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Pernthaler J, Krempaska N, le Moigne A. Small-scale spatial beta diversity of bacteria in the mixed upper layer of a lake. Environ Microbiol 2023; 25:1847-1859. [PMID: 37173811 DOI: 10.1111/1462-2920.16399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/27/2023] [Indexed: 05/15/2023]
Abstract
Bacterial community composition among individual, experimentally generated 'lake snow' particles may be highly variable. Since such aggregates are seasonally abundant in the mixed upper layer of lakes, we hypothesized that particle-attached (PA) bacteria disproportionally contribute to the small-scale spatial beta diversity of pelagic communities. Community composition was analysed in sets of small (10 mL) samples collected from a pre-alpine lake in May, July and October 2018. Bacteria were classified as free-living (FL) or PA depending on their presence in large, 5-μm pre-filtered reference samples. FL exhibited clear seasonal differences in community composition and assembly. They were spatially uniform in May and July, and only a few FL taxa exhibited significant spatial variability. Spatial heterogeneity of FL in October was caused by high alpha and beta diversity of rare taxa, many with a presumably 'tychoplanktic' (alternating attached and free-living) lifestyle. The spatial beta diversity of PA was always high, and only about 10% of their seasonal richness was present in any single sample. Thus, most compositional variability of pelagic bacteria at spatial scales of cm to m either directly or indirectly originated from PA. On a functional level, this genotypic heterogeneity might affect the spatial distribution of rare metabolic traits.
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Affiliation(s)
- Jakob Pernthaler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Natalia Krempaska
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Alizée le Moigne
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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Lin WH, Tsai TS. Comparisons of the Oral Microbiota from Seven Species of Wild Venomous Snakes in Taiwan Using the High-Throughput Amplicon Sequencing of the Full-Length 16S rRNA Gene. BIOLOGY 2023; 12:1206. [PMID: 37759605 PMCID: PMC10525742 DOI: 10.3390/biology12091206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/26/2023] [Accepted: 09/02/2023] [Indexed: 09/29/2023]
Abstract
A venomous snake's oral cavity may harbor pathogenic microorganisms that cause secondary infection at the wound site after being bitten. We collected oral samples from 37 individuals belonging to seven species of wild venomous snakes in Taiwan, including Naja atra (Na), Bungarus multicinctus (Bm), Protobothrops mucrosquamatus (Pm), Trimeresurus stejnegeri (Ts), Daboia siamensis (Ds), Deinagkistrodon acutus (Da), and alpine Trimeresurus gracilis (Tg). Bacterial species were identified using full-length 16S rRNA amplicon sequencing analysis, and this is the first study using this technique to investigate the oral microbiota of multiple Taiwanese snake species. Up to 1064 bacterial species were identified from the snake's oral cavities, with 24 pathogenic and 24 non-pathogenic species among the most abundant ones. The most abundant oral bacterial species detected in our study were different from those found in previous studies, which varied by snake species, collection sites, sampling tissues, culture dependence, and analysis methods. Multivariate analysis revealed that the oral bacterial species compositions in Na, Bm, and Pm each were significantly different from the other species, whereas those among Ts, Ds, Da, and Tg showed fewer differences. Herein, we reveal the microbial diversity in multiple species of wild snakes and provide potential therapeutic implications regarding empiric antibiotic selection for wildlife medicine and snakebite management.
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Affiliation(s)
- Wen-Hao Lin
- Institute of Wildlife Conservation, National Pingtung University of Science and Technology, Pingtung 912301, Taiwan;
| | - Tein-Shun Tsai
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 912301, Taiwan
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Tejman-Yarden N, Robinson A, Davidov Y, Shulman A, Varvak A, Reyes F, Rahav G, Nissan I. Delftibactin-A, a Non-ribosomal Peptide With Broad Antimicrobial Activity. Front Microbiol 2019; 10:2377. [PMID: 31681234 PMCID: PMC6808179 DOI: 10.3389/fmicb.2019.02377] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 09/30/2019] [Indexed: 11/13/2022] Open
Abstract
The rapid emergence of drug resistant bacteria is occurring worldwide, outpacing the development of new antibiotics. It is known that some of the main sources of antibiotics are the bacteria themselves, many of which are secondary metabolites of Gram positive bacteria. Siderophores, which are secondary metabolites, function as natural chelators (e.g., iron). They are produced and secreted by many bacteria and have been experimented on as "carriers" of several types of antibiotics that pass the cell membrane of challenging Gram negative bacteria. Delftibactin A is a non-ribosomal peptide (NRP), which is known to detoxify gold in Delftia spp. and form gold nuggets, and is considered to be a siderophore. In this study we demonstrate that the supernatant from novel environmental isolates of Delftia spp. have antimicrobial activity. We characterized the active fraction and identified delftibactin A as a compound with antimicrobial activity. Delftibactin A exhibits potent antimicrobial activity against Gram positive multi drug resistant (MDR) bacteria like Methicillin-resistant Staphylococcus aureus (MRSA), and Vancomycin resistant Enterococcus (VRE), and also against the Gram negative pathogens Acinetobacter baumannii and Klebsiella pneumoniae. We discovered that the production of delftibactin A is greatly influenced by temperature. Furthermore, we have demonstrated the possibility of utilizing delftibactin A as a siderophore carrier of toxic metals such as gallium into Gram negative bacteria. These findings expose new opportunities of yet unexploited natural products such as delftibactin A, which have been known for other bacterial uses, as potent factors in the battle against MDR bacteria.
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Affiliation(s)
- Noa Tejman-Yarden
- Public Health Regional Laboratory, Southern District, Ministry of Health (Israel), Beer Sheva, Israel.,Laboratory Department, Ministry of Health, Jerusalem, Israel
| | - Ari Robinson
- Infectious Diseases Unit, Sheba Medical Center, Ramat Gan, Israel
| | - Yaakov Davidov
- Infectious Diseases Unit, Sheba Medical Center, Ramat Gan, Israel
| | | | - Alexander Varvak
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | | | - Galia Rahav
- Infectious Diseases Unit, Sheba Medical Center, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Israel Nissan
- Infectious Diseases Unit, Sheba Medical Center, Ramat Gan, Israel.,National Public Health Laboratory, Ministry of Health (Israel), Tel-Aviv, Israel
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Janahiraman V, Anandham R, Kwon SW, Sundaram S, Karthik Pandi V, Krishnamoorthy R, Kim K, Samaddar S, Sa T. Control of Wilt and Rot Pathogens of Tomato by Antagonistic Pink Pigmented Facultative Methylotrophic Delftia lacustris and Bacillus spp. FRONTIERS IN PLANT SCIENCE 2016; 7:1626. [PMID: 27872630 PMCID: PMC5097904 DOI: 10.3389/fpls.2016.01626] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/14/2016] [Indexed: 05/13/2023]
Abstract
The studies on the biocontrol potential of pink pigmented facultative methylotrophic (PPFM) bacteria other than the genus Methylobacterium are scarce. In the present study, we report three facultative methylotrophic isolates; PPO-1, PPT-1, and PPB-1, respectively, identified as Delftia lacustris, Bacillus subtilis, and Bacillus cereus by 16S rRNA gene sequence analysis. Hemolytic activity was tested to investigate the potential pathogenicity of isolates to plants and humans, the results indicates that the isolates PPO-1, PPT-1, and PPB-1 are not pathogenic strains. Under in vitro conditions, D. lacustris PPO-1, B. subtilis PPT-1, and B. cereus PPB-1 showed direct antagonistic effect by inhibiting the mycelial growth of fungal pathogens; Fusarium oxysporum f. sp. lycopersici (2.15, 2.05, and 1.95 cm), Sclerotium rolfsii (2.14, 2.04, and 1.94 cm), Pythium ultimum (2.12, 2.02, and 1.92 cm), and Rhizoctonia solani (2.18, 2.08, and 1.98 cm) and also produced volatile inhibitory compounds. Under plant growth chamber condition methylotrophic bacterial isolates; D. lacustris PPO-1, B. subtilis PPT-1, and B. cereus PPB-1 significantly reduced the disease incidence of tomato. Under greenhouse condition, D. lacustris PPO-1, B. subtilis PPT-1, and B. cereus PPB-1 inoculated tomato plants, when challenged with F. oxysporum f. sp. lycopersici, S. rolfsii, P. ultimum, and R. solani, increased the pathogenesis related proteins (β-1,3-glucanase and chitinase) and defense enzymes (phenylalanine ammonia lyase, peroxidase, polyphenol oxidase, and catalase) on day 5 after inoculation. In the current study, we first report the facultative methylotrophy in pink pigmented D. lacustris, B. subtilis, and B. cereus and their antagonistic potential against fungal pathogens. Direct antagonistic and ISR effects of these isolates against fungal pathogens of tomato evidenced their possible use as a biocontrol agent.
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Affiliation(s)
- Veeranan Janahiraman
- Department of Agricultural Microbiology, Agricultural College and Research Institute, Tamil Nadu Agricultural UniversityMadurai, India
| | - Rangasamy Anandham
- Department of Agricultural Microbiology, Agricultural College and Research Institute, Tamil Nadu Agricultural UniversityMadurai, India
- *Correspondence: Rangasamy Anandham
| | - Soon W. Kwon
- Korean Agricultural Culture Collection, National Academy of Agricultural Science, Rural Development AdministrationJeonju, South Korea
| | - Subbiah Sundaram
- Department of Agricultural Microbiology, Agricultural College and Research Institute, Tamil Nadu Agricultural UniversityMadurai, India
- Department of Environmental and Biological Chemistry, Chungbuk National UniversityCheongju, South Korea
| | - Veeranan Karthik Pandi
- Department of Plant Pathology, Agricultural College and Research Institute, Tamil Nadu Agricultural UniversityCoimbatore, India
| | - Ramasamy Krishnamoorthy
- Department of Agricultural Microbiology, Agricultural College and Research Institute, Tamil Nadu Agricultural UniversityMadurai, India
| | - Kiyoon Kim
- Department of Environmental and Biological Chemistry, Chungbuk National UniversityCheongju, South Korea
| | - Sandipan Samaddar
- Department of Environmental and Biological Chemistry, Chungbuk National UniversityCheongju, South Korea
| | - Tongmin Sa
- Department of Environmental and Biological Chemistry, Chungbuk National UniversityCheongju, South Korea
- Tongmin Sa
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Sohn KM, Baek JY, Cheon S, Kim YS, Koo SH. Ocular infection associated with Delftia lacustris: first report. Braz J Infect Dis 2015; 19:449-50. [PMID: 26095905 PMCID: PMC9427517 DOI: 10.1016/j.bjid.2015.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 05/06/2015] [Indexed: 11/24/2022] Open
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Kang H, Xu X, Fu K, An X, Mi Z, Yin X, Peng F, Pei G, Wang Y, Huang Y, Zhang X, Zhang Z, Wang W, Zhou L, Chen J, Tong Y. Characterization and Genomic Analysis of Quinolone-Resistant Delftia sp. 670 Isolated from a Patient Who Died from Severe Pneumonia. Curr Microbiol 2015; 71:54-61. [PMID: 25935202 DOI: 10.1007/s00284-015-0818-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 03/04/2015] [Indexed: 11/29/2022]
Abstract
Antibiotic-resistant opportunistic pathogens have become a serious concern in recent decades, as they are increasingly responsible for hospital-acquired infections. Here, we describe quinolone-resistant Delftia sp. strain 670, isolated from the sputum of a patient who died from severe pulmonary infection. The draft genome sequence of this strain was obtained by whole-genome shotgun sequencing, and was subjected to comparative genome analysis. Genome analysis revealed that one critical mutation (Ser83Ile in gyrA) might play a decisive role in quinolone resistance. The genome of Delftia sp. strain 670 contains both type II and type VI secretion systems, which were predicted to contribute to the virulence of the strain. Phylogenetic analysis, assimilation tests, and comparative genome analysis indicated that strain 670 differed from the four known Delftia species, suggesting this strain could represent a novel species. Although the study could not determine the strain 670 as the pathogen led to mortality, our findings also presented the pathogenic potential of Delftia species, and the increasing severity of antibiotic resistance among emerging opportunistic pathogens. The whole genome sequencing and comparative analysis improved our understanding of genome evolution in the genus Delftia, and provides the foundation for further study on drug resistance and virulence of Delftia strains.
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Affiliation(s)
- Huaixing Kang
- School of Basic Medical Science Central South University, Changsha, 410013, People's Republic of China,
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Sohn KM, Baek JY. Delftia lacustris septicemia in a pheochromocytoma patient: case report and literature review. Infect Dis (Lond) 2015; 47:349-53. [PMID: 25712727 DOI: 10.3109/00365548.2014.993422] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
We report the first case of true Delftia lacustris bacteremia in a patient with pheochromocytoma. The organism was identified using 16S rRNA gene sequencing and biochemical tests. A peripheral intravenous catheter was the suspected source of infection, and the patient was successfully treated with piperacillin/tazobactam. We also present a review of the literature describing bacteremia caused by Delftia species.
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Affiliation(s)
- Kyung Mok Sohn
- From the Division of Infectious Diseases, Chungnam National University Hospital, Chungnam National University School of Medicine , Daejeon , Republic of Korea
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