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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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2
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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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3
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Fong J, Tang PPY, Deignan LK, Seah JCL, McDougald D, Rice SA, Todd PA. Chemically Mediated Interactions with Macroalgae Negatively Affect Coral Health but Induce Limited Changes in Coral Microbiomes. Microorganisms 2023; 11:2261. [PMID: 37764105 PMCID: PMC10535309 DOI: 10.3390/microorganisms11092261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Allelopathic chemicals facilitated by the direct contact of macroalgae with corals are potentially an important mechanism mediating coral-macroalgal interactions, but only a few studies have explored their impacts on coral health and microbiomes and the coral's ability to recover. We conducted a field experiment on an equatorial urbanized reef to assess the allelopathic effects of four macroalgal species (Bryopsis sp., Endosiphonia horrida, Hypnea pannosa and Lobophora challengeriae) on the health and microbiomes of three coral species (Merulina ampliata, Montipora stellata and Pocillopora acuta). Following 24 h of exposure, crude extracts of all four macroalgal species caused significant coral tissue bleaching and reduction in effective quantum yield. The corals were able to recover within 72 h of the removal of extracts, except those that were exposed to L. challengeriae. While some macroalgal extracts caused an increase in the alpha diversity of coral microbiomes, there were no significant differences in the composition and variability of coral microbiomes between controls and macroalgal extracts at each sampling time point. Nevertheless, DESeq2 differential abundance analyses showed species-specific responses of coral microbiomes. Overall, our findings provide insights on the limited effect of chemically mediated interactions with macroalgae on coral microbiomes and the capacity of corals to recover quickly from the macroalgal chemicals.
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Affiliation(s)
- Jenny Fong
- Experimental Marine Ecology Laboratory, National University of Singapore, Singapore 117558, Singapore; (J.C.L.S.); (P.A.T.)
| | - Peggy P. Y. Tang
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; (P.P.Y.T.); (L.K.D.); (D.M.); (S.A.R.)
| | - Lindsey K. Deignan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; (P.P.Y.T.); (L.K.D.); (D.M.); (S.A.R.)
| | - Jovena C. L. Seah
- Experimental Marine Ecology Laboratory, National University of Singapore, Singapore 117558, Singapore; (J.C.L.S.); (P.A.T.)
| | - Diane McDougald
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; (P.P.Y.T.); (L.K.D.); (D.M.); (S.A.R.)
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Scott A. Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; (P.P.Y.T.); (L.K.D.); (D.M.); (S.A.R.)
| | - Peter A. Todd
- Experimental Marine Ecology Laboratory, National University of Singapore, Singapore 117558, Singapore; (J.C.L.S.); (P.A.T.)
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Richards GP, Watson MA, Williams HN, Jones JL. Predator-Prey Interactions between Halobacteriovorax and Pathogenic Vibrio parahaemolyticus Strains: Geographical Considerations and Influence of Vibrio Hemolysins. Microbiol Spectr 2023; 11:e0235323. [PMID: 37409976 PMCID: PMC10434201 DOI: 10.1128/spectrum.02353-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 06/23/2023] [Indexed: 07/07/2023] Open
Abstract
Halobacteriovorax is a genus of naturally occurring marine predatory bacteria that attack, replicate within, and lyse vibrios and other bacteria. This study evaluated the specificity of four Halobacteriovorax strains against important sequence types (STs) of clinically relevant Vibrio parahaemolyticus, including pandemic strains ST3 and ST36. The Halobacteriovorax bacteria were previously isolated from seawater from the Mid-Atlantic, Gulf of Mexico, and Hawaiian coasts of the United States. Specificity screening was performed using a double agar plaque assay technique on 23 well-characterized and genomically sequenced V. parahaemolyticus strains isolated from infected individuals from widely varying geographic locations within the United States. With few exceptions, results showed that Halobacteriovorax bacteria were excellent predators of the V. parahaemolyticus strains regardless of the origins of the predator or prey. Sequence types and serotypes of V. parahaemolyticus did not influence host specificity, nor did the presence or absence of genes for the thermostable direct hemolysin (TDH) or the TDH-related hemolysin, although faint (cloudy) plaques were present when one or both hemolysins were absent in three of the Vibrio strains. Plaque sizes varied depending on both the Halobacteriovorax and Vibrio strains evaluated, suggesting differences in Halobacteriovorax replication and/or growth rates. The very broad infectivity of Halobacteriovorax toward pathogenic strains of V. parahaemolyticus makes Halobacteriovorax a strong candidate for use in commercial processing applications to enhance the safety of seafoods. IMPORTANCE Vibrio parahaemolyticus is a formidable obstacle to seafood safety. Strains pathogenic to humans are numerous and difficult to control, especially within molluscan shellfish. The pandemic spread of ST3 and ST36 has caused considerable concern, but many other STs are also problematic. The present study demonstrates broad predatory activity of Halobacteriovorax strains obtained along U.S. coastal waters from the Mid-Atlantic, Gulf Coast, and Hawaii toward strains of pathogenic V. parahaemolyticus. This broad activity against clinically relevant V. parahaemolyticus strains suggests a role for Halobacteriovorax in mediating pathogenic V. parahaemolyticus levels in seafoods and their environment as well as the potential application of these predators in the development of new disinfection technologies to reduce pathogenic vibrios in molluscan shellfish and other seafoods.
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Affiliation(s)
- Gary P. Richards
- U.S. Department of Agriculture, Agricultural Research Service, Delaware State University, Dover, Delaware, USA
| | - Michael A. Watson
- U.S. Department of Agriculture, Agricultural Research Service, Delaware State University, Dover, Delaware, USA
| | - Henry N. Williams
- School of the Environment, Florida Agricultural and Mechanical University, Tallahassee, Florida, USA
| | - Jessica L. Jones
- U.S. Food and Drug Administration, Division of Seafood Science and Technology, Gulf Coast Seafood Laboratory, Dauphin Island, Alabama, USA
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5
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Kamada S, Wakabayashi R, Naganuma T. Phylogenetic Revisit to a Review on Predatory Bacteria. Microorganisms 2023; 11:1673. [PMID: 37512846 PMCID: PMC10385382 DOI: 10.3390/microorganisms11071673] [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: 05/29/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Predatory bacteria, along with the biology of their predatory behavior, have attracted interest in terms of their ecological significance and industrial applications, a trend that has been even more pronounced since the comprehensive review in 2016. This mini-review does not cover research trends, such as the role of outer membrane vesicles in myxobacterial predation, but provides an overview of the classification and newly described taxa of predatory bacteria since 2016, particularly with regard to phylogenetic aspects. Among them, it is noteworthy that in 2020 there was a major phylogenetic reorganization that the taxa hosting Bdellovibrio and Myxococcus, formerly classified as Deltaproteobacteria, were proposed as the new phyla Bdellovibrionota and Myxococcota, respectively. Predatory bacteria have been reported from other phyla, especially from the candidate divisions. Predatory bacteria that prey on cyanobacteria and predatory cyanobacteria that prey on Chlorella have also been found. These are also covered in this mini-review, and trans-phylum phylogenetic trees are presented.
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Affiliation(s)
- Saki Kamada
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashihiroshima 739-8528, Japan
| | - Ryoka Wakabayashi
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashihiroshima 739-8528, Japan
| | - Takeshi Naganuma
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashihiroshima 739-8528, Japan
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6
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Da Silva RRP, White CA, Bowman JP, Ross DJ. Composition and functionality of bacterioplankton communities in marine coastal zones adjacent to finfish aquaculture. MARINE POLLUTION BULLETIN 2022; 182:113957. [PMID: 35872476 DOI: 10.1016/j.marpolbul.2022.113957] [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: 05/04/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Finfish aquaculture is a fast-growing primary industry and is increasingly common in coastal ecosystems. Bacterioplankton is ubiquitous in marine environment and respond rapidly to environmental changes. Changes in bacterioplankton community are not well understood in semi-enclosed stratified embayments. This study aims to examine aquaculture effects in the composition and functional profiles of the bacterioplankton community using amplicon sequencing along a distance gradient from two finfish leases in a marine embayment. Results revealed natural stratification in bacterioplankton associated to NOx, conductivity, salinity, temperature and PO4. Among the differentially abundant bacteria in leases, we found members associated with nutrient enrichment and aquaculture activities. Abundant predicted functions near leases were assigned to organic matter degradation, fermentation, and antibiotic resistance. This study provides a first effort to describe changes in the bacterioplankton community composition and function due to finfish aquaculture in a semi-enclosed and highly stratified embayment with a significant freshwater input.
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Affiliation(s)
- R R P Da Silva
- Institute for Marine and Antarctic Studies (IMAS), Nubeena Crescent, Taroona, Tasmania 7053, Australia.
| | - C A White
- Institute for Marine and Antarctic Studies (IMAS), Nubeena Crescent, Taroona, Tasmania 7053, Australia
| | - J P Bowman
- Tasmanian Institute of Agriculture (TIA), University of Tasmania, Hobart, Tasmania 7001, Australia
| | - D J Ross
- Institute for Marine and Antarctic Studies (IMAS), Nubeena Crescent, Taroona, Tasmania 7053, Australia
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7
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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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8
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Hoshiko Y, Nishiyama Y, Moriya T, Kadokami K, López-Jácome LE, Hirano R, García-Contreras R, Maeda T. Quinolone Signals Related to Pseudomonas Quinolone Signal-Quorum Sensing Inhibits the Predatory Activity of Bdellovibrio bacteriovorus. Front Microbiol 2021; 12:722579. [PMID: 34566925 PMCID: PMC8461301 DOI: 10.3389/fmicb.2021.722579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/12/2021] [Indexed: 12/12/2022] Open
Abstract
Bdellovibrio bacteriovorus is one of the predatory bacteria; therefore, it can act as a novel “living antibiotic,” unlike the current antibiotics. Here the predation of Escherichia coli by B. bacteriovorus was inhibited in the presence of Pseudomonas aeruginosa. This study investigated whether P. aeruginosa-induced predation inhibition is associated with bacterial quorum sensing (QS). Each las, rhl, or pqs QS mutant in P. aeruginosa was used to check the predatory activity of E. coli cells using B. bacteriovorus. As a result, the predatory activity of B. bacteriovorus increased in a mutant pqs QS system, whereas wild-type PA14 inhibited the predatory activity. Moreover, the addition of 4-hydroxy-2-heptylquinoline (HHQ) or the analog triggered the low predatory activity of B. bacteriovorus and killed B. bacteriovorus cells. Therefore, a defensive action of P. aeruginosa against B. bacteriovorus is activated by the pqs QS system, which produces some quinolone compounds such as HHQ.
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Affiliation(s)
- Yuki Hoshiko
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Yoshito Nishiyama
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Tae Moriya
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Kiwao Kadokami
- Institute of Environmental Science and Technology, The University of Kitakyushu, Kitakyushu, Japan
| | - Luis Esaú López-Jácome
- Department of Microbiology and Parasitology, Faculty of Medicine, UNAM, Mexico City, Mexico.,Laboratory of Infectology, National Institute of Rehabilitation Luis Guillermo Ibarra Ibarra, Mexico City, Mexico
| | - Ryutaro Hirano
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | | | - Toshinari Maeda
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
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Qian H, Hou C, Liao H, Wang L, Han S, Peng S, Chen W, Huang Q, Luo X. The species evenness of "prey" bacteria correlated with Bdellovibrio-and-like-organisms (BALOs) in the microbial network supports the biomass of BALOs in a paddy soil. FEMS Microbiol Ecol 2021; 96:5911575. [PMID: 32975583 DOI: 10.1093/femsec/fiaa195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 09/23/2020] [Indexed: 11/14/2022] Open
Abstract
To seek how soil biotic and abiotic factors which might shape the Bdellovibrio-and-like-organisms community, we sampled paddy soils under different fertilization treatments including fertilization without nitrogen (Control), the nitrogen use treatment (N) and the nitrogen overuse one (HNK) at three rice growing stages. The abundances of BALOs were impacted by the rice-growing stages but not the fertilization treatments. The abundances of Bdellovibrionaceae-like were positively associated with soil moisture, which showed a negative relationship with Bacteriovoracaceae-like bacteria. High-throughput sequencing analysis of the whole bacterial community revealed that the α-diversity of BALOs was not correlated with any soil properties data. Network analysis detected eight families directly linked to BALOs, namely, Pseudomonadaceae, Peptostreptococcaceae, Flavobacteriaceae, Sediment-4, Verrucomicrobiaceae, OM27, Solirubrobacteraceae and Roseiflexaceae. The richness and composition of OTUs in the eight families were correlated with different soil properties, while the evenness of them had a positive effect on the predicted BALO biomass. These results highlighted that the bottom-up control of BALOs in paddy soil at least partially relied on the changes of soil water content and the diversity of bacteria directly linked to BALOs in the microbial network.
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Affiliation(s)
- Hang Qian
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunli Hou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Liao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Li Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Shun Han
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shaobing Peng
- Crop Physiology and Production Center (CPPC), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuesong Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
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10
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Williams HN, Chen H. Environmental Regulation of the Distribution and Ecology of Bdellovibrio and Like Organisms. Front Microbiol 2020; 11:545070. [PMID: 33193128 PMCID: PMC7658600 DOI: 10.3389/fmicb.2020.545070] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 10/05/2020] [Indexed: 12/21/2022] Open
Abstract
The impact of key environmental factors, salinity, prey, and temperature, on the survival and ecology of Bdellovibrio and like bacteria (BALOs), including the freshwater/terrestrial, non-halotolerant group and the halophilic Halobacteriovorax strains, has been assessed based on a review of data in the literature. These topics have been studied by numerous investigators for nearly six decades now, and much valuable information has been amassed and reported. The collective data shows that salinity, prey, and temperature play a major role in, not only the growth and survival of BALOs, but also the structure and composition of BALO communities and the distribution of the predators. Salinity is a major determinant in the selection of BALO habitats, distribution, prey bacteria, and systematics. Halophilic BALOs require salt for cellular functions and are found only in saltwater habitats, and prey primarily on saltwater bacteria. To the contrary, freshwater/terrestrial BALOs are non-halotolerant and inhibited by salt concentrations greater than 0.5%, and are restricted to freshwater, soils, and other low salt environments. They prey preferentially on bacteria in the same habitats. The halophilic BALOs are further separated on the basis of their tolerance to various salt concentrations. Some strains are found in low salt environments and others in high salt regions. In situ studies have demonstrated that salinity gradients in estuarine systems govern the type of BALO communities that will persist within a specific gradient. Bacterial prey for BALOs functions more than just being a substrate for the predators and include the potential for different prey species to structure the BALO community at the phylotype level. The pattern of susceptibility or resistance of various bacteria species has been used almost universally to differentiate strains of new BALO isolates. However, the method suffers from a lack of uniformity among different laboratories. The use of molecular methods such as comparative analysis of the 16S rDNA gene and metagenomics have provided more specific approaches to distinguished between isolates. Differences in temperature growth range among different BALO groups and strains have been demonstrated in many laboratory experiments. The temperature optima and growth range for the saltwater BALOs is typically lower than that of the freshwater/terrestrial BALOs. The collective data shows not only that environmental factors have a great impact on BALO ecology, but also how the various factors affect BALO populations in nature.
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Affiliation(s)
- Henry N Williams
- School of the Environment, Florida Agricultural and Mechanical University, Tallahassee, FL, United States
| | - Huan Chen
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, United States
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11
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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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12
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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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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: 16] [Impact Index Per Article: 4.0] [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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Ye XS, Chen MX, Li HY, He XY, Zhao Y. Halobacteriovorax vibrionivorans sp. nov., a novel prokaryotic predator isolated from coastal seawater of China. Int J Syst Evol Microbiol 2019; 69:3917-3923. [PMID: 31498060 DOI: 10.1099/ijsem.0.003703] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three prokaryotic predator strains, BL9T, BL10 and BL28, were isolated with Vibrio alginolyticus from coastal seawater of PR China. Cells of the strains were Gram-negative, vibrioid-shaped and motile with a single sheathed flagellum (25-28 nm wide). Cells were around 0.3×0.5-1.0 µm in size. The three strains were obligate predators that exhibited a biphasic life cycle: a free-swimming attack phase and an intraperiplasmic growth phase within the prey. Bdelloplasts were formed. NaCl was required for growth. Optimum growth occurred at ~37 °C, with 2-4 % (w/v) NaCl and at pH 7.0-8.0. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the three strains shared 99.9 % similarity to each other, were affiliated with the genus Halobacteriovorax in the class Oligoflexia, and represented the same new species. Strain BL9T (=MCCC 1K03527T=JCM 32962T) was designated as the type strain. Genome sequencing of strain BL9T revealed a genome size of 3.14 Mb and a G+C content of 35.8 mol%. The estimated digital DNA-DNA hybridization (dDDH) values and the whole genome average nucleotide identity (gANI) values between the genome of strain BL9T and those of Bdellovibrionales and Bacteriovoracales were 12.5-19 and 63.49-76.15 %, respectively. On the basis of life cycle features, results of physiological analyses, gANI data and dDDH data, strain BL9T represents a new species within the genus Halobacteriovorax, for which the name Halobacteriovoraxvibrionivorans sp. nov. is proposed.
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Affiliation(s)
- Xiao-Sheng Ye
- College of Chemical Engineering, Huaqiao University, 668 Jimei Road, Fujian Xiamen 361021, PR China
| | - Ming-Xia Chen
- College of Chemical Engineering, Huaqiao University, 668 Jimei Road, Fujian Xiamen 361021, PR China
- Key Laboratory of Chemical Biology and Molecular Engineering (Huaqiao University), Fujian Province University, 668 Jimei Road, Fujian Xiamen 361021, PR China
| | - He-Yang Li
- Third Institute of Oceanography, Ministry of Natural Resources, 178 Daxue Road, Fujian Xiamen 361005, PR China
| | - Xiao-Yu He
- College of Chemical Engineering, Huaqiao University, 668 Jimei Road, Fujian Xiamen 361021, PR China
| | - Yan Zhao
- College of Chemical Engineering, Huaqiao University, 668 Jimei Road, Fujian Xiamen 361021, PR China
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15
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Im H, Kwon H, Cho G, Kwon J, Choi SY, Mitchell RJ. Viscosity has dichotomous effects on Bdellovibrio bacteriovorus HD100 predation. Environ Microbiol 2019; 21:4675-4684. [PMID: 31498968 DOI: 10.1111/1462-2920.14799] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 09/05/2019] [Indexed: 11/28/2022]
Abstract
Bdellovibrio bacteriovorus HD100 is a highly motile predatory bacterium that consumes other Gram-negative bacteria for its sustenance. Here, we describe the impacts the media viscosity has both on the motility of predator and its attack rates. Experiments performed in polyethylene glycol (PEG) solutions, a linear polymer, found a viscosity of 10 mPa s (5% PEG) negatively impacted predation over a 24-h period. When the viscosity was increased to 27 mPa s (10% PEG), predation was nearly abolished. Tests with three other B. bacteriovorus strains, i.e., 109J and two natural isolates, found identical results. Short-term (2-h) experiments, however, found attack rates were improved in 1% PEG, which had a viscosity of 5.4 mPa s, using bioluminescent prey and their viabilities. In contrast, when experiments were performed in dextran, a branched polymer, no increase in predation was seen even though the viscosity was a comparable 5.1 mPa s. The enhanced attack rates in this solution coincided with a 31% increase in B. bacteriovorus HD100 swimming speeds (62 μm s-1 in 1% PEG vs. 47.5 μm s-1 in HEPES-salt).
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Affiliation(s)
- Hansol Im
- Division of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Heeun Kwon
- Division of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Gayoung Cho
- Division of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Jisoo Kwon
- Division of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Seong Yeol Choi
- Division of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Robert J Mitchell
- Division of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
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16
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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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17
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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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18
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Identification and Characterization of Differentially-Regulated Type IVb Pilin Genes Necessary for Predation in Obligate Bacterial Predators. Sci Rep 2017; 7:1013. [PMID: 28432347 PMCID: PMC5430801 DOI: 10.1038/s41598-017-00951-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/17/2017] [Indexed: 11/08/2022] Open
Abstract
Bdellovibrio bacteriovorus is an obligate predator of bacteria that grows and divides within the periplasm of its prey. Functions involved in the early steps of predation have been identified and characterized, but mediators of prey invasion are still poorly detailed. By combining omics data available for Bdellovibrio and like organisms (BALO’s), we identified 43 genes expressed in B. bacteriovorus during the early interaction with prey. These included genes in a tight adherence (TAD) operon encoding for two type IVb fimbriae-like pilin proteins (flp1 and flp2), and their processing and export machinery. Two additional flp genes (flp3 and flp4) were computationally identified at other locations along the chromosome, defining the largest and most diverse type IVb complement known in bacteria to date. Only flp1, flp2 and flp4 were expressed; their respective gene knock-outs resulted in a complete loss of the predatory ability without losing the ability to adhere to prey cells. Additionally, we further demonstrate differential regulation of the flp genes as the TAD operon of BALOs with different predatory strategies is controlled by a flagellar sigma factor FliA, while flp4 is not. Finally, we show that FliA, a known flagellar transcriptional regulator in other bacteria, is an essential Bdellovibrio gene.
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19
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Si BC, Li JM, Zhu ZB, Zhang YH, Lu JW, Shen RX, Zhang C, Xing XH, Liu Z. Continuous production of biohythane from hydrothermal liquefied cornstalk biomass via two-stage high-rate anaerobic reactors. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:254. [PMID: 27895708 PMCID: PMC5117538 DOI: 10.1186/s13068-016-0666-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 11/10/2016] [Indexed: 05/25/2023]
Abstract
BACKGROUND Biohythane production via two-stage fermentation is a promising direction for sustainable energy recovery from lignocellulosic biomass. However, the utilization of lignocellulosic biomass suffers from specific natural recalcitrance. Hydrothermal liquefaction (HTL) is an emerging technology for the liquefaction of biomass, but there are still several challenges for the coupling of HTL and two-stage fermentation. One particular challenge is the limited efficiency of fermentation reactors at a high solid content of the treated feedstock. Another is the conversion of potential inhibitors during fermentation. Here, we report a novel strategy for the continuous production of biohythane from cornstalk through the integration of HTL and two-stage fermentation. Cornstalk was converted to solid and liquid via HTL, and the resulting liquid could be subsequently fed into the two-stage fermentation systems. The systems consisted of two typical high-rate reactors: an upflow anaerobic sludge blanket (UASB) and a packed bed reactor (PBR). The liquid could be efficiently converted into biohythane via the UASB and PBR with a high density of microbes at a high organic loading rate. RESULTS Biohydrogen production decreased from 2.34 L/L/day in UASB (1.01 L/L/day in PBR) to 0 L/L/day as the organic loading rate (OLR) of the HTL liquid products increased to 16 g/L/day. The methane production rate achieved a value of 2.53 (UASB) and 2.54 L/L/day (PBR), respectively. The energy and carbon recovery of the integrated HTL and biohythane fermentation system reached up to 79.0 and 67.7%, respectively. The fermentation inhibitors, i.e., 5-hydroxymethyl furfural (41.4-41.9% of the initial quantity detected) and furfural (74.7-85.0% of the initial quantity detected), were degraded during hydrogen fermentation. Compared with single-stage fermentation, the methane process during two-stage fermentation had a more efficient methane production rate, acetogenesis, and COD removal. The microbial distribution via Illumina MiSeq sequencing clarified that the biohydrogen process in the two-stage systems functioned not only for biohydrogen production, but also for the degradation of potential inhibitors. The higher distribution of the detoxification family Clostridiaceae, Bacillaceae, and Pseudomonadaceae was found in the biohydrogen process. In addition, a higher distribution of acetate-oxidizing bacteria (Spirochaetaceae) was observed in the biomethane process of the two-stage systems, revealing improved acetogenesis accompanied with an efficient conversion of acetate. CONCLUSIONS Biohythane production could be a promising process for the recovery of energy and degradation of organic compounds from hydrothermal liquefied biomass. The two-stage process not only contributed to the improved quality of the gas fuels but also strengthened the biotransformation process, which resulted from the function of detoxification during biohydrogen production and enhanced acetogenesis during biomethane production.
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Affiliation(s)
- Bu-Chun Si
- Laboratory of Environment-Enhancing Energy (E2E), and Key Laboratory of Agricultural Engineering in Structure and Environment, Ministry of Agriculture, College of Water Resources and Civil Engineering, China Agricultural University, Beijing, 100083 China
| | - Jia-Ming Li
- Laboratory of Environment-Enhancing Energy (E2E), and Key Laboratory of Agricultural Engineering in Structure and Environment, Ministry of Agriculture, College of Water Resources and Civil Engineering, China Agricultural University, Beijing, 100083 China
| | - Zhang-Bing Zhu
- Laboratory of Environment-Enhancing Energy (E2E), and Key Laboratory of Agricultural Engineering in Structure and Environment, Ministry of Agriculture, College of Water Resources and Civil Engineering, China Agricultural University, Beijing, 100083 China
| | - Yuan-Hui Zhang
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, 61801 USA
| | - Jian-Wen Lu
- Laboratory of Environment-Enhancing Energy (E2E), and Key Laboratory of Agricultural Engineering in Structure and Environment, Ministry of Agriculture, College of Water Resources and Civil Engineering, China Agricultural University, Beijing, 100083 China
| | - Rui-Xia Shen
- Laboratory of Environment-Enhancing Energy (E2E), and Key Laboratory of Agricultural Engineering in Structure and Environment, Ministry of Agriculture, College of Water Resources and Civil Engineering, China Agricultural University, Beijing, 100083 China
| | - Chong Zhang
- Key Laboratory of Industrial Biocatalysis of Ministry of Education of China, Beijing, 100084 China
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, 100084 China
| | - Xin-Hui Xing
- Key Laboratory of Industrial Biocatalysis of Ministry of Education of China, Beijing, 100084 China
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing, 100084 China
| | - Zhidan Liu
- Laboratory of Environment-Enhancing Energy (E2E), and Key Laboratory of Agricultural Engineering in Structure and Environment, Ministry of Agriculture, College of Water Resources and Civil Engineering, China Agricultural University, Beijing, 100083 China
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20
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Li N, Wang K, Williams HN, Sun J, Ding C, Leng X, Dong K. Analysis of gene gain and loss in the evolution of predatory bacteria. Gene 2016; 598:63-70. [PMID: 27825775 DOI: 10.1016/j.gene.2016.10.039] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 10/11/2016] [Accepted: 10/27/2016] [Indexed: 01/18/2023]
Abstract
Predatory bacteria are ubiquitously distributed in nature in including in aquatic environments, sewage, intestinal tracts of animals and humans, rhizophere and, soils. However, our understanding of their evolutionary history is limited. Results of recent studies have shown that acquiring novel genes is a major force driving bacterial evolution. Therefore, to gain a better understanding of the impact of gene gain and loss in the evolution of bacterial predators, this study employed comparative genomic approaches to identify core-set gene families and species-specific gene families, and model gene gain and loss events among 11 genomes that represented diverse lineages. In total, 1977 gene families were classified. Of these 509 (pattern 11111111111) were present all of the 11 species. Among the non-core set gene families, 52 were present only in saltwater bacteria predators and had no ortholog in the other genomes. Similarly 109 and 44 were present only in the genomes of Micavibrio spp. and Bdellovibrio spp., respectively. In this study, the gain loss mapping engine GLOOME was selected to analyze and estimate the expectations and probabilities of both gain and loss events in the predatory bacteria. In total, 354 gene families were involved in significant gene gain events, and 407 gene families were classified into gene loss events with high supported value. Moreover, 18 families from the core set gene family were identified as putative genes under positive selection. The results of this study suggest that acquisition of particular genes that encode functional proteins in metabolism and cellular processes and signaling, especially ABC systems, may help bacterial predators adapt to surrounding environmental changes and present different predation strategies for survival in their habitats.
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Affiliation(s)
- Nan Li
- College of Marine Science and Environmental Sciences, Tianjin University of Science and Technology, Tianjin 300457, China; School of the Environment, Florida A&M University, Tallahassee, FL, USA.
| | - Kai Wang
- Institute of Biochemistry and Cell Biology, Shanghai Institute of Biological Science, Chinese Academy of Science, Shanghai, China
| | - Henry N Williams
- School of the Environment, Florida A&M University, Tallahassee, FL, USA
| | - Jun Sun
- College of Marine Science and Environmental Sciences, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Changling Ding
- College of Marine Science and Environmental Sciences, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xiaoyun Leng
- College of Marine Science and Environmental Sciences, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Ke Dong
- Department of Biological Sciences, Seoul National University, Seoul 151-742, South Korea
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21
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Microbial Surface Colonization and Biofilm Development in Marine Environments. Microbiol Mol Biol Rev 2015; 80:91-138. [PMID: 26700108 DOI: 10.1128/mmbr.00037-15] [Citation(s) in RCA: 462] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.
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22
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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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23
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Halobacteriovorax, an underestimated predator on bacteria: potential impact relative to viruses on bacterial mortality. ISME JOURNAL 2015; 10:491-9. [PMID: 26251870 DOI: 10.1038/ismej.2015.129] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 06/16/2015] [Accepted: 06/24/2015] [Indexed: 12/11/2022]
Abstract
Predation on bacteria and accompanying mortality are important mechanisms in controlling bacterial populations and recycling of nutrients through the microbial loop. The agents most investigated and seen as responsible for bacterial mortality are viruses and protists. However, a body of evidence suggests that predatory bacteria such as the Halobacteriovorax (formerly Bacteriovorax), a Bdellovibrio-like organism, contribute substantially to bacterial death. Until now, conclusive evidence has been lacking. The goal of this study was to better understand the contributors to bacterial mortality by addressing the poorly understood role of Halobacteriovorax and how their role compares with that of viruses. The results revealed that when a concentrated suspension of Vibrio parahaemolyticus was added into microcosms of estuarine waters, the native Halobacteriovorax were the predators that responded first and most rapidly. Their numbers increased by four orders of magnitude, whereas V. parahaemolyticus prey numbers decreased by three orders of magnitude. In contrast, the extant virus population showed little increase and produced little change in the prey density. An independent experiment with stable isotope probing confirmed that Halobacteriovorax were the predators primarily responsible for the mortality of the V. parahaemolyticus. The results show that Halobacteriovorax have the potential to be significant contributors to bacterial mortality, and in such cases, predation by Halobacteriovorax may be an important mechanism of nutrient recycling. These conclusions add another dimension to bacterial mortality and the recycling of nutrients.
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24
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Li N, Chen H, Williams HN. Genome-wide comparative analysis of ABC systems in the Bdellovibrio-and-like organisms. Gene 2015; 562:132-7. [PMID: 25707746 DOI: 10.1016/j.gene.2015.02.062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/14/2015] [Accepted: 02/19/2015] [Indexed: 11/28/2022]
Abstract
Bdellovibrio-and-like organisms (BALOs) are gram-negative, predatory bacteria with wide variations in genome sizes and GC content and ecological habitats. The ATP-binding cassette (ABC) systems have been identified in several prokaryotes, fungi and plants and have a role in transport of materials in and out of cells and in cellular processes. However, knowledge of the ABC systems of BALOs remains obscure. A total of 269 putative ABC proteins were identified in BALOs. The genes encoding these ABC systems occupy nearly 1.3% of the gene content in freshwater Bdellovibrio strains and about 0.7% in their saltwater counterparts. The proteins found belong to 25 ABC system families based on their structural characteristics and functions. Among these, 16 families function as importers, 6 as exporters and 3 are involved in various cellular processes. Eight of these 25 ABC system families were deduced to be the core set of ABC systems conserved in all BALOs. All Bacteriovorax strains have 28 or less ABC systems. On the contrary, the freshwater Bdellovibrio strains have more ABC systems, typically around 51. In the genome of Bdellovibrio exovorus JSS (CP003537.1), 53 putative ABC systems were detected, representing the highest number among all the BALO genomes examined in this study. Unexpected high numbers of ABC systems involved in cellular processes were found in all BALOs. Phylogenetic analysis suggests that the majority of ABC proteins can be assigned into many separate families with high bootstrap supports (>50%). In this study, a general framework of sequence-structure-function connections for the ABC systems in BALOs was revealed providing novel insights for future investigations.
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Affiliation(s)
- Nan Li
- School of the Environment, Florida A&M University, Tallahassee, FL, USA
| | - Huan Chen
- National High Magnetic Field Laboratory, Tallahassee, FL, USA
| | - Henry N Williams
- School of the Environment, Florida A&M University, Tallahassee, FL, USA.
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25
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Chen H, Brinkac LM, Mishra P, Li N, Lymperopoulou DS, Dickerson TL, Gordon-Bradley N, Williams HN, Badger JH. Draft genome sequences for the obligate bacterial predators Bacteriovorax spp. of four phylogenetic clusters. Stand Genomic Sci 2015. [PMID: 26203326 PMCID: PMC4511183 DOI: 10.1186/1944-3277-10-11] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Bacteriovorax is the halophilic genus of the obligate bacterial predators, Bdellovibrio and like organisms. The predators are known for their unique biphasic life style in which they search for and attack their prey in the free living phase; penetrate, grow, multiply and lyse the prey in the intraperiplasmic phase. Bacteriovorax isolates representing four phylogenetic clusters were selected for genomic sequencing. Only one type strain genome has been published so far from the genus Bacteriovorax. We report the genomes from non-type strains isolated from aquatic environments. Here we describe and compare the genomic features of the four strains, together with the classification and annotation.
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Affiliation(s)
- Huan Chen
- Florida A&M University, Tallahassee, USA ; National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310-4005, USA
| | | | | | - Nan Li
- Florida A&M University, Tallahassee, USA
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26
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Koval SF, Williams HN, Stine OC. Reclassification of Bacteriovorax marinus as Halobacteriovorax marinus gen. nov., comb. nov. and Bacteriovorax litoralis as Halobacteriovorax litoralis comb. nov.; description of Halobacteriovoraceae fam. nov. in the class Deltaproteobacteria. Int J Syst Evol Microbiol 2014; 65:593-597. [PMID: 25406234 DOI: 10.1099/ijs.0.070201-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic status of saltwater Bdellovibrio-like prokaryotic predators has been revised to assign species to Halobacteriovorax gen. nov. A reclassification of Bacteriovorax marinus as Halobacteriovorax marinus comb. nov. (type strain ATCC BAA-682(T) = DSM 15412(T)) and Bacteriovorax litoralis as Halobacteriovorax litoralis comb. nov. (type strain ATCC BAA-684(T) = DSM 15409(T)) is proposed. This revision is necessary because a previous proposal to retain saltwater isolates as species of Bacteriovorax and reclassify Bacteriovorax stolpii as Bacteriolyticum stolpii was not approved. The type species of a genus cannot be reassigned to another genus. Bacteriovorax stolpii is thus retained as the type species of Bacteriovorax and Halobacteriovorax marinus is the type species of Halobacteriovorax and of Halobacteriovoraceae fam. nov.
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Affiliation(s)
- Susan F Koval
- Department of Microbiology and Immunology, University of Western Ontario, London, ON N6A 5C1, Canada
| | - Henry N Williams
- School of the Environment, Florida A&M University, Tallahassee, FL 32307, USA
| | - O Colin Stine
- Department of Epidemiology and Public Health, University of Maryland, Baltimore, MD 21201, USA
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27
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Li N, Williams HN. 454 Pyrosequencing reveals diversity of Bdellovibrio and like organisms in fresh and salt water. Antonie van Leeuwenhoek 2014; 107:305-11. [PMID: 25380719 DOI: 10.1007/s10482-014-0327-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 10/31/2014] [Indexed: 12/21/2022]
Abstract
Bdellovibrio-and-like organisms (BALOs) are Gram-negative, predatory bacteria that inhabit terrestrial, freshwater and saltwater environments. They have been detected primarily by culture-dependent methods which have limitations. In this study, diversity and community structure of BALOs in freshwater and saltwater samples were characterized by 16S rRNA gene pyrosequencing with specific BALO group primers. Novel Bacteriovorax 16S rDNA sequences were found both in saltwater enrichment cultures and in situ environmental samples, but no new operational taxonomic units were detected in the freshwater samples. The results revealed unexpected diversity of BALOs and advance understanding of the similarities and differences between Bdellovibrio and Bacteriovorax diversity and distribution in the environment.
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Affiliation(s)
- Nan Li
- School of the Environment, Florida A& M University, 1515 S Martin Luther King, Jr Blvd, Tallahassee, FL, 32307, USA,
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28
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Wen C, Xue M, Liang H, Zhou S. Evaluating the potential of marine Bacteriovorax sp. DA5 as a biocontrol agent against vibriosis in Litopenaeus vannamei larvae. Vet Microbiol 2014; 173:84-91. [DOI: 10.1016/j.vetmic.2014.07.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 07/22/2014] [Accepted: 07/24/2014] [Indexed: 11/17/2022]
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29
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Seasonal levels of the Vibrio predator bacteriovorax in atlantic, pacific, and gulf coast seawater. Int J Microbiol 2013; 2013:375371. [PMID: 24454382 PMCID: PMC3881529 DOI: 10.1155/2013/375371] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 11/04/2013] [Accepted: 11/05/2013] [Indexed: 12/02/2022] Open
Abstract
Bacteriovorax were quantified in US Atlantic, Gulf, and Pacific seawater to determine baseline levels of these predatory bacteria and possible seasonal fluctuations in levels. Surface seawater was analyzed monthly for 1 year from Kailua-Kona, Hawaii; the Gulf Coast of Alabama; and four sites along the Delaware Bay. Screening for Bacteriovorax was performed on lawns of V. parahaemolyticus host cells. Direct testing of 7.5 mL portions of seawater from the Atlantic, Pacific, and Gulf coasts gave mean annual counts ≤12.2 PFU. Spikes in counts were observed at 3 out of 4 sites along the Delaware Bay 1 week after Hurricane Sandy. A comparison of summer versus winter counts showed significantly more Bacteriovorax (P ≤ 0.0001)
in the Delaware Bay during the summer and significantly more (P ≤ 0.0001)
in the Gulf during the winter, but no significant seasonal differences (P > 0.05) for Hawaiian seawater. Bacteriovorax counts only correlated with seawater salinity and temperature at one Delaware site (r = 0.79 and r = 0.65, resp.). There was a relatively strong negative correlation between temperature and Bacteriovorax levels (r = −0.585) for Gulf seawater. Selected isolates were sequenced and identified by phylogenetic analysis as Bacteriovorax clusters IX, X, XI, and XII.
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30
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Pineiro S, Chauhan A, Berhane TK, Athar R, Zheng G, Wang C, Dickerson T, Liang X, Lymperopoulou DS, Chen H, Christman M, Louime C, Babiker W, Stine OC, Williams HN. Niche partition of Bacteriovorax operational taxonomic units along salinity and temporal gradients in the Chesapeake Bay reveals distinct estuarine strains. MICROBIAL ECOLOGY 2013; 65:652-660. [PMID: 23463183 DOI: 10.1007/s00248-013-0186-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 01/14/2013] [Indexed: 06/01/2023]
Abstract
The predatory Bacteriovorax are Gram-negative bacteria ubiquitous in saltwater systems that prey upon other Gram-negative bacteria in a similar manner to the related genus Bdellovibrio. Among the phylogenetically defined clusters of Bacteriovorax, cluster V has only been isolated from estuaries suggesting that it may be a distinct estuarine phylotype. To assess this hypothesis, the spatial and temporal distribution of cluster V and other Bacteriovorax phylogenetic assemblages along the salinity gradient of Chesapeake Bay were determined. Cluster V was expected to be found in significantly greater numbers in low to moderate salinity waters compared to high salinity areas. The analyses of water and sediment samples from sites in the bay revealed cluster V to be present at the lower salinity and not high salinity sites, consistent with it being an estuarine phylotype. Cluster IV had a similar distribution pattern and may also be specifically adapted to estuaries. While the distribution of clusters V and IV were similar for salinity, they were distinct on temperature gradients, being found in cooler and in warmer temperatures, respectively. The differentiation of phylotype populations along the salinity and temporal gradients in Chesapeake Bay revealed distinct niches inhabited by different phylotypes of Bacteriovorax and unique estuarine phylotypes.
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Affiliation(s)
- Silvia Pineiro
- School of Medicine, University of Maryland, Baltimore, MD 21201, USA
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31
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A small predatory core genome in the divergent marine Bacteriovorax marinus SJ and the terrestrial Bdellovibrio bacteriovorus. ISME JOURNAL 2012; 7:148-60. [PMID: 22955231 PMCID: PMC3526173 DOI: 10.1038/ismej.2012.90] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Bacteriovorax marinus SJ is a predatory delta-proteobacterium isolated from a marine environment. The genome sequence of this strain provides an interesting contrast to that of the terrestrial predatory bacterium Bdellovibrio bacteriovorus HD100. Based on their predatory lifestyle, Bacteriovorax were originally designated as members of the genus Bdellovibrio but subsequently were re-assigned to a new genus and family based on genetic and phenotypic differences. B. marinus attaches to Gram-negative bacteria, penetrates through the cell wall to form a bdelloplast, in which it replicates, as shown using microscopy. Bacteriovorax is distinct, as it shares only 30% of its gene products with its closest sequenced relatives. Remarkably, 34% of predicted genes over 500 nt in length were completely unique with no significant matches in the databases. As expected, Bacteriovorax shares several characteristic loci with the other delta-proteobacteria. A geneset shared between Bacteriovorax and Bdellovibrio that is not conserved among other delta-proteobacteria such as Myxobacteria (which destroy prey bacteria externally via lysis), or the non-predatory Desulfo-bacteria and Geobacter species was identified. These 291 gene orthologues common to both Bacteriovorax and Bdellovibrio may be the key indicators of host-interaction predatory-specific processes required for prey entry. The locus from Bdellovibrio bacteriovorus is implicated in the switch from predatory to prey/host-independent growth. Although the locus is conserved in B. marinus, the sequence has only limited similarity. The results of this study advance understanding of both the similarities and differences between Bdellovibrio and Bacteriovorax and confirm the distant relationship between the two and their separation into different families.
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Predatory bacteria as natural modulators of Vibrio parahaemolyticus and Vibrio vulnificus in seawater and oysters. Appl Environ Microbiol 2012; 78:7455-66. [PMID: 22904049 DOI: 10.1128/aem.01594-12] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
This study shows that naturally occurring Vibrio predatory bacteria (VPB) exert a major role in controlling pathogenic vibrios in seawater and shellfish. The growth and persistence of Vibrio parahaemolyticus and Vibrio vulnificus were assessed in natural seawater and in the Eastern oyster, Crassostrea virginica. The pathogens examined were V. vulnificus strain VV1003, V. parahaemolyticus O1:KUT (KUT stands for K untypeable), and V. parahaemolyticus O3:K6 and corresponding O3:K6 mutants deficient in the toxRS virulence regulatory gene or the rpoS alternative stress response sigma factor gene. Vibrios were selected for streptomycin resistance, which facilitated their enumeration. In natural seawater, oysters bioconcentrated each Vibrio strain for 24 h at 22°C; however, counts rapidly declined to near negligible levels by 72 h. In natural seawater with or without oysters, vibrios decreased more than 3 log units to near negligible levels within 72 h. Neither toxRS nor rpoS had a significant effect on Vibrio levels. In autoclaved seawater, V. parahaemolyticus O3:K6 counts increased 1,000-fold over 72 h. Failure of the vibrios to persist in natural seawater and oysters led to screening of the water samples for VPB on lawns of V. parahaemolyticus O3:K6 host cells. Many VPB, including Bdellovibrio and like organisms (BALOs; Bdellovibrio bacteriovorus and Bacteriovorax stolpii) and Micavibrio aeruginosavorus-like predators, were detected by plaque assay and electron microscopic analysis of plaque-purified isolates from Atlantic, Gulf Coast, and Hawaiian seawater. When V. parahaemolyticus O3:K6 was added to natural seawater containing trace amounts of VPB, Vibrio counts diminished 3 log units to nondetectable levels, while VPB increased 3 log units within 48 h. We propose a new paradigm that VPB are important modulators of pathogenic vibrios in seawater and oysters.
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33
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Jurkevitch E. Isolation and classification of Bdellovibrio and like organisms. CURRENT PROTOCOLS IN MICROBIOLOGY 2012; Chapter 7:Unit7B.1. [PMID: 22875568 DOI: 10.1007/978-3-642-39044-9_379] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Bdellovibrio and like organisms (BALOs) are obligate predators of Gram-negative bacteria. BALOs are isolated as plaques growing at the expense of their prey and are cultivated as two-member cultures. The growth cycle is composed of an extracellular attack phase and an intraperiplasmic elongation and replication phase. However, there are methods for obtaining host-independent (HI) mutants that grow without prey on rich media. BALOs are commonly found in the environment but generally constitute small populations; therefore, their isolation may require enrichment steps. Contamination by other bacteria during isolation necessitates efficient separation between the smaller BALO cells from the majority of larger bacteria. BALOs can also be directly detected and quantified in environmental samples using specific PCR. Synchronous cultures of both wild-type and HI derivatives can be obtained to study the different growth phases. These can be further separated by centrifugation. Classification is based on 16S rDNA analysis. Protocols relevant to these aspects of BALO detection, isolation, growth, classification, and quantitation are presented in this unit.
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Affiliation(s)
- Edouard Jurkevitch
- Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, Israel
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34
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Predatory Bacteriovorax communities ordered by various prey species. PLoS One 2012; 7:e34174. [PMID: 22461907 PMCID: PMC3312913 DOI: 10.1371/journal.pone.0034174] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 02/28/2012] [Indexed: 02/01/2023] Open
Abstract
The role of predation in altering microbial communities has been studied for decades but few examples are known for bacterial predators. Bacteriovorax are halophilic prokaryotes that prey on susceptible Gram-negative bacteria. We recently reported novel observations on the differential selection of Bacteriovorax phylotypes by two different prey, Vibrio parahaemolyticus and Vibrio vulnificus. However, the conclusion is restricted by the limited number of prey tested. In this study, we have conducted two independent investigations involving eight species of prey bacteria while using V. vulnificus and V. parahaemolytics as reference strains. Water samples collected from Dry Bar, Apalachicola Bay were used to establish microcosms which were respectively spiked with prey strains Vibrio cholerae, Escherichia coli or Pseudomonas putida to examine the response of native Bacteriovorax to freshwater bacteria. Indigenous Vibrio sp., Pseudoalteromonas sp., Photobacterium sp. and a clinical strain of V. vulnificus were also tested for the impact of saltwater prey on the Bacteriovorax community. At 24 hour intervals, optical density of the microcosm samples and the abundance of Bacteriovorax were measured over five days. The predominant Bacteriovorax plaques were selected and analyzed by 16S rRNA gene amplification and sequencing. In addition, the impacts of prey on predator population and bacterial community composition were investigated using culture independent denaturing gradient gel electrophoresis. Strikingly, Cluster IV was found consistently as the predominant phylotype produced by the freshwater prey. For all saltwater prey, subgroups of Bacteriovorax phylotype IX were the major predators recovered. The results suggest that prey is an important factor along with temperature, salinity and other environmental parameters in shaping Bacteriovorax communities in aquatic systems.
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35
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Chen H, Athar R, Zheng G, Williams HN. Prey bacteria shape the community structure of their predators. ISME JOURNAL 2011; 5:1314-22. [PMID: 21326335 DOI: 10.1038/ismej.2011.4] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Although predator-prey interactions among higher organisms have been studied extensively, only few examples are known for microbes other than protists and viruses. Among the bacteria, the most studied obligate predators are the Bdellovibrio and like organisms (BALOs) that prey on many other bacteria. In the macroscopical world, both predator and prey influence the population size of the other's community, and may have a role in selection. However, selective pressures among prey and predatory bacteria have been rarely investigated. In this study, Bacteriovorax, a predator within the group of BALOs, in environmental waters were fed two prey bacteria, Vibrio vulnificus and Vibrio parahaemolyticus. The two prey species yielded distinct Bacteriovorax populations, evidence that selective pressures shaped the predator community and diversity. The results of laboratory experiments confirmed the differential predation of Bacteriovorax phylotypes on the two bacteria species. Not only did Bacteriovorax Cluster IX exhibit the versatility to be the exclusive efficient predator on Vibrio vulnificus, thereby, behaving as a specialist, but was also able to prey with similar efficiency on Vibrio parahaemolyticus, indicative of a generalist. Therefore, we proposed a designation of versatilist for this predator. This initiative should provide a basis for further efforts to characterize the predatory patterns of bacterial predators. The results of this study have revealed impacts of the prey on Bacteriovorax predation and in structuring the predator community, and advanced understanding of predation behavior in the microbial world.
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Affiliation(s)
- Huan Chen
- Environmental Sciences Institute, Florida A&M University, 1515 S. Martin Luther King, Jr. Blvd, Tallahassee, FL 32307, USA
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Affiliation(s)
- Renee Elizabeth Sockett
- Institute of Genetics, School of Biology, University of Nottingham, Medical School, Nottingham NG7 2UH, United Kingdom;
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Chauhan A, Fortenberry GZ, Lewis DE, Williams HN. Increased diversity of predacious Bdellovibrio-like organisms (blos) as a function of eutrophication in Kumaon Lakes of India. Curr Microbiol 2009; 59:1-8. [PMID: 19319600 DOI: 10.1007/s00284-009-9385-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Revised: 02/04/2009] [Accepted: 02/12/2009] [Indexed: 11/30/2022]
Abstract
Predation by Bdellovibrio-like organisms (BLOs) results in bacterial community succession in aquatic ecosystems. The effects of nutrient loading on the distribution and phylogeny of BLOs remain largely unknown. To this end, we present our findings on BLO diversity from four north-Indian lakes that are variable in their trophic status; Nainital is eutrophic, both, Bhimtal and Naukuchiatal are mesotrophic and Sattal remains oligotrophic, respectively. Initially, total heterotrophic bacteria and BLOs were quantified by most probable number (MPN) analyses using Pseudomonas putida and Escherichia coli as prey bacteria. Total bacterial numbers were at least two-logs higher in the eutrophic lake samples compared with oligotrophic lake. Similarly, BLO numbers were approximately 39-fold higher using Pseudomonas sp., which is likely the preferred prey within these lakes. Conversely, significant differences were not observed between mesotrophic and oligotrophic BLO numbers when E. coli was used as the prey. PCR-RFLP of small subunit rDNA (SSU rDNA) of BLOs, followed by cloning, sequencing, and taxonomic categorization revealed distinct differences such that, eutrophic lake consisted of higher BLO diversity compared with mesotrophic and oligotrophic lake, most likely due to both, higher numbers and availability of a diverse population of prey bacteria resulting from nutrient loading in this ecosystem.
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Affiliation(s)
- Ashvini Chauhan
- Environmental Sciences Institute, Florida A&M University, 1515, S. MLK Blvd., Tallahassee, FL 32307, USA.
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Impact of sideways and bottom-up control factors on bacterial community succession over a tidal cycle. Proc Natl Acad Sci U S A 2009; 106:4301-6. [PMID: 19251645 DOI: 10.1073/pnas.0809671106] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In aquatic systems, bacterial community succession is a function of top-down and bottom-up factors, but little information exists on "sideways" controls, such as bacterial predation by Bdellovibrio-like organisms (BLOs), which likely impacts nutrient cycling within the microbial loop and eventual export to higher trophic groups. Here we report transient response of estuarine microbiota and BLO spp. to tidal-associated dissolved organic matter supply in a river-dominated estuary, Apalachicola Bay, Florida. Both dissolved organic carbon and dissolved organic nitrogen concentrations oscillated over the course of the tidal cycle with relatively higher concentrations observed at low tide. Concurrent with the shift in dissolved organic matter (DOM) supply at low tide, a synchronous increase in numbers of bacteria and predatorial BLOs were observed. PCR-restriction fragment length polymorphism of small subunit rDNA, cloning, and sequence analyses revealed distinct shifts such that, at low tide, significantly higher phylotype abundances were observed from gamma-Proteobacteria, delta-Proteobacteria, Bacteroidetes, and high G+C gram-positive bacteria. Conversely, diversity of alpha-Proteobacteria, beta-Proteobacteria, and Chlamydiales-Verrucomicrobia group increased at high tides. To identify metabolically active BLO guilds, tidal microcosms were spiked with six (13)C-labeled bacteria as potential prey and studied using an adaptation of stable isotope probing. At low tide, representative of higher DOM and increased prey but lower salinity, BLO community also shifted such that mesohaline clusters I and VI were more active; with an increased salinity at high tide, halotolerant clusters III, V, and X were predominant. Eventually, (13)C label was identified from higher micropredators, indicating that trophic interactions within the estuarine microbial food web are potentially far more complex than previously thought.
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Wen CQ, Lai XT, Xue M, Huang YL, Li HX, Zhou SN. Molecular typing and identification of Bdellovibrio-and-like organisms isolated from seawater shrimp ponds and adjacent coastal waters. J Appl Microbiol 2009; 106:1154-62. [PMID: 19191952 DOI: 10.1111/j.1365-2672.2008.04081.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS To apply and compare two PCR-based methods for typing saltwater Bdellovibrio-and-like organisms (BALOs) and to understand ecological and phylogenetic aspects of the BALOs isolated from shrimp mariculture systems. METHODS AND RESULTS Using double-layer agar technique, the numbers of culturable BALOs that lyse Vibrio alginolyticus were found to be 10-10(3) PFU ml(-1) in the surface water samples. A total of 130 BALOs isolates were differentiated into five phylotypes by denaturing gradient gel electrophoresis targeting the 16S rDNA V3 region and four phylotypes by amplified rDNA restriction analysis of the Bacteriovoracaceae-specific 16S rDNA fragment respectively. Phylogenetic analysis of representative isolates showed that all of them were identified as Bacteriovorax spp., but affiliated with four different clusters in the family Bacteriovoracaceae. CONCLUSIONS The two PCR-based methods both can be chosen to rapidly type the saltwater BALOs at cluster level. And the relatively large numbers of BALOs with various phylotypes recovered from the same habitats suggested that these predators might play important ecological role in shrimp mariculture environments. SIGNIFICANCE AND IMPACT OF THE STUDY We proposed two effective methods to distinguish rapidly large numbers of BALOs isolates and our results would be helpful to understand the diversity and function of BALOs in mariculture environments.
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Affiliation(s)
- C-Q Wen
- Sun Yat-Sen University, Guangzhou, China
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Little AEF, Robinson CJ, Peterson SB, Raffa KF, Handelsman J. Rules of engagement: interspecies interactions that regulate microbial communities. Annu Rev Microbiol 2008; 62:375-401. [PMID: 18544040 DOI: 10.1146/annurev.micro.030608.101423] [Citation(s) in RCA: 252] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microbial communities comprise an interwoven matrix of biological diversity modified by physical and chemical variation over space and time. Although these communities are the major drivers of biosphere processes, relatively little is known about their structure and function, and predictive modeling is limited by a dearth of comprehensive ecological principles that describe microbial community processes. Here we discuss working definitions of central ecological terms that have been used in various fashions in microbial ecology, provide a framework by focusing on different types of interactions within communities, review the status of the interface between evolutionary and ecological study, and highlight important similarities and differences between macro- and microbial ecology. We describe current approaches to study microbial ecology and progress toward predictive modeling.
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Affiliation(s)
- Ainslie E F Little
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, 53706, USA.
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Nguyen NAT, Sallans L, Kaneshiro ES. The Major Glycerophospholipids of the Predatory and Parasitic Bacterium Bdellovibrio bacteriovorus HID5. Lipids 2008; 43:1053-63. [DOI: 10.1007/s11745-008-3235-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Accepted: 08/20/2008] [Indexed: 11/29/2022]
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Zheng G, Wang C, Williams HN, Pineiro SA. Development and evaluation of a quantitative real-time PCR assay for the detection of saltwater Bacteriovorax. Environ Microbiol 2008; 10:2515-26. [PMID: 18631362 DOI: 10.1111/j.1462-2920.2008.01676.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bdellovibrio-and-like-organisms (BALOs) are small, Gram-negative predatory bacteria with the ability to prey on a wide variety of Gram-negative bacteria, and which may have a significant ecological role. Detection and quantification of BALOs by culture-dependent methods are complicated, as their reproduction is dependent upon the use of appropriate prey. For this reason, a sensitive and specific molecular detection method was developed. This paper describes a SYBR Green-based real-time PCR (quantitative PCR) assay that combines the use of a specific 16S rDNA primer with a universal primer for quantitative detection of halophilic Bacteriovorax. 16S rDNA sequences from 174 BALO strains, including both halophilic and freshwater, were aligned and a consensus region was identified that is unique to the halophilic Bacteriovorax strains. A specific primer was designed and analysed for specificity. The PCR conditions were optimized to obtain high specificity and sensitivity. The specificity was evaluated by testing a series of halophilic Bacteriovorax samples and prey specimens, including both pure cultures and environmental saltwater samples. A linear and reproducible standard curve was obtained over a range of 10(1)-10(6) gene copies and the detection limit was determined to be 10 copies of 16S rRNA gene per reaction. The results presented in this study validate the procedure as a rapid, sensitive and accurate method for the detection and quantification of halophilic Bacteriovorax in environmental saltwater samples. It is anticipated that this culture-independent method will facilitate future investigations of the distribution and population dynamics of these interesting predatory bacteria, leading to a better understanding of their ecological role.
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Affiliation(s)
- Guili Zheng
- School of Medicine, University of Maryland Baltimore, Baltimore, MD 21201, USA
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Pineiro SA, Williams HN, Stine OC. Phylogenetic relationships amongst the saltwater members of the genus Bacteriovorax using rpoB sequences and reclassification of Bacteriovorax stolpii as Bacteriolyticum stolpii gen. nov., comb. nov. Int J Syst Evol Microbiol 2008; 58:1203-9. [DOI: 10.1099/ijs.0.65710-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Chauhan A, Williams HN. Biostimulation of estuarine microbiota on substrate coated agar slides: a novel approach to study diversity of autochthonous Bdellovibrio- and like organisms. MICROBIAL ECOLOGY 2008; 55:640-650. [PMID: 17968612 DOI: 10.1007/s00248-007-9307-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2007] [Revised: 07/10/2007] [Accepted: 07/16/2007] [Indexed: 05/25/2023]
Abstract
Characterization of Bdellovibrio- and like organisms (BALOs) from environmental samples involves growing them in the presence of Gram-negative prey bacteria and isolation of BALO plaques. This labor-intensive enrichment and isolation procedure may impede the detection and phylogenetic characterization of uncultivable BALOs. In this article, we describe a simple slide biofilm assay to improve detection and characterization of BALO microbiota. Agar spiked with biostimulants such as yeast extract (YE), casamino acids (CA), or concentrated cells of Vibrio parahaemolyticus P5 (most widely used prey bacteria for isolation of halophilic BALOs) was plated onto buffed glass slides and exposed to water samples collected from Apalachicola Bay, Florida. After incubating for a week, diversity of the biofilm bacterial community was studied by culture-dependent and culture-independent molecular methods. The results revealed that most probable numbers (MPNs) of BALOs and total culturable bacteria recovered from YE agar slide were significantly higher than the numbers on CA- or P5-spiked agar slides. Polymerase chain reaction-restriction fragment length polymorphism followed by 16S rDNA sequencing of clones from different biostimulants resulted in identification of a plethora of Gram-negative bacteria predominantly from the alpha, gamma, delta-proteobacteria, and the Cytophaga-Flavobacterium-Bacteroides group. Corresponding to the higher biomass on the YE agar slide, the BALO clone library from YE was most diverse, consisting of Bacteriovorax spp. and a novel clade representing Peredibacter spp. Microbiota from all three biostimulated biofilms were exclusively Gram-negative, and each bacterial guild represented potential prey for BALOs. We propose the use of this simple yet novel slide biofilm assay to study oligotrophic aquatic bacterial diversity which could also potentially be utilized to isolate marine bacteria with novel traits.
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Affiliation(s)
- Ashvini Chauhan
- Marine Molecular Microbial Ecology Laboratory, Environmental Sciences Institute, Florida A&M University, 1515, S. MLK Blvd., 305 FSHSRC, Tallahassee, FL 32307, USA.
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