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Li Y, Zhang X, He K, Song X, Yu J, Guo Z, Xu M. Isolation and Identification of Bacillus subtilis LY-1 and Its Antifungal and Growth-Promoting Effects. PLANTS (BASEL, SWITZERLAND) 2023; 12:4158. [PMID: 38140485 PMCID: PMC10747398 DOI: 10.3390/plants12244158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/29/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023]
Abstract
Peanut root rot, caused by Fusarium spp., is a devastating fungal disease. As part of a program to obtain a biocontrol agent to control peanut root rot in the field, a bacterial strain LY-1 capable of inhibiting the growth of the fungus in vitro was isolated from rhizosphere soil samples collected from wild mint by agar disk dilution and dual-culture assay. Strain LY-1 was identified as Bacillus subtilis based on morphological characteristics, 16S rDNA, and gyrA sequence analyses. The bacterial suspension and cell-free culture filtrate of LY-1 could significantly inhibit the growth of Fusarium oxysporum, Fusarium proliferatum and Fusarium solani, but volatile organic compounds from the cultures had only a weak effect on mycelial growth. The percentage inhibition of 20% concentration of the cell-free culture filtrate of LY-1 on conidium production of each of the three Fusarium species was greater than 72.38%, and the percentage inhibition by the culture filtration on the germination of conidia of the three species was at least 62.37%. The production of extracellular enzyme activity by LY-1 was studied in functional assays, showing protease, cellulase, amylase, chitinase, and β-1,3-glucanase activity, while LY-1 contained a gene encoding iturin, an antifungal lipopeptide. In addition, under pot culture in a greenhouse, culture filtrate of LY-1 significantly promoted the growth of peanut, increasing the fresh and dry mass of the plant by 30.77% and 27.27%, respectively, in comparison with the no-filtrate control. The culture filtrate of LY-1 increased the resistance of peanut plants to F. oxysporum, with the biocontrol efficiency reaching 44.71%. In conclusion, B. subtilis LY-1, a plant-growth-promoting rhizobacterium, was able to protect peanuts from Fusarium spp. infection.
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Affiliation(s)
- Ying Li
- Shandong Peanut Research Institute, Qingdao 266100, China; (Y.L.); (X.Z.); (K.H.); (X.S.); (J.Y.); (Z.G.)
- National Engineering Research Center for Peanut, Qingdao 266100, China
| | - Xia Zhang
- Shandong Peanut Research Institute, Qingdao 266100, China; (Y.L.); (X.Z.); (K.H.); (X.S.); (J.Y.); (Z.G.)
- National Engineering Research Center for Peanut, Qingdao 266100, China
| | - Kang He
- Shandong Peanut Research Institute, Qingdao 266100, China; (Y.L.); (X.Z.); (K.H.); (X.S.); (J.Y.); (Z.G.)
- National Engineering Research Center for Peanut, Qingdao 266100, China
| | - Xinying Song
- Shandong Peanut Research Institute, Qingdao 266100, China; (Y.L.); (X.Z.); (K.H.); (X.S.); (J.Y.); (Z.G.)
- National Engineering Research Center for Peanut, Qingdao 266100, China
| | - Jing Yu
- Shandong Peanut Research Institute, Qingdao 266100, China; (Y.L.); (X.Z.); (K.H.); (X.S.); (J.Y.); (Z.G.)
- National Engineering Research Center for Peanut, Qingdao 266100, China
| | - Zhiqing Guo
- Shandong Peanut Research Institute, Qingdao 266100, China; (Y.L.); (X.Z.); (K.H.); (X.S.); (J.Y.); (Z.G.)
- National Engineering Research Center for Peanut, Qingdao 266100, China
| | - Manlin Xu
- Shandong Peanut Research Institute, Qingdao 266100, China; (Y.L.); (X.Z.); (K.H.); (X.S.); (J.Y.); (Z.G.)
- National Engineering Research Center for Peanut, Qingdao 266100, China
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2
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Çam S, Küçük Ç, Almaca A. Bacillus strains exhibit various plant growth promoting traits and their biofilm-forming capability correlates to their salt stress alleviation effect on maize seedlings. J Biotechnol 2023; 369:35-42. [PMID: 37207853 DOI: 10.1016/j.jbiotec.2023.05.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/29/2023] [Accepted: 05/16/2023] [Indexed: 05/21/2023]
Abstract
Soil salinity interferes with plant growth and development. Bacillus genus has been used to increase the growth and productivity of a wide variety of crops by alleviating the effects of salt stress. A total of thirty two Bacillus isolates were obtained from maize rhizosphere, and their plant growth-promoting (PGP) traits and biocontrol activities were tested. Bacillus isolates displayed varying degrees of PGP properties-the production of extracellular enzymes, indole acetic acid, hydrogen cyanide, phosphate solubilization, biofilm formation, and antifungal potential against several fungal pathogens. The phosphate-solubilizing isolates belong to B. safensis, B. thuringiensis, B. cereus, and B. megaterium species. Each Bacillus isolate demonstrated different levels of antifungal activity against the fungal pathogens tested. Biofilm production by some salt-tolerant isolates significantly increased at elevated levels of NaCl (p<0.05). The strains B. safensis B24, B. halotolerans B7/B18, B. subtilis B26, and B. thuringiensis B10 significantly increased the length of root (by 32.7-38.2%) and shoot (by 19.5-29.8%) of maize (p<0.05). Maize plants treated with some Bacillus strains displayed significantly greater chlorophyll content with an increase of 26.7-32.1% (p <0.05). Among PGP properties, enhanced biofilm formation played a more important role in maize growth under higher salinity. These salt-tolerant biofilm-forming strains could be efficiently used as bio-inoculant for maize under salinity stress.
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Affiliation(s)
- Sedat Çam
- Department of Biology, Faculty of Arts and Sciences, Harran University, Haliliye/Şanlıurfa, 63050, Turkey.
| | - Çiğdem Küçük
- Department of Biology, Faculty of Arts and Sciences, Harran University, Haliliye/Şanlıurfa, 63050, Turkey
| | - Ahmet Almaca
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Harran University, Haliliye/Şanlıurfa, Turkey
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3
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Wang Y, Shahid MQ. Genome sequencing and resequencing identified three horizontal gene transfers and uncovered the genetic mechanism on the intraspecies adaptive evolution of Gastrodia elata Blume. FRONTIERS IN PLANT SCIENCE 2023; 13:1035157. [PMID: 36684780 PMCID: PMC9848658 DOI: 10.3389/fpls.2022.1035157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Horizontal gene transfer is a rare and useful genetic mechanism in higher plants. Gastrodia elata Blume (GE) (Orchidaceae), well known as traditional medicinal material in East Asia, adopts a heterotrophic lifestyle, thus being considered to be more prone to horizontal gene transfer (HGT). GE is a "polytypic species" that currently comprised of five recognized forms according to the plant morphology. G. elata Blume forma elata (GEE) and G. elata Bl.f.glauca (GEG) are two common forms that naturally grow in different habitats with difference in altitude and latitude. G. elata Bl.f.viridis (GEV) often occurs sporadically in cultivated populations of GEE and GEG. However, the genetic relationships and genetic mechanism underpinned the divergent ecological adaptations of GEE and GEG have not been revealed. Here, we assembled a chromosome-level draft genome of GEE with 1.04 Gb. Among predicted 17,895 protein coding genes, we identified three HGTs. Meanwhile, we resequenced 10 GEE accessions, nine GEG accessions, and 10 GEV accessions, and identified two independent genetic lineages: GEG_pedigree (GEG individuals and GEV individuals collected from GEG populations) and GEE_pedigree (GEE individuals and GEV individuals collected from GEE populations), which strongly support the taxonomic status of GEE and GEG as subspecies, not as different forms. In highly differentiated genomic regions of GEE_pedigree and GEG_pedigree, three chalcone synthase-encoding genes and one Phox/Bem1p (PB1) domain of encoding Auxin (AUX)/Indoleacetic acid (IAA) were identified in selection sweeping genome regions, which suggested that differentiation between GEE_pedigree and GEG_pedigree was promoted by the selection of genes related to photoresponse and growth and development. Overall, this new genome would be helpful for breeding and utilization of GE and the new findings would deepen the understanding about ecological adaptation and evolution of GE.
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Affiliation(s)
- Yunsheng Wang
- School of Health and Life Science, Kaili University, Kaili, Guizhou, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
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Target and Enhance Ethanol and Butyrate Production from Anaerobic Fermentation via the pH and Organic Loading Rate Combined Strategy. Appl Biochem Biotechnol 2022; 194:6367-6385. [PMID: 35921030 DOI: 10.1007/s12010-021-03729-z] [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: 07/24/2021] [Accepted: 10/21/2021] [Indexed: 11/02/2022]
Abstract
The large capacity production and low utilization rate increase the difficulty of fruit and vegetable wastes (FVW) treatment. Efficient and targeted recovery strategies can solve these problems. This study investigated and proposed combined strategies via pH and organic loading rate (OLR) to target and enhance ethanol- and butyrate-dominant acidogenic production in the FVW mixed culture fermentation. Under pH 4.0, OLR 18 gCOD/(L∙d), and mesophilic (35 °C), ethanol-dominant fermentation was formed. The long-term operation (168 days) showed that the highest ethanol yield was 0.33 g/gCOD which was greater than that in other studies. Also, the hydrolysis rate of ethanol-type fermentation reached 74.5%. Besides, butyrate-type fermentation was stable at yield 0.39 g/gCOD following conditions: pH 6.0, OLR 28 gCOD/(L∙d), and 35 °C, of which hydrolysis and acidogenic rate were 78.0% and 62.0%, respectively. The high relative abundance of Lactobacillus, Olsenella, and Bifidobacterium played positive role in achieving ethanol, butyrate, and lactate production among various metabolic pathways. The results revealed the pH value together with OLR was the valid parameter to affect product formation and composition during FVW fermentation.
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Coastal Transient Niches Shape the Microdiversity Pattern of a Bacterioplankton Population with Reduced Genomes. mBio 2022; 13:e0057122. [PMID: 35880883 PMCID: PMC9426536 DOI: 10.1128/mbio.00571-22] [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] [Indexed: 12/01/2022] Open
Abstract
Globally dominant marine bacterioplankton lineages are often limited in metabolic versatility, owing to their extensive genome reductions, and thus cannot take advantage of transient nutrient patches. It is therefore perplexing how the nutrient-poor bulk seawater sustains the pelagic streamlined lineages, each containing numerous populations. Here, we sequenced the genomes of 33 isolates of the recently discovered CHUG lineage (~2.6 Mbp), which have some of the smallest genomes in the globally abundant Roseobacter group (commonly over 4 Mbp). These genome-reduced bacteria were isolated from a transient habitat: seawater surrounding the brown alga, Sargassum hemiphyllum. Population genomic analyses showed that: (i) these isolates, despite sharing identical 16S rRNA genes, were differentiated into several genetically isolated populations through successive speciation events; (ii) only the first speciation event led to the genetic separation of both core and accessory genomes; and (iii) populations resulting from this event are differentiated at many loci involved in carbon utilization and oxygen respiration, corroborated by BiOLOG phenotype microarray assays and oxygen uptake kinetics experiments, respectively. These differentiated traits match well with the dynamic nature of the macroalgal seawater, in which the quantity and quality of carbon sources and the concentration of oxygen likely vary spatially and temporally, though other habitats, like fresh organic aggregates, cannot be ruled out. Our study implies that transient habitats in the overall nutrient-poor ocean can shape the microdiversity and population structure of genome-reduced bacterioplankton lineages.
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Canário Viana MV, Profeta R, Cerqueira JC, Wattam AR, Barh D, Silva A, Azevedo V. Evidence of episodic positive selection in Corynebacterium diphtheriae complex of species and its implementations in identification of drug and vaccine targets. PeerJ 2022; 10:e12662. [PMID: 35190783 PMCID: PMC8857904 DOI: 10.7717/peerj.12662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/30/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Within the pathogenic bacterial species Corynebacterium genus, six species that can produce diphtheria toxin (C. belfantii, C. diphtheriae, C. pseudotuberculosis, C. rouxii, C. silvaticum and C. ulcerans) form a clade referred to as the C. diphtheria complex. These species have been found in humans and other animals, causing diphtheria or other diseases. Here we show the results of a genome scale analysis to identify positive selection in protein-coding genes that may have resulted in the adaptations of these species to their ecological niches and suggest drug and vaccine targets. METHODS Forty genomes were sampled to represent species, subspecies or biovars of Corynebacterium. Ten phylogenetic groups were tested for positive selection using the PosiGene pipeline, including species and biovars from the C. diphtheria complex. The detected genes were tested for recombination and had their sequences alignments and homology manually examined. The final genes were investigated for their function and a probable role as vaccine or drug targets. RESULTS Nineteen genes were detected in the species C. diphtheriae (two), C. pseudotuberculosis (10), C. rouxii (one), and C. ulcerans (six). Those were found to be involved in defense, translation, energy production, and transport and in the metabolism of carbohydrates, amino acids, nucleotides, and coenzymes. Fourteen were identified as essential genes, and six as virulence factors. Thirteen from the 19 genes were identified as potential drug targets and four as potential vaccine candidates. These genes could be important in the prevention and treatment of the diseases caused by these bacteria.
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Affiliation(s)
- Marcus Vinicius Canário Viana
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil,Departamento de Genética, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Rodrigo Profeta
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Janaína Canário Cerqueira
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Alice Rebecca Wattam
- Biocomplexity Institute, University of Virginia, Charlottesville, Virginia, United States
| | - Debmalya Barh
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil,Institute of Integrative Omics and Applied Biotechnology, Nonakuri, West Bengal, India
| | - Artur Silva
- Departamento de Genética, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Vasco Azevedo
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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7
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Igai K, Kitade O, Fu J, Omata K, Yonezawa T, Ohkuma M, Hongoh Y. Fine-scale genetic diversity and putative ecotypes of oxymonad protists coinhabiting the hindgut of Reticulitermes speratus. Mol Ecol 2021; 31:1317-1331. [PMID: 34865251 DOI: 10.1111/mec.16309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 11/22/2021] [Accepted: 11/30/2021] [Indexed: 11/29/2022]
Abstract
The hindgut of lower termites is generally coinhabited by multiple morphologically identifiable protist species. However, it is unclear how many protist species truly coexist in this miniaturized environment, and moreover, it is difficult to define the fundamental unit of protist diversity. Species delineation of termite gut protists has therefore been guided without a theory-based concept of species. Here, we focused on the hindgut of the termite Reticulitermes speratus, where 10 or 11 morphologically distinct oxymonad cell types, that is, morphospecies, coexist. We elucidated the phylogenetic structure of all co-occurring oxymonads and addressed whether their diversity can be explained by the "ecotype" hypothesis. Oxymonad-specific 18S rRNA gene amplicon sequencing analyses of whole-gut samples, combined with single-cell 18S rRNA sequencing of the oxymonad morphospecies, identified 210 one-nucleotide-level variants. The phylogenetic analysis of these variants revealed the presence of microdiverse clusters typically within 1% sequence divergence. Each known oxymonad morphospecies comprised one to several monophyletic or paraphyletic microdiverse clusters. Using these sequence data sets, we conducted computational simulation to predict the rates of ecotype formation and periodic selection, and to demarcate putative ecotypes. Our simulations suggested that the oxymonad genetic divergence is constrained primarily by strong selection, in spite of limited population size and possible bottlenecks during intergenerational transmission. A total of 33 oxymonad ecotypes were predicted, and most of the putative ecotypes were consistently detected among different colonies and host individuals. These findings provide a possible theoretical basis for species diversity and underlying mechanisms of coexistence of termite gut protists.
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Affiliation(s)
- Katsura Igai
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Osamu Kitade
- College of Science, Ibaraki University, Ibaraki, Japan
| | - Jieyang Fu
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Kazumi Omata
- Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan.,Department of Hematology, Rheumatology and Infectious Disease, Kumamoto University Hospital, Kumamoto, Japan
| | - Takahiro Yonezawa
- Department of Animal Science, Faculty of Agriculture, Tokyo University of Agriculture, Kanagawa, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Ibaraki, Japan
| | - Yuichi Hongoh
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.,Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center, Ibaraki, Japan
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8
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Tucker SJ, Freel KC, Monaghan EA, Sullivan CES, Ramfelt O, Rii YM, Rappé MS. Spatial and temporal dynamics of SAR11 marine bacteria across a nearshore to offshore transect in the tropical Pacific Ocean. PeerJ 2021; 9:e12274. [PMID: 34760357 PMCID: PMC8572523 DOI: 10.7717/peerj.12274] [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: 03/22/2021] [Accepted: 09/19/2021] [Indexed: 01/04/2023] Open
Abstract
Surveys of microbial communities across transitions coupled with contextual measures of the environment provide a useful approach to dissect the factors determining distributions of microorganisms across ecological niches. Here, monthly time-series samples of surface seawater along a transect spanning the nearshore coastal environment within Kāneʻohe Bay on the island of Oʻahu, Hawaiʻi, and the adjacent offshore environment were collected to investigate the diversity and abundance of SAR11 marine bacteria (order Pelagibacterales) over a 2-year time period. Using 16S ribosomal RNA gene amplicon sequencing, the spatiotemporal distributions of major SAR11 subclades and exact amplicon sequence variants (ASVs) were evaluated. Seven of eight SAR11 subclades detected in this study showed distinct subclade distributions across the coastal to offshore environments. The SAR11 community was dominated by seven (of 106 total) SAR11 ASVs that made up an average of 77% of total SAR11. These seven ASVs spanned five different SAR11 subclades (Ia, Ib, IIa, IV, and Va), and were recovered from all samples collected from either the coastal environment, the offshore, or both. SAR11 ASVs were more often restricted spatially to coastal or offshore environments (64 of 106 ASVs) than they were shared among coastal, transition, and offshore environments (39 of 106 ASVs). Overall, offshore SAR11 communities contained a higher diversity of SAR11 ASVs than their nearshore counterparts, with the highest diversity within the little-studied subclade IIa. This study reveals ecological differentiation of SAR11 marine bacteria across a short physiochemical gradient, further increasing our understanding of how SAR11 genetic diversity partitions into distinct ecological units.
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Affiliation(s)
- Sarah J Tucker
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States.,Marine Biology Graduate Program, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States
| | - Kelle C Freel
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States
| | - Elizabeth A Monaghan
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States.,Marine Biology Graduate Program, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States
| | - Clarisse E S Sullivan
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States
| | - Oscar Ramfelt
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States.,Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, Hawai'i, United States
| | - Yoshimi M Rii
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States.,He'eia National Estuarine Research Reserve, Kāne'ohe, Hawai'i, United States
| | - Michael S Rappé
- Hawai'i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States
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9
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Kaasalainen U, Tuovinen V, Mwachala G, Pellikka P, Rikkinen J. Complex Interaction Networks Among Cyanolichens of a Tropical Biodiversity Hotspot. Front Microbiol 2021; 12:672333. [PMID: 34177853 PMCID: PMC8220813 DOI: 10.3389/fmicb.2021.672333] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/26/2021] [Indexed: 11/13/2022] Open
Abstract
Interactions within lichen communities include, in addition to close mutualistic associations between the main partners of specific lichen symbioses, also more elusive relationships between members of a wider symbiotic community. Here, we analyze association patterns of cyanolichen symbionts in the tropical montane forests of Taita Hills, southern Kenya, which is part of the Eastern Afromontane biodiversity hotspot. The cyanolichen specimens analyzed represent 74 mycobiont taxa within the order Peltigerales (Ascomycota), associating with 115 different variants of the photobionts genus Nostoc (Cyanobacteria). Our analysis demonstrates wide sharing of photobionts and reveals the presence of several photobiont-mediated lichen guilds. Over half of all mycobionts share photobionts with other fungal species, often from different genera or even families, while some others are strict specialists and exclusively associate with a single photobiont variant. The most extensive symbiont network involves 24 different fungal species from five genera associating with 38 Nostoc photobionts. The Nostoc photobionts belong to two main groups, the Nephroma-type Nostoc and the Collema/Peltigera-type Nostoc, and nearly all mycobionts associate only with variants of one group. Among the mycobionts, species that produce cephalodia and those without symbiotic propagules tend to be most promiscuous in photobiont choice. The extent of photobiont sharing and the structure of interaction networks differ dramatically between the two major photobiont-mediated guilds, being both more prevalent and nested among Nephroma guild fungi and more compartmentalized among Peltigera guild fungi. This presumably reflects differences in the ecological characteristics and/or requirements of the two main groups of photobionts. The same two groups of Nostoc have previously been identified from many lichens in various lichen-rich ecosystems in different parts of the world, indicating that photobiont sharing between fungal species is an integral part of lichen ecology globally. In many cases, symbiotically dispersing lichens can facilitate the dispersal of sexually reproducing species, promoting establishment and adaptation into new and marginal habitats and thus driving evolutionary diversification.
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Affiliation(s)
- Ulla Kaasalainen
- Department of Geobiology, University of Göttingen, Göttingen, Germany.,Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Veera Tuovinen
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | | | - Petri Pellikka
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland.,State Key Laboratory of Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University, Wuhan, China
| | - Jouko Rikkinen
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland.,Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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10
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Van Rossum T, Ferretti P, Maistrenko OM, Bork P. Diversity within species: interpreting strains in microbiomes. Nat Rev Microbiol 2020; 18:491-506. [PMID: 32499497 PMCID: PMC7610499 DOI: 10.1038/s41579-020-0368-1] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2020] [Indexed: 02/06/2023]
Abstract
Studying within-species variation has traditionally been limited to culturable bacterial isolates and low-resolution microbial community fingerprinting. Metagenomic sequencing and technical advances have enabled culture-free, high-resolution strain and subspecies analyses at high throughput and in complex environments. This holds great scientific promise but has also led to an overwhelming number of methods and terms to describe infraspecific variation. This Review aims to clarify these advances by focusing on the diversity within bacterial and archaeal species in the context of microbiomics. We cover foundational microevolutionary concepts relevant to population genetics and summarize how within-species variation can be studied and stratified directly within microbial communities with a focus on metagenomics. Finally, we describe how common applications of within-species variation can be achieved using metagenomic data. We aim to guide the selection of appropriate terms and analytical approaches to facilitate researchers in benefiting from the increasing availability of large, high-resolution microbiome genetic sequencing data.
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Affiliation(s)
- Thea Van Rossum
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Pamela Ferretti
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Oleksandr M Maistrenko
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany.
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany.
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
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11
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Simonsen AK, Barrett LG, Thrall PH, Prober SM. Novel model-based clustering reveals ecologically differentiated bacterial genomes across a large climate gradient. Ecol Lett 2019; 22:2077-2086. [PMID: 31612601 DOI: 10.1111/ele.13389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 07/28/2019] [Accepted: 08/19/2019] [Indexed: 12/19/2022]
Abstract
A pervasive challenge in microbial ecology is understanding the genetic level where ecological units can be differentiated. Ecological differentiation often occurs at fine genomic levels, yet it is unclear how to utilise ecological information to define ecotypes given the breadth of environmental variation among microbial taxa. Here, we present an analytical framework that infers clusters along genome-based microbial phylogenies according to shared environmental responses. The advantage of our approach is the ability to identify genomic clusters that best fit complex environmental information whilst characterising cluster niches through model predictions. We apply our method to determine climate-associated ecotypes in populations of nitrogen-fixing symbionts using whole genomes, explicitly sampled to detect climate differentiation across a heterogeneous landscape. Although soil and plant host characteristics strongly influence distribution patterns of inferred ecotypes, our flexible statistical method enabled us to identify climate-associated genomic clusters using environmental data, providing solid support for ecological specialisation in soil symbionts.
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Affiliation(s)
- Anna K Simonsen
- Research School of Biology, Australian National University, Acton, ACT, Australia.,Land and Water, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Luke G Barrett
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Peter H Thrall
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Suzanne M Prober
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
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12
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Lassalle F, Planel R, Penel S, Chapulliot D, Barbe V, Dubost A, Calteau A, Vallenet D, Mornico D, Bigot T, Guéguen L, Vial L, Muller D, Daubin V, Nesme X. Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium. Genome Biol Evol 2018; 9:3413-3431. [PMID: 29220487 PMCID: PMC5739047 DOI: 10.1093/gbe/evx255] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2017] [Indexed: 12/12/2022] Open
Abstract
Horizontal gene transfer (HGT) is considered as a major source of innovation in bacteria, and as such is expected to drive adaptation to new ecological niches. However, among the many genes acquired through HGT along the diversification history of genomes, only a fraction may have actively contributed to sustained ecological adaptation. We used a phylogenetic approach accounting for the transfer of genes (or groups of genes) to estimate the history of genomes in Agrobacterium biovar 1, a diverse group of soil and plant-dwelling bacterial species. We identified clade-specific blocks of cotransferred genes encoding coherent biochemical pathways that may have contributed to the evolutionary success of key Agrobacterium clades. This pattern of gene coevolution rejects a neutral model of transfer, in which neighboring genes would be transferred independently of their function and rather suggests purifying selection on collectively coded acquired pathways. The acquisition of these synapomorphic blocks of cofunctioning genes probably drove the ecological diversification of Agrobacterium and defined features of ancestral ecological niches, which consistently hint at a strong selective role of host plant rhizospheres.
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Affiliation(s)
- Florent Lassalle
- Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, France.,Biométrie et Biologie Evolutive, CNRS, UCBL, Université de Lyon, Villeurbanne, France.,Ecole Normale Supérieure de Lyon, Lyon, France
| | - Rémi Planel
- Biométrie et Biologie Evolutive, CNRS, UCBL, Université de Lyon, Villeurbanne, France
| | - Simon Penel
- Biométrie et Biologie Evolutive, CNRS, UCBL, Université de Lyon, Villeurbanne, France
| | - David Chapulliot
- Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, France
| | - Valérie Barbe
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA) Direction de la Recherche Fondamentale, Institut de Biologie Francois-Jacob (IBFJ), Genoscope, Evry, France
| | - Audrey Dubost
- Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, France
| | - Alexandra Calteau
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA) Direction de la Recherche Fondamentale, Institut de Biologie Francois-Jacob (IBFJ), Genoscope, Evry, France.,Laboratoire d'Analyse Bioinformatiques pour la Génomique et le Métabolisme, CNRS, UMR 8030, Evry, France.,UEVE, Université d'Evry Val d'Essonne, France
| | - David Vallenet
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA) Direction de la Recherche Fondamentale, Institut de Biologie Francois-Jacob (IBFJ), Genoscope, Evry, France.,Laboratoire d'Analyse Bioinformatiques pour la Génomique et le Métabolisme, CNRS, UMR 8030, Evry, France.,UEVE, Université d'Evry Val d'Essonne, France
| | - Damien Mornico
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA) Direction de la Recherche Fondamentale, Institut de Biologie Francois-Jacob (IBFJ), Genoscope, Evry, France.,Laboratoire d'Analyse Bioinformatiques pour la Génomique et le Métabolisme, CNRS, UMR 8030, Evry, France.,UEVE, Université d'Evry Val d'Essonne, France
| | - Thomas Bigot
- Biométrie et Biologie Evolutive, CNRS, UCBL, Université de Lyon, Villeurbanne, France
| | - Laurent Guéguen
- Biométrie et Biologie Evolutive, CNRS, UCBL, Université de Lyon, Villeurbanne, France
| | - Ludovic Vial
- Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, France
| | - Daniel Muller
- Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, France
| | - Vincent Daubin
- Biométrie et Biologie Evolutive, CNRS, UCBL, Université de Lyon, Villeurbanne, France
| | - Xavier Nesme
- Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Villeurbanne, France
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13
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Abstract
Any two lineages, no matter how distant they are now, began their divergence as one population splitting into two lineages that could coexist indefinitely. The rate of origin of higher-level taxa is therefore the product of the rate of speciation times the probability that two new species coexist long enough to reach a particular level of divergence. Here I have explored these two parameters of disparification in bacteria. Owing to low recombination rates, sexual isolation is not a necessary milestone of bacterial speciation. Rather, irreversible and indefinite divergence begins with ecological diversification, that is, transmission of a bacterial lineage to a new ecological niche, possibly to a new microhabitat but at least to new resources. Several algorithms use sequence data from a taxon of focus to identify phylogenetic groups likely to bear the dynamic properties of species. Identifying these newly divergent lineages allows us to characterize the genetic bases of speciation, as well as the ecological dimensions upon which new species diverge. Speciation appears to be least frequent when a given lineage has few new resources it can adopt, as exemplified by photoautotrophs, C1 heterotrophs, and obligately intracellular pathogens; speciation is likely most rapid for generalist heterotrophs. The genetic basis of ecological divergence may determine whether ecological divergence is irreversible and whether lineages will diverge indefinitely into the future. Long-term coexistence is most likely when newly divergent lineages utilize at least some resources not shared with the other and when the resources themselves will coexist into the remote future.
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14
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Larkin AA, Martiny AC. Microdiversity shapes the traits, niche space, and biogeography of microbial taxa. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:55-70. [PMID: 28185400 DOI: 10.1111/1758-2229.12523] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/31/2017] [Accepted: 02/01/2017] [Indexed: 06/06/2023]
Abstract
With rapidly improving sequencing technologies, scientists have recently gained the ability to examine diverse microbial communities at high genomic resolution, revealing that both free-living and host-associated microbes partition their environment at fine phylogenetic scales. This 'microdiversity,' or closely related (> 97% similar 16S rRNA gene) but ecologically and physiologically distinct sub-taxonomic groups, appears to be an intrinsic property of microorganisms. However, the functional implications of microdiversity as well as its effects on microbial biogeography are poorly understood. Here, we present two theoretical models outlining the evolutionary mechanisms that drive the formation of microdiverse 'sub-taxa.' Additionally, we review recent literature and reveal that microdiversity influences a wide range of functional traits across diverse ecosystems and microbes. Moving to higher levels of organization, we use laboratory data from marine, soil, and host-associated bacteria to demonstrate that the aggregated trait-based response of microdiverse sub-taxa modifies the fundamental niche of microbes. The correspondence between microdiversity and niche space represents a critical tool for future studies of microbial ecology. By combining growth experiments on diverse isolates with examinations of environmental abundance patterns, researchers can better quantify the fundamental and realized niches of microbes and improve understanding of microbial biogeography and response to future environmental change.
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Affiliation(s)
- Alyse A Larkin
- Department of Earth System Science, University of California, Irvine, CA, 92697, USA
| | - Adam C Martiny
- Department of Earth System Science, University of California, Irvine, CA, 92697, USA
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
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15
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Microdiversification of a Pelagic Polynucleobacter Species Is Mainly Driven by Acquisition of Genomic Islands from a Partially Interspecific Gene Pool. Appl Environ Microbiol 2017; 83:AEM.02266-16. [PMID: 27836842 DOI: 10.1128/aem.02266-16] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 11/07/2016] [Indexed: 12/13/2022] Open
Abstract
Microdiversification of a planktonic freshwater bacterium was studied by comparing 37 Polynucleobacter asymbioticus strains obtained from three geographically separated sites in the Austrian Alps. Genome comparison of nine strains revealed a core genome of 1.8 Mb, representing 81% of the average genome size. Seventy-five percent of the remaining flexible genome is clustered in genomic islands (GIs). Twenty-four genomic positions could be identified where GIs are potentially located. These positions are occupied strain specifically from a set of 28 GI variants, classified according to similarities in their gene content. One variant, present in 62% of the isolates, encodes a pathway for the degradation of aromatic compounds, and another, found in 78% of the strains, contains an operon for nitrate assimilation. Both variants were shown in ecophysiological tests to be functional, thus providing the potential for microniche partitioning. In addition, detected interspecific horizontal exchange of GIs indicates a large gene pool accessible to Polynucleobacter species. In contrast to core genes, GIs are spread more successfully across spatially separated freshwater habitats. The mobility and functional diversity of GIs allow for rapid evolution, which may be a key aspect for the ubiquitous occurrence of Polynucleobacter bacteria. IMPORTANCE Assessing the ecological relevance of bacterial diversity is a key challenge for current microbial ecology. The polyphasic approach which was applied in this study, including targeted isolation of strains, genome analysis, and ecophysiological tests, is crucial for the linkage of genetic and ecological knowledge. Particularly great importance is attached to the high number of closely related strains which were investigated, represented by genome-wide average nucleotide identities (ANI) larger than 97%. The extent of functional diversification found on this narrow phylogenetic scale is compelling. Moreover, the transfer of metabolically relevant genomic islands between more distant members of the Polynucleobacter community provides important insights toward a better understanding of the evolution of these globally abundant freshwater bacteria.
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16
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Mardanova AM, Fanisovna Hadieva G, Tafkilevich Lutfullin M, Valer’evna Khilyas I, Farvazovna Minnullina L, Gadelevna Gilyazeva A, Mikhailovna Bogomolnaya L, Rashidovna Sharipova M. <i>Bacillus subtilis Strains</i> with Antifungal Activity against the Phytopathogenic Fungi. ACTA ACUST UNITED AC 2017. [DOI: 10.4236/as.2017.81001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Klinger CR, Lau JA, Heath KD. Ecological genomics of mutualism decline in nitrogen-fixing bacteria. Proc Biol Sci 2016; 283:20152563. [PMID: 26962142 DOI: 10.1098/rspb.2015.2563] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Anthropogenic changes can influence mutualism evolution; however, the genomic regions underpinning mutualism that are most affected by environmental change are generally unknown, even in well-studied model mutualisms like the interaction between legumes and their nitrogen (N)-fixing rhizobia. Such genomic information can shed light on the agents and targets of selection maintaining cooperation in nature. We recently demonstrated that N-fertilization has caused an evolutionary decline in mutualistic partner quality in the rhizobia that form symbiosis with clover. Here, population genomic analyses of N-fertilized versus control rhizobium populations indicate that evolutionary differentiation at a key symbiosis gene region on the symbiotic plasmid (pSym) contributes to partner quality decline. Moreover, patterns of genetic variation at selected loci were consistent with recent positive selection within N-fertilized environments, suggesting that N-rich environments might select for less beneficial rhizobia. By studying the molecular population genomics of a natural bacterial population within a long-term ecological field experiment, we find that: (i) the N environment is indeed a potent selective force mediating mutualism evolution in this symbiosis, (ii) natural variation in rhizobium partner quality is mediated in part by key symbiosis genes on the symbiotic plasmid, and (iii) differentiation at selected genes occurred in the context of otherwise recombining genomes, resembling eukaryotic models of adaptation.
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Affiliation(s)
- Christie R Klinger
- Department of Plant Biology, University of Illinois Urbana-Champaign, 505 South Goodwin Avenue, Urbana, IL 61801, USA
| | - Jennifer A Lau
- W.K. Kellogg Biological Station and Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Katy D Heath
- Department of Plant Biology, University of Illinois Urbana-Champaign, 505 South Goodwin Avenue, Urbana, IL 61801, USA
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18
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Katyal I, Chaban B, Hill JE. Comparative Genomics of cpn60-Defined Enterococcus hirae Ecotypes and Relationship of Gene Content Differences to Competitive Fitness. MICROBIAL ECOLOGY 2016; 72:917-930. [PMID: 26566933 DOI: 10.1007/s00248-015-0708-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 11/02/2015] [Indexed: 06/05/2023]
Abstract
Natural microbial communities undergo selection-driven succession with changes in environmental conditions and available nutrients. In a previous study of the pig faecal Enterococcus community, we demonstrated that cpn60 universal target (UT) sequences could resolve phenotypically and genotypically distinct ecotypes of Enterococcus spp. that emerged over time in the faecal microbiome of growing pigs. In this study, we characterized genomic diversity in the identified Enterococcus hirae ecotypes in order to define further the nature and degree of genome content differences between taxa resolved by cpn60 UT sequences. Genome sequences for six representative isolates (two from each of three ecotypes) were compared. Differences in phosphotransferase systems and amino acid metabolism pathways for glutamine, proline and selenocysteine were observed. Differences in the lac family phosphotransferase system corresponded to lactose utilization phenotypes of the isolates. Competitive fitness of the E. hirae ecotypes was evaluated by in vitro growth competition assays in pig faecal extract medium. Isolates from E. hirae-1 and E. hirae-2 ecotypes were able to out-compete isolates from the E. hirae-3 ecotype, consistent with the relatively low abundance of E. hirae-3 relative to E. hirae-1 and E. hirae-2 previously observed in the pig faecal microbiome, and with observed differences between the ecotypes in gene content related to biosynthetic capacity. Results of this study provide a genomic basis for the definition of ecotypes within E. hirae and confirm the utility of the cpn60 UT sequence for high-resolution profiling of complex microbial communities.
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Affiliation(s)
- Isha Katyal
- Department of Veterinary Microbiology, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK, S7N 5B4, Canada
| | - Bonnie Chaban
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Janet E Hill
- Department of Veterinary Microbiology, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK, S7N 5B4, Canada.
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19
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Walker LM, Stephenson SL. The Species Problem in Myxomycetes Revisited. Protist 2016; 167:319-338. [DOI: 10.1016/j.protis.2016.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 05/12/2016] [Accepted: 05/27/2016] [Indexed: 11/27/2022]
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20
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Structure of bacterial communities in soil following cover crop and organic fertilizer incorporation. Appl Microbiol Biotechnol 2016; 100:9331-9341. [DOI: 10.1007/s00253-016-7736-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 07/04/2016] [Accepted: 07/10/2016] [Indexed: 11/29/2022]
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21
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Abstract
One theory of bacterial speciation states that bacterial and animal species share the property of cohesion, meaning that diversity within a species is constrained. A new study provides direct evidence that genome-wide sweeps can limit diversity within bacterial species.
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Affiliation(s)
- Frederick M Cohan
- Department of Biology, Wesleyan University, Middletown, CT 06459, USA.
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22
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Adelskov J, Patel BKC. A molecular phylogenetic framework for Bacillus subtilis using genome sequences and its application to Bacillus subtilis subspecies stecoris strain D7XPN1, an isolate from a commercial food-waste degrading bioreactor. 3 Biotech 2016; 6:96. [PMID: 28330166 PMCID: PMC4809863 DOI: 10.1007/s13205-016-0408-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 02/28/2016] [Indexed: 11/25/2022] Open
Abstract
A thermophilic, heterotrophic and facultatively anaerobic bacterium designated strain D7XPN1 was isolated from Baku BakuKing™, a commercial food-waste degrading bioreactor (composter). The strain grew optimally at 45 °C (growth range between 24 and 50 °C) and pH 7 (growth pH range between pH 5 and 9) in Luria Broth supplemented with 0.3 % glucose. Strain D7XPN1 tolerated up to 7 % NaCl and showed amylolytic and xylanolytic activities. 16S rRNA gene analysis placed strain D7XPN1 in the cluster represented by Bacillus subtilis and the genome analysis of the 4.1 Mb genome sequence determined using RAST (Rapid Annotation using Subsystem Technology) indicated a total of 5116 genomic features were present of which 2320 features could be grouped into several subsystem categories. Of these, 615 features were related to carbohydrate metabolism which included a range of enzymes with potential in the biodegradation of food wastes, a property consistent with the ecological habitat of the isolate. ANIb (Average Nucleotide Identity based on BLAST) analysis with 49 Bacillus subtilis genomes indicated that it was distantly related to the three currently taxonomically validated B. subtilis subspecies namely B. subtilis subsp. subtilis (95.6 %), B. subtilis subsp. spizizenii (93 %) and B. subtilis subsp. inaquosorum (92 %) and based on our current knowledge warranted that it be included as a separate cluster together with strain JS which it was closely related (98.69 %). The close relationship of strains D7XPN1 and JS is also supported from our results from electronic DNA–DNA Hybridization (e-DDH) studies. Furthermore, our additional in-depth phylogenomic analyses using three different datasets unequivocally supported the creation of a fourth B. subtilis subspecies to include strains D7XPN1 and JS for which we propose strain D7XPN1T (=KCTC 33554T, JCM 30051T) as the type strain, and designate it as B. subtilis subsp. stecoris.
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Affiliation(s)
- Joseph Adelskov
- Microbial Gene Research and Resources Facility, School of Natural Sciences, Griffith University, Brisbane, QLD, 4111, Australia
| | - Bharat K C Patel
- Microbial Gene Research and Resources Facility, School of Natural Sciences, Griffith University, Brisbane, QLD, 4111, Australia.
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23
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Whiteside MD, Laing CR, Manji A, Kruczkiewicz P, Taboada EN, Gannon VPJ. SuperPhy: predictive genomics for the bacterial pathogen Escherichia coli. BMC Microbiol 2016; 16:65. [PMID: 27067409 PMCID: PMC4828761 DOI: 10.1186/s12866-016-0680-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 03/29/2016] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Predictive genomics is the translation of raw genome sequence data into a phenotypic assessment of the organism. For bacterial pathogens, these phenotypes can range from environmental survivability, to the severity of human disease. Significant progress has been made in the development of generic tools for genomic analyses that are broadly applicable to all microorganisms; however, a fundamental missing component is the ability to analyze genomic data in the context of organism-specific phenotypic knowledge, which has been accumulated from decades of research and can provide a meaningful interpretation of genome sequence data. RESULTS In this study, we present SuperPhy, an online predictive genomics platform ( http://lfz.corefacility.ca/superphy/ ) for Escherichia coli. The platform integrates the analytical tools and genome sequence data for all publicly available E. coli genomes and facilitates the upload of new genome sequences from users under public or private settings. SuperPhy provides real-time analyses of thousands of genome sequences with results that are understandable and useful to a wide community, including those in the fields of clinical medicine, epidemiology, ecology, and evolution. SuperPhy includes identification of: 1) virulence and antimicrobial resistance determinants 2) statistical associations between genotypes, biomarkers, geospatial distribution, host, source, and phylogenetic clade; 3) the identification of biomarkers for groups of genomes on the based presence/absence of specific genomic regions and single-nucleotide polymorphisms and 4) in silico Shiga-toxin subtype. CONCLUSIONS SuperPhy is a predictive genomics platform that attempts to provide an essential link between the vast amounts of genome information currently being generated and phenotypic knowledge in an organism-specific context.
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Affiliation(s)
- Matthew D. Whiteside
- National Microbiology Laboratory @ Lethbridge, Public Health Agency of Canada, Lethbridge, AB T1J 3Z4 Canada
| | - Chad R. Laing
- National Microbiology Laboratory @ Lethbridge, Public Health Agency of Canada, Lethbridge, AB T1J 3Z4 Canada
| | - Akiff Manji
- National Microbiology Laboratory @ Lethbridge, Public Health Agency of Canada, Lethbridge, AB T1J 3Z4 Canada
| | - Peter Kruczkiewicz
- National Microbiology Laboratory @ Lethbridge, Public Health Agency of Canada, Lethbridge, AB T1J 3Z4 Canada
| | - Eduardo N. Taboada
- National Microbiology Laboratory @ Lethbridge, Public Health Agency of Canada, Lethbridge, AB T1J 3Z4 Canada
| | - Victor P. J. Gannon
- National Microbiology Laboratory @ Lethbridge, Public Health Agency of Canada, Lethbridge, AB T1J 3Z4 Canada
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24
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Melendrez MC, Becraft ED, Wood JM, Olsen MT, Bryant DA, Heidelberg JF, Rusch DB, Cohan FM, Ward DM. Recombination Does Not Hinder Formation or Detection of Ecological Species of Synechococcus Inhabiting a Hot Spring Cyanobacterial Mat. Front Microbiol 2016; 6:1540. [PMID: 26834710 PMCID: PMC4712262 DOI: 10.3389/fmicb.2015.01540] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 12/21/2015] [Indexed: 12/15/2022] Open
Abstract
Recent studies of bacterial speciation have claimed to support the biological species concept—that reduced recombination is required for bacterial populations to diverge into species. This conclusion has been reached from the discovery that ecologically distinct clades show lower rates of recombination than that which occurs among closest relatives. However, these previous studies did not attempt to determine whether the more-rapidly recombining close relatives within the clades studied may also have diversified ecologically, without benefit of sexual isolation. Here we have measured the impact of recombination on ecological diversification within and between two ecologically distinct clades (A and B') of Synechococcus in a hot spring microbial mat in Yellowstone National Park, using a cultivation-free, multi-locus approach. Bacterial artificial chromosome (BAC) libraries were constructed from mat samples collected at 60°C and 65°C. Analysis of multiple linked loci near Synechococcus 16S rRNA genes showed little evidence of recombination between the A and B' lineages, but a record of recombination was apparent within each lineage. Recombination and mutation rates within each lineage were of similar magnitude, but recombination had a somewhat greater impact on sequence diversity than mutation, as also seen in many other bacteria and archaea. Despite recombination within the A and B' lineages, there was evidence of ecological diversification within each lineage. The algorithm Ecotype Simulation identified sequence clusters consistent with ecologically distinct populations (ecotypes), and several hypothesized ecotypes were distinct in their habitat associations and in their adaptations to different microenvironments. We conclude that sexual isolation is more likely to follow ecological divergence than to precede it. Thus, an ecology-based model of speciation appears more appropriate than the biological species concept for bacterial and archaeal diversification.
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Affiliation(s)
- Melanie C Melendrez
- Department of Land Resources and Environmental Science, Montana State University Bozeman, MT, USA
| | - Eric D Becraft
- Department of Land Resources and Environmental Science, Montana State University Bozeman, MT, USA
| | - Jason M Wood
- Department of Land Resources and Environmental Science, Montana State University Bozeman, MT, USA
| | - Millie T Olsen
- Department of Land Resources and Environmental Science, Montana State University Bozeman, MT, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, Pennsylvania State University University Park, PA, USA
| | - John F Heidelberg
- Department of Biological Sciences, College of Letters, Arts and Sciences, University of Southern California Los Angeles, CA, USA
| | - Douglas B Rusch
- Informatics Group, J. Craig Venter Institute Rockville, MD, USA
| | | | - David M Ward
- Department of Land Resources and Environmental Science, Montana State University Bozeman, MT, USA
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25
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Lassalle F, Muller D, Nesme X. Ecological speciation in bacteria: reverse ecology approaches reveal the adaptive part of bacterial cladogenesis. Res Microbiol 2015; 166:729-41. [DOI: 10.1016/j.resmic.2015.06.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 06/28/2015] [Accepted: 06/30/2015] [Indexed: 11/30/2022]
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26
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Kin discrimination between sympatric Bacillus subtilis isolates. Proc Natl Acad Sci U S A 2015; 112:14042-7. [PMID: 26438858 DOI: 10.1073/pnas.1512671112] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Kin discrimination, broadly defined as differential treatment of conspecifics according to their relatedness, could help biological systems direct cooperative behavior toward their relatives. Here we investigated the ability of the soil bacterium Bacillus subtilis to discriminate kin from nonkin in the context of swarming, a cooperative multicellular behavior. We tested a collection of sympatric conspecifics from soil in pairwise combinations and found that despite their history of coexistence, the vast majority formed distinct boundaries when the swarms met. Some swarms did merge, and most interestingly, this behavior was only seen in the most highly related strain pairs. Overall the swarm interaction phenotype strongly correlated with phylogenetic relatedness, indicative of kin discrimination. Using a subset of strains, we examined cocolonization patterns on plant roots. Pairs of kin strains were able to cocolonize roots and formed a mixed-strain biofilm. In contrast, inoculating roots with pairs of nonkin strains resulted in biofilms consisting primarily of one strain, suggestive of an antagonistic interaction among nonkin strains. This study firmly establishes kin discrimination in a bacterial multicellular setting and suggests its potential effect on ecological interactions.
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Kumar N, Lad G, Giuntini E, Kaye ME, Udomwong P, Shamsani NJ, Young JPW, Bailly X. Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum. Open Biol 2015; 5:140133. [PMID: 25589577 PMCID: PMC4313370 DOI: 10.1098/rsob.140133] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Biological species may remain distinct because of genetic isolation or ecological adaptation, but these two aspects do not always coincide. To establish the nature of the species boundary within a local bacterial population, we characterized a sympatric population of the bacterium Rhizobium leguminosarum by genomic sequencing of 72 isolates. Although all strains have 16S rRNA typical of R. leguminosarum, they fall into five genospecies by the criterion of average nucleotide identity (ANI). Many genes, on plasmids as well as the chromosome, support this division: recombination of core genes has been largely within genospecies. Nevertheless, variation in ecological properties, including symbiotic host range and carbon-source utilization, cuts across these genospecies, so that none of these phenotypes is diagnostic of genospecies. This phenotypic variation is conferred by mobile genes. The genospecies meet the Mayr criteria for biological species in respect of their core genes, but do not correspond to coherent ecological groups, so periodic selection may not be effective in purging variation within them. The population structure is incompatible with traditional ‘polyphasic taxonomy′ that requires bacterial species to have both phylogenetic coherence and distinctive phenotypes. More generally, genomics has revealed that many bacterial species share adaptive modules by horizontal gene transfer, and we envisage a more consistent taxonomic framework that explicitly recognizes this. Significant phenotypes should be recognized as ‘biovars' within species that are defined by core gene phylogeny.
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Affiliation(s)
- Nitin Kumar
- Department of Biology, University of York, York YO10 5DD, UK
| | - Ganesh Lad
- Department of Biology, University of York, York YO10 5DD, UK
| | - Elisa Giuntini
- Department of Biology, University of York, York YO10 5DD, UK
| | - Maria E Kaye
- Department of Biology, University of York, York YO10 5DD, UK
| | | | | | - J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK
| | - Xavier Bailly
- Department of Biology, University of York, York YO10 5DD, UK
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Becraft ED, Wood JM, Rusch DB, Kühl M, Jensen SI, Bryant DA, Roberts DW, Cohan FM, Ward DM. The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park. Front Microbiol 2015; 6:590. [PMID: 26157420 PMCID: PMC4475828 DOI: 10.3389/fmicb.2015.00590] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/29/2015] [Indexed: 01/18/2023] Open
Abstract
Based on the Stable Ecotype Model, evolution leads to the divergence of ecologically distinct populations (e.g., with different niches and/or behaviors) of ecologically interchangeable membership. In this study, pyrosequencing was used to provide deep sequence coverage of Synechococcus psaA genes and transcripts over a large number of habitat types in the Mushroom Spring microbial mat. Putative ecological species [putative ecotypes (PEs)], which were predicted by an evolutionary simulation based on the Stable Ecotype Model (Ecotype Simulation), exhibited distinct distributions relative to temperature-defined positions in the effluent channel and vertical position in the upper 1 mm-thick mat layer. Importantly, in most cases variants predicted to belong to the same PE formed unique clusters relative to temperature and depth in the mat in canonical correspondence analysis, supporting the hypothesis that while the PEs are ecologically distinct, the members of each ecotype are ecologically homogeneous. PEs responded differently to experimental perturbations of temperature and light, but the genetic variation within each PE was maintained as the relative abundances of PEs changed, further indicating that each population responded as a set of ecologically interchangeable individuals. Compared to PEs that predominate deeper within the mat photic zone, the timing of transcript abundances for selected genes differed for PEs that predominate in microenvironments closer to upper surface of the mat with spatiotemporal differences in light and O2 concentration. All of these findings are consistent with the hypotheses that Synechococcus species in hot spring mats are sets of ecologically interchangeable individuals that are differently adapted, that these adaptations control their distributions, and that the resulting distributions constrain the activities of the species in space and time.
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Affiliation(s)
- Eric D. Becraft
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MTUSA
- Single Cell Genomics Center, Bigelow Laboratory for Ocean Sciences, East Boothbay, MEUSA
| | - Jason M. Wood
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MTUSA
| | | | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, HelsingørDenmark
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Ultimo, NSWAustralia
| | - Sheila I. Jensen
- Marine Biological Section, Department of Biology, University of Copenhagen, HelsingørDenmark
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, HellerupDenmark
| | - Donald A. Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PAUSA
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MTUSA
| | | | | | - David M. Ward
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MTUSA
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29
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Oslizlo A, Stefanic P, Vatovec S, Beigot Glaser S, Rupnik M, Mandic-Mulec I. Exploring ComQXPA quorum-sensing diversity and biocontrol potential of Bacillus spp. isolates from tomato rhizoplane. Microb Biotechnol 2015; 8:527-40. [PMID: 25757097 PMCID: PMC4408185 DOI: 10.1111/1751-7915.12258] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 11/20/2014] [Accepted: 12/03/2014] [Indexed: 01/06/2023] Open
Abstract
Bacillus subtilis is a widespread and diverse bacterium t exhibits a remarkable intraspecific diversity of the ComQXPA quorum-sensing (QS) system. This manifests in the existence of distinct communication groups (pherotypes) that can efficiently communicate within a group, but not between groups. Similar QS diversity was also found in other bacterial species, and its ecological and evolutionary meaning is still being explored. Here we further address the ComQXPA QS diversity among isolates from the tomato rhizoplane, a natural habitat of B. subtilis, where these bacteria likely exist in their vegetative form. Because this QS system regulates production of anti-pathogenic and biofilm-inducing substances such as surfactins, knowledge on cell-cell communication of this bacterium within rhizoplane is also important from the biocontrol perspective. We confirm the presence of pherotype diversity within B. subtilis strains isolated from a rhizoplane of a single plant. We also show that B. subtilis rhizoplane isolates show a remarkable diversity of surfactin production and potential plant growth promoting traits. Finally, we discover that effects of surfactin deletion on biofilm formation can be strain specific and unexpected in the light of current knowledge on its role it this process.
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Affiliation(s)
- A Oslizlo
- Department of Food Science and Technology, Biotechnical Faculty, University of LjubljanaLjubljana, Slovenia
| | - P Stefanic
- Department of Food Science and Technology, Biotechnical Faculty, University of LjubljanaLjubljana, Slovenia
| | - S Vatovec
- Department of Food Science and Technology, Biotechnical Faculty, University of LjubljanaLjubljana, Slovenia
| | - S Beigot Glaser
- National Laboratory for Health, Environment and FoodMaribor, Slovenia
| | - M Rupnik
- National Laboratory for Health, Environment and FoodMaribor, Slovenia
- Faculty of Medicine, University of MariborMaribor, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of ProteinsLjubljana, Slovenia
| | - I Mandic-Mulec
- Department of Food Science and Technology, Biotechnical Faculty, University of LjubljanaLjubljana, Slovenia
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Huang CL, Pu PH, Huang HJ, Sung HM, Liaw HJ, Chen YM, Chen CM, Huang MB, Osada N, Gojobori T, Pai TW, Chen YT, Hwang CC, Chiang TY. Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts. BMC Genomics 2015; 16:188. [PMID: 25879893 PMCID: PMC4372319 DOI: 10.1186/s12864-015-1369-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 02/20/2015] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Comparative genomics provides insights into the diversification of bacterial species. Bacterial speciation usually takes place with lasting homologous recombination, which not only acts as a cohering force between diverging lineages but brings advantageous alleles favored by natural selection, and results in ecologically distinct species, e.g., frequent host shift in Xanthomonas pathogenic to various plants. RESULTS Using whole-genome sequences, we examined the genetic divergence in Xanthomonas campestris that infected Brassicaceae, and X. citri, pathogenic to a wider host range. Genetic differentiation between two incipient races of X. citri pv. mangiferaeindicae was attributable to a DNA fragment introduced by phages. In contrast to most portions of the genome that had nearly equivalent levels of genetic divergence between subspecies as a result of the accumulation of point mutations, 10% of the core genome involving with homologous recombination contributed to the diversification in Xanthomonas, as revealed by the correlation between homologous recombination and genomic divergence. Interestingly, 179 genes were under positive selection; 98 (54.7%) of these genes were involved in homologous recombination, indicating that foreign genetic fragments may have caused the adaptive diversification, especially in lineages with nutritional transitions. Homologous recombination may have provided genetic materials for the natural selection, and host shifts likely triggered ecological adaptation in Xanthomonas. To a certain extent, we observed positive selection nevertheless contributed to ecological divergence beyond host shifting. CONCLUSION Altogether, mediated with lasting gene flow, species formation in Xanthomonas was likely governed by natural selection that played a key role in helping the deviating populations to explore novel niches (hosts) or respond to environmental cues, subsequently triggering species diversification.
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Affiliation(s)
- Chao-Li Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Pei-Hua Pu
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Hao-Jen Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Huang-Mo Sung
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Hung-Jiun Liaw
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Yi-Min Chen
- Institute of Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Chien-Ming Chen
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, 202, Taiwan.
| | - Ming-Ban Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Naoki Osada
- National Institute of Genetics, Mishima, Shizuoka, 411-8540, Yata, Japan.
| | - Takashi Gojobori
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
- National Institute of Genetics, Mishima, Shizuoka, 411-8540, Yata, Japan.
- Computational Bioscience Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia.
| | - Tun-Wen Pai
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, 202, Taiwan.
| | - Yu-Tin Chen
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Chi-Chuan Hwang
- Department of Engineering Science and Supercomputing Research Center, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Tzen-Yuh Chiang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
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