabolic activity of the intestine microbiome, and digestive and immune-related gene expression in Litopenaeus vannamei fed with diets containing different levels of CB: basal diet (control), 2.5 × 109 CFU kg-1 diet (CB1), 5.0 × 109 CFU kg-1 diet (CB2), and 1.0 × 1010 CFU kg-1 diet (CB3) for 56 days. Dietary CB altered the composition of the intestine microbiome. Specifically, the dominant bacterial phylum Proteobacteria was enriched in the CB3 group and weakened in the CB1 and CB2 groups. The Bacteroidetes was enriched in the CB1 and CB2 groups and weakened in the CB3 group. The Firmicutes was enriched in all three CB groups. At the genus level, the potential pathogen (Desulfovibrio and Desulfobulbus) were weakened, and beneficial bacteria (Bacillus, Clostridium, Lachmoclostridium, Lachnospiraceae, and Lactobacillus) were enriched in response to dietary CB; these might contribute to the expression of the host digestive genes (α-amylase, lipase, trypsin, fatty acid-binding protein, and fatty acid synthase) and immune-related genes (prophenoloxidase, lipopolysaccharide and β-1,3-glucan binding protein, lysozyme, crustin, and superoxide dismutase). Additionally, CB enhanced the bacterial metabolism, especially that of carbohydrates, polymers, amino acids, carboxylic acids, and amines. These results revealed that dietary CB had a beneficial effect on the intestine health of L. vannamei by modulating the composition of the intestine microbiome, enhancing the microbial metabolism activity, and promoting the digestion and immunity of the host. The optimal dietary supplementation dosage was found to be 5.0 × 109 CFU kg-1 in the diet.
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Affiliation(s)
- Yafei Duan
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fishery Ecology and Environment, Guangdong Province, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Yun Wang
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fishery Ecology and Environment, Guangdong Province, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Hongbiao Dong
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fishery Ecology and Environment, Guangdong Province, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Xian Ding
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fishery Ecology and Environment, Guangdong Province, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Qingsong Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fishery Ecology and Environment, Guangdong Province, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Hua Li
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fishery Ecology and Environment, Guangdong Province, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jiasong Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fishery Ecology and Environment, Guangdong Province, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Dalin Xiong
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fishery Ecology and Environment, Guangdong Province, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
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Ottaviani D, Chierichetti S, Angelico G, Forte C, Rocchegiani E, Manuali E, Leoni F. Halobacteriovorax isolated from marine water of the Adriatic sea, Italy, as an effective predator of Vibrio parahaemolyticus, non-O1/O139 V. cholerae, V. vulnificus. J Appl Microbiol 2018; 125:1199-1207. [PMID: 29931749 DOI: 10.1111/jam.14027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 06/04/2018] [Accepted: 06/15/2018] [Indexed: 12/01/2022]
Abstract
AIM To detect marine Bdellovibrio and like organisms (BALOs) which are able to infect Vibrio parahaemolyticus from seawater of the Adriatic, Italy. To test, prey specificity and predation efficiency of our Halobacteriovorax isolate, named HBXCO1, towards 17 Vibrio and 7 non-Vibrio strains linked to the Adriatic sea, Italy. METHODS AND RESULTS Double layer agar plating technique was used to enumerate BALOs and to evaluate their prey specificity and predation efficiency. Transmission electron microscopy and 16S rRNA analysis were used to identify them. Means of BALOs counts ranged from 5·0 PFU per ml (March 2017) to 98·6 PFU per ml (August 2016). HBXCO1 had the ability to attack all tested prey strains of V. parahaemolyticus, Vibrio cholerae non-O1/O139 and Vibrio vulnificus, but it did not prey on non-Vibrio strains and V. alginolyticus under the tested conditions. CONCLUSIONS Bdellovibrio and like organisms capable of infecting pathogenic vibrios are naturally present in seawater of the Adriatic, Italy. Isolate HBXCO1 shows prey specificity preferentially for the Vibrio genus and high predatory efficiency towards a wide range of pathogenic strains. SIGNIFICANCE AND IMPACT OF THE STUDY The public impact of V. parahaemolyticus, non-O1/O139 V. cholerae and V. vulnificus in bivalves is relevant and current decontamination processes are not always effective. We believe that the predator HBXCO1 represents a potential candidate for the development of strategies of biocontrol of pathogenic vibrios in bivalves from harvesting to trade.
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Affiliation(s)
- D Ottaviani
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Laboratorio Nazionale di Riferimento per il controllo delle Contaminazioni Batteriche dei Molluschi Bivalvi Vivi, Ancona, Italy
| | - S Chierichetti
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Laboratorio Nazionale di Riferimento per il controllo delle Contaminazioni Batteriche dei Molluschi Bivalvi Vivi, Ancona, Italy
| | - G Angelico
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Laboratorio Nazionale di Riferimento per il controllo delle Contaminazioni Batteriche dei Molluschi Bivalvi Vivi, Ancona, Italy
| | - C Forte
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Laboratorio Nazionale di Riferimento per il controllo delle Contaminazioni Batteriche dei Molluschi Bivalvi Vivi, Ancona, Italy
| | - E Rocchegiani
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Laboratorio Nazionale di Riferimento per il controllo delle Contaminazioni Batteriche dei Molluschi Bivalvi Vivi, Ancona, Italy
| | - E Manuali
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Laboratorio Nazionale di Riferimento per il controllo delle Contaminazioni Batteriche dei Molluschi Bivalvi Vivi, Ancona, Italy
| | - F Leoni
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Laboratorio Nazionale di Riferimento per il controllo delle Contaminazioni Batteriche dei Molluschi Bivalvi Vivi, Ancona, Italy
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Relative Contributions of Halobacteriovorax and Bacteriophage to Bacterial Cell Death under Various Environmental Conditions. mBio 2018; 9:mBio.01202-18. [PMID: 30087166 PMCID: PMC6083911 DOI: 10.1128/mbio.01202-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The role of protists and bacteriophages in bacterial predation in the microbial food web has been well studied. There is mounting evidence that Bdellovibrio and like organisms (BALOs) also contribute to bacterial mortality and, in some cases, more so than bacteriophages. A full understanding of the ecologic function of the microbial food web requires recognition of all major predators and the magnitude of each predator’s contribution. Here we investigated the contribution of Halobacteriovorax, one of the BALOs, and bacteriophages when incubated with their common prey, Vibrio vulnificus, in a seawater microcosm. We observed that Halobacteriovorax was the greatest responder to the prey, increasing 18-fold with a simultaneous 4.4-log-unit reduction of V. vulnificus at 40 h, whereas the bacteriophage population showed no significant increase. In subsequent experiments to formulate a medium that would support the predatory activities and replication of both predators, low-nutrient media favored the predation and replication of the Halobacteriovorax, whereas higher-nutrient media enhanced phage growth. The greatest prey reduction and replication of both Halobacteriovorax and phage were observed in media with moderate nutrient levels. Additional experiments show that the predatory activities of both predators were influenced by environmental conditions, specifically, temperature and salinity. The two predators combined exerted greater control on V. vulnificus, a synergism that may be exploited for practical applications to reduce bacterial populations. These findings suggest that along with bacteriophage and protists, Halobacteriovorax has the potential to have a prominent role in bacterial mortality and cycling of nutrients, two vital ecologic functions. Although much has been reported about the marine microbial food web and the role of micropredators, specifically viruses and protists, the contribution of Bdellovibrio-like predators has largely been ignored, posing a major gap in understanding food web processes. A complete scenario of the microbial food web cannot be developed until the roles of all major micropredators and the magnitude of their contributions to bacterial mortality, structuring of microbial communities, and cycling of nutrients are assessed. Here we show compelling evidence that Halobacteriovorax, a predatory bacterium, is a significant contributor to bacterial death and, in some cases, may rival viruses as agents of bacterial mortality. These results advance current understanding of the microbial loop and top-down control on the bacterial community.
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38
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Liu J, Tian Z, Zhang P, Qiu G, Wu Y, Zhang H, Xu R, Fang W, Ye J, Song Y, Zeng G. Influence of reflux ratio on two-stage anoxic/oxic with MBR for leachate treatment: Performance and microbial community structure. BIORESOURCE TECHNOLOGY 2018; 256:69-76. [PMID: 29428616 DOI: 10.1016/j.biortech.2018.01.146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/27/2018] [Accepted: 01/31/2018] [Indexed: 06/08/2023]
Abstract
A lab-scale two-stage Anoxic/Oxic with MBR (AO/AO-MBR) system was operated for 81 days for leachate treatment with different reflux ratio (R). The best system performances were observed with a R value of 150%, and the average removal efficiencies of chemical oxygen demand, ammonia and total nitrogen were 85.6%, 99.1%, and 77.6%, respectively. The microbial community were monitored and evaluated using high-throughput sequencing. Proteobacteria were dominant in all process. Phylogenetic trees were described at species level, genus Thiopseudomonas, Amaricoccus, Nitrosomonas and Nitrobacter played significant roles in nitrogen removal. Co-occurrence analyzing top 20 genera showed that Nitrosomonas-Nitrobacter presented perfect positive relationship, as well as Paracoccus-Brevundimonas and Pusillimonas-Halobacteriovorax.
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Affiliation(s)
- Jianbo Liu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
| | - Zhiyong Tian
- Department of Urban Water Environmental Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Panyue Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China; School of Environmental and Chemical Engineering, Chongqing Three Gorges University, Chongqing 404632, China.
| | - Guanglei Qiu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Yan Wu
- School of Environmental and Chemical Engineering, Chongqing Three Gorges University, Chongqing 404632, China
| | - Haibo Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
| | - Rui Xu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
| | - Wei Fang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
| | - Jie Ye
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
| | - Yonghui Song
- Department of Urban Water Environmental Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
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Prey Range and Genome Evolution of Halobacteriovorax marinus Predatory Bacteria from an Estuary. mSphere 2018; 3:mSphere00508-17. [PMID: 29359184 PMCID: PMC5760749 DOI: 10.1128/msphere.00508-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/05/2017] [Indexed: 02/04/2023] Open
Abstract
Predatory bacteria attack and digest other bacteria and therefore may play a role in shaping microbial communities. To investigate phenotypic and genotypic variation in saltwater-adapted predatory bacteria, we isolated Halobacteriovorax marinus BE01 from an estuary in Rhode Island, assayed whether it could attack different prey bacteria, and sequenced and analyzed its genome. We found that BE01 is a prey generalist, attacking bacteria from different phylogenetic groups and environments. Gene order and amino acid sequences are highly conserved between BE01 and the H. marinus type strain, SJ. By comparative genomics, we detected two regions of gene content difference that likely occurred via horizontal gene transfer events. Acquired genes encode functions such as modification of DNA, membrane synthesis and regulation of gene expression. Understanding genome evolution and variation in predation phenotypes among predatory bacteria will inform their development as biocontrol agents and clarify how they impact microbial communities. Halobacteriovorax strains are saltwater-adapted predatory bacteria that attack Gram-negative bacteria and may play an important role in shaping microbial communities. To understand how Halobacteriovorax strains impact ecosystems and develop them as biocontrol agents, it is important to characterize variation in predation phenotypes and investigate Halobacteriovorax genome evolution. We isolated Halobacteriovorax marinus BE01 from an estuary in Rhode Island using Vibrio from the same site as prey. Small, fast-moving, attack-phase BE01 cells attach to and invade prey cells, consistent with the intraperiplasmic predation strategy of the H. marinus type strain, SJ. BE01 is a prey generalist, forming plaques on Vibrio strains from the estuary, Pseudomonas from soil, and Escherichia coli. Genome analysis revealed extremely high conservation of gene order and amino acid sequences between BE01 and SJ, suggesting strong selective pressure to maintain the genome in this H. marinus lineage. Despite this, we identified two regions of gene content difference that likely resulted from horizontal gene transfer. Analysis of modal codon usage frequencies supports the hypothesis that these regions were acquired from bacteria with different codon usage biases than H. marinus. In one of these regions, BE01 and SJ carry different genes associated with mobile genetic elements. Acquired functions in BE01 include the dnd operon, which encodes a pathway for DNA modification, and a suite of genes involved in membrane synthesis and regulation of gene expression that was likely acquired from another Halobacteriovorax lineage. This analysis provides further evidence that horizontal gene transfer plays an important role in genome evolution in predatory bacteria. IMPORTANCE Predatory bacteria attack and digest other bacteria and therefore may play a role in shaping microbial communities. To investigate phenotypic and genotypic variation in saltwater-adapted predatory bacteria, we isolated Halobacteriovorax marinus BE01 from an estuary in Rhode Island, assayed whether it could attack different prey bacteria, and sequenced and analyzed its genome. We found that BE01 is a prey generalist, attacking bacteria from different phylogenetic groups and environments. Gene order and amino acid sequences are highly conserved between BE01 and the H. marinus type strain, SJ. By comparative genomics, we detected two regions of gene content difference that likely occurred via horizontal gene transfer events. Acquired genes encode functions such as modification of DNA, membrane synthesis and regulation of gene expression. Understanding genome evolution and variation in predation phenotypes among predatory bacteria will inform their development as biocontrol agents and clarify how they impact microbial communities.
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40
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Draft Genome Sequence of the Predatory Marine Bacterium Halobacteriovorax sp. Strain JY17. GENOME ANNOUNCEMENTS 2018; 6:6/1/e01416-17. [PMID: 29301887 PMCID: PMC5754496 DOI: 10.1128/genomea.01416-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A draft genome sequence of Halobacteriovorax sp. strain JY17 was assembled from a metagenomic data set. The 3.47-Mbp genome of this unusual predatory bacterium contains 3,263 protein-coding sequences, 33 tRNAs, and 2 copies each of the 16S, 23S, and 5S rRNA genes. This is only the third sequenced representative of this genus.
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41
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Johnke J, Boenigk J, Harms H, Chatzinotas A. Killing the killer: predation between protists and predatory bacteria. FEMS Microbiol Lett 2017; 364:3746136. [PMID: 28444379 DOI: 10.1093/femsle/fnx089] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/20/2017] [Indexed: 02/05/2023] Open
Abstract
Predation by microbes is one of the main drivers of bacterial mortality in the environment. In most ecosystems multiple micropredators compete at least partially for the same bacterial resource. Predatory interactions between these micropredators might lead to shifts within microbial communities. Integrating these interactions is therefore crucial for the understanding of ecosystem functioning. In this study, we investigated the predation between two groups of micropredators, i.e. phagotrophic protists and Bdellovibrio and like organisms (BALOs). BALOs are obligate predators of Gram-negative bacteria. We hypothesised that protists can prey upon BALOs despite the small size and high swimming speed of the latter, which makes them potentially hard to capture. Predation experiments including three protists, i.e. one filter feeder and two interception feeder, showed that BALOs are a relevant prey for these protists. The growth rate on BALOs differed for the respective protists. The filter feeding ciliate was growing equally well on the BALOs and on Escherichia coli, whereas the two flagellate species grew less well on the BALOs compared to E. coli. However, BALOs might not be a favourable food source in resource-rich environments as they are not enabling all protists to grow as much as on bacteria of bigger volume.
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Affiliation(s)
- Julia Johnke
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany
| | - Jens Boenigk
- Biodiversity Department and Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, 45117 Essen, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
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42
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Johnke J, Baron M, de Leeuw M, Kushmaro A, Jurkevitch E, Harms H, Chatzinotas A. A Generalist Protist Predator Enables Coexistence in Multitrophic Predator-Prey Systems Containing a Phage and the Bacterial Predator Bdellovibrio. Front Ecol Evol 2017. [DOI: 10.3389/fevo.2017.00124] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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43
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Jurkevitch É, Jacquet S. [Bdellovibrio and like organisms: outstanding predators!]. Med Sci (Paris) 2017; 33:519-527. [PMID: 28612728 DOI: 10.1051/medsci/20173305016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Obligate predatory bacteria, i.e. bacteria requiring a Gram negative prey cell in order to complete their cell cycle, belong to the polyphyletic group referred to as the Bdellovibrio And Like Organisms (BALO). Predatory interactions between bacteria are complex, yet their dynamics and impact on bacterial communities in the environment are becoming better understood. BALO have unique life cycles: they grow epibiotically with the predator remaining attached to the prey's envelope, dividing in a binary manner or periplasmically, i.e. by penetrating the prey's periplasm to generate a number of progeny cells. The periplasmic life cycle includes unique gene and protein patterns and unique signaling features. These ecological and cellular features, along with applications of the BALO in the medical, agricultural and environmental fields are surveyed.
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Affiliation(s)
- Édouard Jurkevitch
- Faculté d'Agriculture, de l'Alimentation et de l'Environnement, Université Hébraïque de Jérusalem, Rehovot, Israël
| | - Stéphan Jacquet
- INRA, UMR CARRTEL, 75, avenue de Corzent, 74200 Thonon-les-Bains, France
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44
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Welsh RM, Rosales SM, Zaneveld JR, Payet JP, McMinds R, Hubbs SL, Vega Thurber RL. Alien vs. predator: bacterial challenge alters coral microbiomes unless controlled by Halobacteriovorax predators. PeerJ 2017; 5:e3315. [PMID: 28584701 PMCID: PMC5455293 DOI: 10.7717/peerj.3315] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 04/14/2017] [Indexed: 12/26/2022] Open
Abstract
Coral microbiomes are known to play important roles in organismal health, response to environmental stress, and resistance to disease. The coral microbiome contains diverse assemblages of resident bacteria, ranging from defensive and metabolic symbionts to opportunistic bacteria that may turn harmful in compromised hosts. However, little is known about how these bacterial interactions influence the mechanism and controls of overall structure, stability, and function of the microbiome. We sought to test how coral microbiome dynamics were affected by interactions between two bacteria: Vibrio coralliilyticus, a known temperature-dependent pathogen of some corals, and Halobacteriovorax, a unique bacterial predator of Vibrio and other gram-negative bacteria. We challenged reef-building coral with V. coralliilyticus in the presence or absence of Halobacteriovorax predators, and monitored microbial community dynamics with 16S rRNA gene profiling time-series. Vibrio coralliilyticus inoculation increased the mean relative abundance of Vibrios by greater than 35% from the 4 to 8 hour time point, but not in the 24 & 32 hour time points. However, strong secondary effects of the Vibrio challenge were also observed for the rest of the microbiome such as increased richness (observed species), and reduced stability (increased beta-diversity). Moreover, after the transient increase in Vibrios, two lineages of bacteria (Rhodobacterales and Cytophagales) increased in coral tissues, suggesting that V. coralliilyticus challenge opens niche space for these known opportunists. Rhodobacterales increased from 6.99% (±0.05 SEM) to a maximum mean relative abundance of 48.75% (±0.14 SEM) in the final time point and Cytophagales from <0.001% to 3.656%. Halobacteriovorax predators are commonly present at low-abundance on coral surfaces. Based on the keystone role of predators in many ecosystems, we hypothesized that Halobacteriovorax predators might help protect corals by consuming foreign or "alien" gram negative bacteria. Halobacteriovorax inoculation also altered the microbiome but to a lesser degree than V. coralliilyticus, and Halobacteriovorax were never detected after inoculation. Simultaneous challenge with both V. coralliilyticus and predatory Halobacteriovorax eliminated the increase in V. coralliilyticus, ameliorated changes to the rest of the coral microbiome, and prevented the secondary blooms of opportunistic Rhodobacterales and Cytophagales seen in the V. coralliilyticus challenge. These data suggest that, under certain circumstances, host-associated bacterial predators may mitigate the ability of other bacteria to destabilize the microbiome.
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Affiliation(s)
- Rory M Welsh
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | | | - Jesse R Zaneveld
- Department of Microbiology, Oregon State University, Corvallis, OR, USA.,Department of Biological Sciences, University of Washington Bothell, Bothell, WA, USA
| | - Jérôme P Payet
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | - Ryan McMinds
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | - Steven L Hubbs
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
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45
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López-Pérez M, Kimes NE, Haro-Moreno JM, Rodriguez-Valera F. Not All Particles Are Equal: The Selective Enrichment of Particle-Associated Bacteria from the Mediterranean Sea. Front Microbiol 2016; 7:996. [PMID: 27446036 PMCID: PMC4916215 DOI: 10.3389/fmicb.2016.00996] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 06/09/2016] [Indexed: 11/13/2022] Open
Abstract
We have used two metagenomic approaches, direct sequencing of natural samples and sequencing after enrichment, to characterize communities of prokaryotes associated to particles. In the first approximation, different size filters (0.22 and 5 μm) were used to identify prokaryotic microbes of free-living and particle-attached bacterial communities in the Mediterranean water column. A subtractive metagenomic approach was used to characterize the dominant microbial groups in the large size fraction that were not present in the free-living one. They belonged mainly to Actinobacteria, Planctomycetes, Flavobacteria and Proteobacteria. In addition, marine microbial communities enriched by incubation with different kinds of particulate material have been studied by metagenomic assembly. Different particle kinds (diatomaceous earth, sand, chitin and cellulose) were colonized by very different communities of bacteria belonging to Roseobacter, Vibrio, Bacteriovorax, and Lacinutrix that were distant relatives of genomes already described from marine habitats. Besides, using assembly from deep metagenomic sequencing from the particle-specific enrichments we were able to determine a total of 20 groups of contigs (eight of them with >50% completeness) and reconstruct de novo five new genomes of novel species within marine clades (>79% completeness and <1.8% contamination). We also describe for the first time the genome of a marine Rhizobiales phage that seems to infect a broad range of Alphaproteobacteria and live in habitats as diverse as soil, marine sediment and water column. The metagenomic recruitment of the communities found by direct sequencing of the large size filter and by enrichment had nearly no overlap. These results indicate that these reconstructed genomes are part of the rare biosphere which exists at nominal levels under natural conditions.
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46
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Modenutti BE, Balseiro EG, Bastidas Navarro MA, Lee ZM, Souza MS, Corman JR, Elser JJ. Effects of Volcanic Pumice Inputs on Microbial Community Composition and Dissolved C/P Ratios in Lake Waters: an Experimental Approach. MICROBIAL ECOLOGY 2016; 71:18-28. [PMID: 26563321 DOI: 10.1007/s00248-015-0707-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 11/02/2015] [Indexed: 06/05/2023]
Abstract
Volcanic eruptions discharge massive amounts of ash and pumice that decrease light penetration in lakes and lead to concomitant increases in phosphorus (P) concentrations and shifts in soluble C/P ratios. The consequences of these sudden changes for bacteria community composition, metabolism, and enzymatic activity remain unclear, especially for the dynamic period immediately after pumice deposition. Thus, the main aim of our study was to determine how ambient bacterial communities respond to pumice inputs in lakes that differ in dissolved organic carbon (DOC) and P concentrations and to what extent these responses are moderated by substrate C/P stoichiometry. We performed an outdoor experiment with natural lake water from two lakes that differed in dissolved organic carbon (DOC) concentration. We measured nutrient concentrations, alkaline phosphatase activity (APA), and DOC consumption rates and assessed different components of bacterial community structure using next-generation sequencing of the 16S rRNA gene. Pumice inputs caused a decrease in the C/P ratio of dissolved resources, a decrease in APA, and an increase in DOC consumption, indicating reduced P limitation. These changes in bacteria metabolism were coupled with modifications in the assemblage composition and an increase in diversity, with increases in bacterial taxa associated with biofilm and sediments, in predatory bacteria, and in bacteria with gliding motility. Our results confirm that volcanic eruptions have the potential to alter nutrient partitioning and light penetration in receiving waterways which can have dramatic impacts on microbial community dynamics.
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Affiliation(s)
- B E Modenutti
- Laboratorio de Limnología, INIBIOMA, CONICET-University of Comahue, Quintral 1250, 8400, Bariloche, Argentina.
| | - E G Balseiro
- Laboratorio de Limnología, INIBIOMA, CONICET-University of Comahue, Quintral 1250, 8400, Bariloche, Argentina
| | - M A Bastidas Navarro
- Laboratorio de Limnología, INIBIOMA, CONICET-University of Comahue, Quintral 1250, 8400, Bariloche, Argentina
| | - Z M Lee
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - M S Souza
- Laboratorio de Limnología, INIBIOMA, CONICET-University of Comahue, Quintral 1250, 8400, Bariloche, Argentina
| | - J R Corman
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Center for Limnology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - J J Elser
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
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47
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Welsh RM, Zaneveld JR, Rosales SM, Payet JP, Burkepile DE, Thurber RV. Bacterial predation in a marine host-associated microbiome. ISME JOURNAL 2015; 10:1540-4. [PMID: 26613338 DOI: 10.1038/ismej.2015.219] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 10/14/2015] [Accepted: 10/25/2015] [Indexed: 11/09/2022]
Abstract
In many ecological communities, predation has a key role in regulating community structure or function. Although predation has been extensively explored in animals and microbial eukaryotes, predation by bacteria is less well understood. Here we show that predatory bacteria of the genus Halobacteriovorax are prevalent and active predators on the surface of several genera of reef-building corals. Across a library of 198 16S rRNA samples spanning three coral genera, 79% were positive for carriage of Halobacteriovorax. Cultured Halobacteriovorax from Porites asteroides corals tested positive for predation on the putative coral pathogens Vibrio corallyticus and Vibrio harveyii. Co-occurrence network analysis showed that Halobacteriovorax's interactions with other bacteria are influenced by temperature and inorganic nutrient concentration, and further suggested that this bacterial predator's abundance may be driven by prey availability. Thus, animal microbiomes can harbor active bacterial predators, which may regulate microbiome structure and protect the host by consuming potential pathogens.
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Affiliation(s)
- Rory M Welsh
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | - Jesse R Zaneveld
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | | | - Jérôme P Payet
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | - Deron E Burkepile
- Department of Biological Sciences, Florida International University, North Miami, FL, USA.,Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
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48
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Purification and Host Specificity of Predatory Halobacteriovorax Isolates from Seawater. Appl Environ Microbiol 2015; 82:922-7. [PMID: 26590288 DOI: 10.1128/aem.03136-15] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 11/17/2015] [Indexed: 11/20/2022] Open
Abstract
Halobacteriovorax (formerly Bacteriovorax) is a small predatory bacterium found in the marine environment and modulates bacterial pathogens in shellfish. Four strains of Halobacteriovorax originally isolated in Vibrio parahaemolyticus O3:K6 host cells were separated from their prey by an enrichment-filtration-dilution technique for specificity testing in other bacteria. This technique was essential, since 0.45-μm filtration alone was unable to remove infectious Vibrio minicells, as determined by scanning electron microscopy and cultural methods. Purified Halobacteriovorax strains were screened for predation against other V. parahaemolyticus strains and against Vibrio vulnificus, Vibrio alginolyticus, Escherichia coli O157:H7, and Salmonella enterica serovar Typhimurium DT104, all potential threats to seafood safety. They showed high host specificity and were predatory only against strains of V. parahaemolyticus. In addition, strains of Halobacteriovorax that were predatory for E. coli O157:H7 and S. Typhimurium DT104 were isolated from a tidal river at 5 ppt salinity. In a modified plaque assay agar, they killed their respective prey over a broad range of salinities (5 to 30 ppt). Plaques became smaller as the salinity levels rose, suggesting that the lower salinities were optimal for the predators' replication. These species also showed broader host specificity, infectious against each other's original hosts as well as against V. parahaemolyticus strains. In summary, this study characterized strains of Halobacteriovorax which may be considered for use in the development of broad-based biocontrol technologies to enhance the safety of commercially marketed shellfish and other foods.
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