PeerJ Preprints: Microbiologyhttps://peerj.com/preprints/index.atom?journal=peerj&subject=2000Microbiology articles published in PeerJ PreprintsIsolation and characterization of psychrotrophic proteolytic bacteria from landfill site under temperate climatic conditions of Kashmir Himalayahttps://peerj.com/preprints/273912019-12-212019-12-21Basharat HamidArshid JehangirZahoor Ahmad BabaMuneer Ahmad WaniImran Khan
The temperate climatic regions face the problem of waste accumulation due to lower environmental temperatures. However, these regions harbor cold active microbes viz. psychrotrophic proteolytic bacteria that play an important role in the degradation of protenaceous materials of the waste stream. Hence in the present study psychrotrophic proteolytic bacteria were isolated from waste samples collected from landfill site by using random sampling method under environmental temperature of 10oC. By using serial dilution and spread plate technique a total of 8 morphologically different psychrotrophic proteolytic bacteria were isolated on skim milk agar media at pH of 7.0 and temperature of 10°C after 48hours. Under in-vitro conditions all the isolates produced significant quantities of protease over the control and diameters of hydrolysis zones ranged between 2 to 18 mm at temperature range of 5 to 20oC and after 72 hours. The corresponding quantitative protease activities of the isolates was significant that ranged between 0.5 to 2.25 U/ml and the isolate PB2 was most efficient with highest protease activity of 2.25U/ml at 20oC. Based on 16SrRNA analysis the isolate was identified as Pseudomonas florescence with 96% similarity. It was concluded that the isolates can grow in wide ranges of temperature and could be used for enhanced decomposition of organic wastes during lower temperature conditions in cold regions. Further the isolates could have industrial applications due to the production of cold active proteases that would help economic benefits through energy conservation.
The temperate climatic regions face the problem of waste accumulation due to lower environmental temperatures. However, these regions harbor cold active microbes viz. psychrotrophic proteolytic bacteria that play an important role in the degradation of protenaceous materials of the waste stream. Hence in the present study psychrotrophic proteolytic bacteria were isolated from waste samples collected from landfill site by using random sampling method under environmental temperature of 10oC. By using serial dilution and spread plate technique a total of 8 morphologically different psychrotrophic proteolytic bacteria were isolated on skim milk agar media at pH of 7.0 and temperature of 10°C after 48hours. Under in-vitro conditions all the isolates produced significant quantities of protease over the control and diameters of hydrolysis zones ranged between 2 to 18 mm at temperature range of 5 to 20oC and after 72 hours. The corresponding quantitative protease activities of the isolates was significant that ranged between 0.5 to 2.25 U/ml and the isolate PB2 was most efficient with highest protease activity of 2.25U/ml at 20oC. Based on 16SrRNA analysis the isolate was identified as Pseudomonas florescence with 96% similarity. It was concluded that the isolates can grow in wide ranges of temperature and could be used for enhanced decomposition of organic wastes during lower temperature conditions in cold regions. Further the isolates could have industrial applications due to the production of cold active proteases that would help economic benefits through energy conservation.An introduction to phylosymbiosishttps://peerj.com/preprints/278792019-12-112019-12-11Shen Jean LimSeth R Bordenstein
Phylosymbiosis was recently formulated to support a hypothesis-driven framework for the characterization of a new, cross-system trend in host-associated microbiomes. Defining phylosymbiosis as “microbial community relationships that recapitulate the phylogeny of their host”, we review the relevant literature and data in the last decade, emphasizing frequently used methods and regular patterns observed in analyses. Quantitative support for phylosymbiosis is provided by statistical methods evaluating higher microbiome variation between host species than within host species, topological similarities between the host phylogeny and microbiome dendrogram, and a positive association between host genetic relationships and microbiome beta diversity. Significant degrees of phylosymbiosis are prevalent, but not universal, in microbiomes of plants and animals from terrestrial and aquatic habitats. Consistent with natural selection shaping phylosymbiosis, microbiome transplant experiments demonstrate reduced host performance and/or fitness upon host-microbiome mismatches. Hybridization can also disrupt phylosymbiotic microbiomes and cause hybrid pathologies. The pervasiveness of phylosymbiosis carries several important implications for advancing knowledge of eco-evolutionary processes that impact host-microbiome interactions and future applications of precision microbiology. Important future steps will be to examine phylosymbiosis beyond bacterial communities, apply evolutionary modeling for an increasingly sophisticated understanding of phylosymbiosis, and unravel the host and microbial mechanisms that contribute to the pattern. This review serves as a gateway to experimental, conceptual, and quantitative themes of phylosymbiosis and outlines opportunities ripe for investigations from a diversity of disciplines.
Phylosymbiosis was recently formulated to support a hypothesis-driven framework for the characterization of a new, cross-system trend in host-associated microbiomes. Defining phylosymbiosis as “microbial community relationships that recapitulate the phylogeny of their host”, we review the relevant literature and data in the last decade, emphasizing frequently used methods and regular patterns observed in analyses. Quantitative support for phylosymbiosis is provided by statistical methods evaluating higher microbiome variation between host species than within host species, topological similarities between the host phylogeny and microbiome dendrogram, and a positive association between host genetic relationships and microbiome beta diversity. Significant degrees of phylosymbiosis are prevalent, but not universal, in microbiomes of plants and animals from terrestrial and aquatic habitats. Consistent with natural selection shaping phylosymbiosis, microbiome transplant experiments demonstrate reduced host performance and/or fitness upon host-microbiome mismatches. Hybridization can also disrupt phylosymbiotic microbiomes and cause hybrid pathologies. The pervasiveness of phylosymbiosis carries several important implications for advancing knowledge of eco-evolutionary processes that impact host-microbiome interactions and future applications of precision microbiology. Important future steps will be to examine phylosymbiosis beyond bacterial communities, apply evolutionary modeling for an increasingly sophisticated understanding of phylosymbiosis, and unravel the host and microbial mechanisms that contribute to the pattern. This review serves as a gateway to experimental, conceptual, and quantitative themes of phylosymbiosis and outlines opportunities ripe for investigations from a diversity of disciplines.A lipid-invasion model for Alzheimer’s Diseasehttps://peerj.com/preprints/278112019-11-182019-11-18Jonathan D Rudge
This paper describes a potential new explanation for Alzheimer’s disease (AD), referred to here as the lipid-invasion model. It proposes that AD is primarily caused by the influx of lipids following the breakdown of the blood brain barrier (BBB). The model argues that a principal role of the BBB is to protect the brain from external lipid access. When the BBB is damaged, it allows a mass influx of (mainly albumin-bound) free fatty acids (FFAs) and lipid-rich lipoproteins to the brain, which in turn causes neurodegeneration, amyloidosis, tau tangles and other AD characteristics. The model also argues that, whilst β-amyloid causes neurodegeneration, as is widely argued, its principal role in the disease lies in damaging the BBB. It is the external lipids, entering as a consequence, that are the primary drivers of neurodegeneration in AD., especially FFAs, which induce oxidative stress, stimulate microglia-driven neuroinflammation, and inhibit neurogenesis. Simultaneously, the larger, more lipid-laden lipoproteins, characteristic of the external plasma but not the CNS, cause endosomal-lysosomal abnormalities, amyloidosis and the formation of tau tangles, all characteristic of AD. In most cases (certainly in late-onset, noninherited forms of the disease) amyloidosis and tau tangle formation are consequences of this external lipid invasion, and in many ways more symptomatic of the disease than causative. In support of this, it is argued that the pattern of damage caused by the influx of FFAs into the brain is likely to resemble the neurodegeneration seen in alcohol-related brain damage (ARBD), a disease that shows many similarities to AD, including the areas of the brain it affects. The fact that neurodegeneration is far more pronounced in AD than in ARBD, and characterised by other features, such as amyloidosis and tau tangles, most likely results from the greater heterogeneity of the lipid assault in AD compared with ethanol alone. The lipid-invasion model, described here, arguably provides the first cohesive, multi-factorial explanation of AD that accounts for all currently known major risk factors, and explains all AD-associated pathologies, including those, such as endosomal-lysosomal dysfunction and excessive lipid droplet formation, that are not well-accounted for in other explanation of this disease.
This paper describes a potential new explanation for Alzheimer’s disease (AD), referred to here as the lipid-invasion model. It proposes that AD is primarily caused by the influx of lipids following the breakdown of the blood brain barrier (BBB). The model argues that a principal role of the BBB is to protect the brain from external lipid access. When the BBB is damaged, it allows a mass influx of (mainly albumin-bound) free fatty acids (FFAs) and lipid-rich lipoproteins to the brain, which in turn causes neurodegeneration, amyloidosis, tau tangles and other AD characteristics. The model also argues that, whilst β-amyloid causes neurodegeneration, as is widely argued, its principal role in the disease lies in damaging the BBB. It is the external lipids, entering as a consequence, that are the primary drivers of neurodegeneration in AD., especially FFAs, which induce oxidative stress, stimulate microglia-driven neuroinflammation, and inhibit neurogenesis. Simultaneously, the larger, more lipid-laden lipoproteins, characteristic of the external plasma but not the CNS, cause endosomal-lysosomal abnormalities, amyloidosis and the formation of tau tangles, all characteristic of AD. In most cases (certainly in late-onset, noninherited forms of the disease) amyloidosis and tau tangle formation are consequences of this external lipid invasion, and in many ways more symptomatic of the disease than causative. In support of this, it is argued that the pattern of damage caused by the influx of FFAs into the brain is likely to resemble the neurodegeneration seen in alcohol-related brain damage (ARBD), a disease that shows many similarities to AD, including the areas of the brain it affects. The fact that neurodegeneration is far more pronounced in AD than in ARBD, and characterised by other features, such as amyloidosis and tau tangles, most likely results from the greater heterogeneity of the lipid assault in AD compared with ethanol alone. The lipid-invasion model, described here, arguably provides the first cohesive, multi-factorial explanation of AD that accounts for all currently known major risk factors, and explains all AD-associated pathologies, including those, such as endosomal-lysosomal dysfunction and excessive lipid droplet formation, that are not well-accounted for in other explanation of this disease.Bacillus induced to biosynthesize VOCs & nitriles may benefit agriculture.https://peerj.com/preprints/26112019-09-302019-09-30Guenevere PerryDiane Perry
The scope of the project was to identify the possible agricultural applications for bacteria induced to synthesize nitriles and VOCs. The study was randomized. Cucurbit seeds and Bacillus licheniformis were selected as the plant and microbial models for two trial studies. In trial 1, 90 cucumber seeds were cultured with B.licheniformis induced to synthesize VOCs (including ethanol, 3-methyl-1-butanol, pentanol), esters (ethyl acetate), and acetonitriles. After 2 weeks the induced bacteria increased seed germination by 68% compared to control samples. Several seedlings were transferred to a small garden, infested with soil nematodes. Roots of control and induced samples appeared affected. Control samples appeared stunted in growth with decreased productivity, but cucumber plants initially planted with induced bacteria were noticeably larger in size with good productivity. Induced Bacillus increased the number of blossoms and cucumber per plant by 125% compared to control samples. Induced Bacillus did not increase solubility of nitrogen, phosphorous, or potassium in the soil, but appeared to increase plant health and defenses against pathogenic infections. Though the study findings are preliminary, soil microbes induced to synthesize VOCs and nitriles may improve plant health and productivity in cucurbit plants.
The scope of the project was to identify the possible agricultural applications for bacteria induced to synthesize nitriles and VOCs. The study was randomized. Cucurbit seeds and Bacillus licheniformis were selected as the plant and microbial models for two trial studies. In trial 1, 90 cucumber seeds were cultured with B.licheniformis induced to synthesize VOCs (including ethanol, 3-methyl-1-butanol, pentanol), esters (ethyl acetate), and acetonitriles. After 2 weeks the induced bacteria increased seed germination by 68% compared to control samples. Several seedlings were transferred to a small garden, infested with soil nematodes. Roots of control and induced samples appeared affected. Control samples appeared stunted in growth with decreased productivity, but cucumber plants initially planted with induced bacteria were noticeably larger in size with good productivity. Induced Bacillus increased the number of blossoms and cucumber per plant by 125% compared to control samples. Induced Bacillus did not increase solubility of nitrogen, phosphorous, or potassium in the soil, but appeared to increase plant health and defenses against pathogenic infections. Though the study findings are preliminary, soil microbes induced to synthesize VOCs and nitriles may improve plant health and productivity in cucurbit plants.Ethylene induced soil delays ripening in organic bananas.https://peerj.com/preprints/5062019-09-252019-09-25Guenevere PerryDiane Williams
The scope of the project was to develop a method to induce soil bacteria to biosynthesize compounds that retard the effects of ethylene induced ripening in climacteric fruits. The study was randomized. Organic bananas selected for the study were visibly inspected to ensure the fruit was unripen with no visible signs of bruising, spotting, or infection from a local distributor. Four trials were conducted from June 5th - August 5th 2014 with 3 replicates (3-4 bananas per experimental unit) in 4 trial studies for 3 days at room temperature. A mixed culture of plant growth promoting rhizobacteria (PGPR) were collected from soil surrounding the roots of young fruit bearing trees. Microbes were mixed with no-carbon source media, and cultured with an ethylene for 3 d at room temperature in a closed container. Induced soil was used to delay ripening. Microbes induced with media and ethylene delayed ripening 100% of the time in all experimental units compared to control samples, while microbes cultured with media (no ethylene) delayed ripening less than 10% of the time compared to the control. These cells also appeared to increase the incidence of fungal infection in the fruit. The findings suggest induced microbes may convert ethylene into ethanol then acetaldehyde. The two compounds may form an acetaldehyde/ethanol vapor that delays ripening, and a secondary nitrile compound that inhibits fungal growth.
The scope of the project was to develop a method to induce soil bacteria to biosynthesize compounds that retard the effects of ethylene induced ripening in climacteric fruits. Thestudy was randomized. Organic bananas selected for the study were visibly inspected to ensure the fruit was unripen with no visible signs of bruising, spotting, or infection from a local distributor. Four trials were conducted from June 5th - August 5th 2014 with 3 replicates (3-4 bananas per experimental unit) in 4 trial studies for 3 days at room temperature. A mixed culture of plant growth promoting rhizobacteria (PGPR) were collected from soil surrounding the roots of young fruit bearing trees. Microbes were mixed with no-carbon source media, and cultured with an ethylene for 3 d at room temperature in a closed container. Induced soil was used to delay ripening. Microbes induced with media and ethylene delayed ripening 100% of the time in all experimental units compared to control samples, while microbes cultured with media (no ethylene) delayed ripening less than 10% of the time compared to the control. These cells also appeared to increase the incidence of fungal infection in the fruit. The findings suggest induced microbes may convert ethylene into ethanol then acetaldehyde. The two compounds may form an acetaldehyde/ethanol vapor that delays ripening, and a secondary nitrile compound that inhibits fungal growth.Antimicrobial resistance and genetic relationship among enterococci from siblings and non-siblings Heliconius erato phyllis caterpillarshttps://peerj.com/preprints/279762019-09-232019-09-23Rosana HuffRebeca Inhoque PereiraCaroline PissettiAldo Mellender de AraújoPedro Alves d’AzevedoJeverson FrazzonAna Paula Guedes Frazzon
Background: Studies evaluating bacterial in insects could provide information about host-microorganism-environment interactions. The gut community is recognized to have a profound effect on various physiological functions of the insects. Enterococcus is part of the gut community in humans andanimals, as well as in the guts of insects. The presence and antimicrobialresistance profileof enterococci are well studied in different animals; however, data in Heliconius erato phyllis (Lepidoptera; Nymphalidae), do not yet exist. Therefore, the aims of this study were to evaluate species distribution, antimicrobial resistance profile, virulence genes and genetic relationship amongenterococci isolated from fecal samples of siblings and non-siblings H. erato phyllis caterpillars collected from different places in South Brazil.
Methods: Three H. erato phyllis females were captured (two from a forest fragment and one from an urban area), and kept individually in open-air insectaries. Eggs were collected and caterpillars (siblings and non-siblings) were fed daily with Passiflora suberosa leaves. Fecal samples (n=12) were collected from fifth instar caterpillars, inoculated in selective medium and fifteen colonies were randomly selected from each sample. Enterococci were identified by PCR and MALDI-TOF, submitted to antimicrobial susceptibility tests by disk diffusion method, and screened for resistance and virulence genes by PCR. The genetic relationships among the strains were determined using pulsed-field gel electrophoresis (PFGE).
Results: A total of 178 enterococci were identified as: Enterococcus casseliflavus (74.15%; n=132),E. mundtii (21.34%; n=38), E. faecalis (1.12%; n=2) and Enterococcus sp. (3.37%; n=6). High rates of resistance to rifampicin (56%) and erythromycin (31%) were observed. One hundred and twenty (67.41%) out of the 178 isolates showed resistance to at least one compound and 6 (3.37%) were multidrug-resistant.None of the erythromycin-resistant strains was positive to erm(B) and msrC genes. The virulence genes esp, ace and gelE were observed in 35%, 7% and 1% of the strains, respectively. PFGE separated the enterococci into 22 patterns, being four patterns composed by strains from sibling caterpillars.
Conclusion: Enterococcus casseliflavus was the dominant species in fecal samples of fifth instar caterpillars. Resistant enterococci strains could be related to environmental pollution or linked to environmental resistome. The PFGE analysis showed related genetic relationship among some strains, suggesting that the enterococci isolated from fecal samples of fifth instar sibling caterpillars might have come from common sources, by diet (herbivory) and/or via vertical transmission (through egg surface). Further studies will be conducted to better understand the role of Enterococcus on the microbial gastrointestinal tract community of these insects, and the mechanisms involved in acquisition and maintenance of these bacteria.
Background: Studies evaluating bacterial in insects could provide information about host-microorganism-environment interactions. The gut community is recognized to have a profound effect on various physiological functions of the insects. Enterococcus is part of the gut community in humans andanimals, as well as in the guts of insects. The presence and antimicrobialresistance profileof enterococci are well studied in different animals; however, data in Heliconius erato phyllis (Lepidoptera; Nymphalidae), do not yet exist. Therefore, the aims of this study were to evaluate species distribution, antimicrobial resistance profile, virulence genes and genetic relationship amongenterococci isolated from fecal samples of siblings and non-siblings H. erato phyllis caterpillars collected from different places in South Brazil.Methods: Three H. erato phyllis females were captured (two from a forest fragment and one from an urban area), and kept individually in open-air insectaries. Eggs were collected and caterpillars (siblings and non-siblings) were fed daily with Passiflora suberosa leaves. Fecal samples (n=12) were collected from fifth instar caterpillars, inoculated in selective medium and fifteen colonies were randomly selected from each sample. Enterococci were identified by PCR and MALDI-TOF, submittedto antimicrobial susceptibility tests by disk diffusion method, and screened for resistance and virulencegenes by PCR. The genetic relationships among the strains were determined using pulsed-field gel electrophoresis (PFGE).Results: A total of 178 enterococci were identified as: Enterococcus casseliflavus (74.15%; n=132),E. mundtii (21.34%; n=38), E. faecalis (1.12%; n=2) and Enterococcus sp. (3.37%; n=6). High rates of resistance to rifampicin (56%) and erythromycin (31%) were observed. One hundred and twenty (67.41%) out of the 178 isolates showed resistance to at least one compound and 6 (3.37%) were multidrug-resistant.None of the erythromycin-resistant strains was positive to erm(B) and msrC genes. The virulence genes esp, ace and gelE were observed in 35%, 7% and 1% of the strains, respectively. PFGE separated the enterococci into 22 patterns, being four patterns composed by strains from sibling caterpillars.Conclusion: Enterococcus casseliflavus was the dominant species in fecal samples of fifth instarcaterpillars. Resistant enterococci strains could be related to environmental pollution or linked to environmental resistome. The PFGE analysis showed related genetic relationship among some strains, suggesting that the enterococci isolated from fecal samples of fifth instar sibling caterpillars might have come from common sources, by diet (herbivory) and/or via vertical transmission (through egg surface). Further studies will be conducted to better understand the role of Enterococcus on the microbial gastrointestinal tract community of these insects, and the mechanisms involved in acquisition and maintenance of these bacteria.Rhodococcus sp. may convert ethylene to acetaldehyde to slow ripening in climacteric fruit.https://peerj.com/preprints/33982019-09-172019-09-17Guenevere Perry
Pre-Print Update. Previous studies suggested Rhodococcus rhodochrous and Bacillus licheniformis cells converted ethylene to a nitrile compound to delay the effects of ripening, (Perry, G. Nov. 9, 2017). However, there may be an alternative compound that plays a more significant role in induced Rhodococcus and Bacillus ability to delay ripening. It has been known for years that Rhodococcus can convert the alkyne compound acetylene to acetaldehyde and potentially ethanol as a secondary product (DeBont, 1980).
This pre-print revisit re-examines the prior data to determine if the tri-phasic system previously discussed in 2017, induced bacteria to convert ethylene and/or propylene into acetaldehyde (a primary product), ethanol (a secondary product), and acetonitrile (a product of ethanol and a subsequent ammoxidation reaction). The acetaldehyde may delay the effects of ripening and inhibit fungal growth, while the nitrile by products enhance early plant development including germination and root elongation. Experimental results suggest an inducible monooxygenase or dioxygenase like enzyme is required to facilitate this process.
Pre-Print Update. Previous studies suggested Rhodococcus rhodochrous and Bacillus licheniformis cells converted ethylene to a nitrile compound to delay the effects of ripening, (Perry, G. Nov. 9, 2017). However, there may be an alternative compound that plays a more significant role in induced Rhodococcus and Bacillus ability to delay ripening. It has been known for years that Rhodococcus can convert the alkyne compound acetylene to acetaldehyde and potentially ethanol as a secondary product (DeBont, 1980).This pre-print revisit re-examines the prior data to determine if the tri-phasic system previously discussed in 2017, induced bacteria to convert ethylene and/or propylene into acetaldehyde (a primary product), ethanol (a secondary product), and acetonitrile (a product of ethanol and a subsequent ammoxidation reaction). The acetaldehyde may delay the effects of ripening and inhibit fungal growth, while the nitrile by products enhance early plant development including germination and root elongation. Experimental results suggest an inducible monooxygenase or dioxygenase like enzyme is required to facilitate this process.Epiphytic fungi induced pathogen resistance of invasive plant Ipomoea cairica against Colletotrichum gloeosporioideshttps://peerj.com/preprints/279562019-09-112019-09-11Hua XuMinjie ZhuShaoshan LiWeibin RuanCan Xie
Background. Ipomoea cairica (L.) Sweet is a destructive invasive weed in South China but rarely infected with pathogens in nature. Its pathogen resistance mechanism is largely unknown at present. Some non-pathogenic isolates of Fusarium oxysporum and Fusarium fujikuroi are prevalent on many plant species and function as pathogen resistance inducers of host plants. The objective of the present research is to investigate whether the symbiosis between the both fungi and I. cairica is present, and thereby induce pathogen resistance of I. cairica. Methods. Through field investigation, we explored the occurrence rates of F. oxysporum and F. fujikuroi on leaf surfaces of I. cairica plants in natural habitats and compared their abundance between healthy leaves and leaves infected with Colletotrichum gloeosporioides, a natural pathogen. With artificial inoculation, we assessed their pathogencity to I. cairica and study their contribution of pathogen resistance to I. cairica against C. gloeosporioides. Results. We found that F. oxysporum and F. fujikuroi were widely epiphytic on healthy leaf surfaces of I. cairica in sunny non-saline, shady non-saline and sunny saline habitats. Their occurrence rates reached up to 100%. Moreover, we found that the abundance of F. oxysporum and F. fujikuroi on leaves infected with C. gloeosporioides were significantly lower than that of healthy leaves. With artificial inoculation, we empirically confirmed that F. oxysporum and F. fujikuroi were non-pathogenic to I. cairica. It was interesting that colonization by F. fujikuroi, F. oxysporum alone and a mixture of both fungi resulted in a reduction of C. gloeosporioides infection to I. cairica accompanied by lower lesion area to leaf surface area ratio, increased H2O2 concentration and salicylic acid (SA) level relative to the control. However, NPR1 expression, chitinase and β -1,3-glucanase activities as well as stem length and biomass of I. cairica plant only could be significantly improved by F. oxysporum and a mixture of both fungi but not by F. fujikuroi. In addition, as compared to colonization by F. oxysporum and a mixture of both fungi, F. fujikuroi induced significantly higher jasmonic acid (JA) level but significantly lower β -1,3-glucanase activity in leaves of I. cairica plants. Thus, our findings indicated the symbiosis of epiphytic fungi F. fujikuroi and F. oxysporum facilitated the fitness of I. cairica via the induced systemic resistance of host plant against C. gloeosporioides. F. oxysporum played a dominant role in inducing pathogen resistance of I. cairica. Its presence alleviated the antagonism of the JA signaling on SA-dependent β -1,3-glucanase activity and enabled I. cairica plants to maintain relatively higher level of resistance against C. gloeosporioides.
Background. Ipomoea cairica (L.) Sweet is a destructive invasive weed in South China but rarely infected with pathogens in nature. Its pathogen resistance mechanism is largely unknown at present. Some non-pathogenic isolates of Fusarium oxysporum and Fusarium fujikuroi are prevalent on many plant species and function as pathogen resistance inducers of host plants. The objective of the present research is to investigate whether the symbiosis between the both fungi and I. cairica is present, and thereby induce pathogen resistance of I. cairica.Methods. Through field investigation, we explored the occurrence rates of F. oxysporum and F. fujikuroi on leaf surfaces of I. cairica plants in natural habitats and compared their abundance between healthy leaves and leaves infected with Colletotrichum gloeosporioides, a natural pathogen. With artificial inoculation, we assessed their pathogencity to I. cairica and study their contribution of pathogen resistance to I. cairica against C. gloeosporioides.Results. We found that F. oxysporum and F. fujikuroi were widely epiphytic on healthy leaf surfaces of I. cairica in sunny non-saline, shady non-saline and sunny saline habitats. Their occurrence rates reached up to 100%. Moreover, we found that the abundance of F. oxysporum and F. fujikuroi on leaves infected with C. gloeosporioides were significantly lower than that of healthy leaves. With artificial inoculation, we empirically confirmed that F. oxysporum and F. fujikuroi were non-pathogenic to I. cairica. It was interesting that colonization by F. fujikuroi, F. oxysporum alone and a mixture of both fungi resulted in a reduction of C. gloeosporioides infection to I. cairica accompanied by lower lesion area to leaf surface area ratio, increased H2O2 concentration and salicylic acid (SA) level relative to the control. However, NPR1 expression, chitinase and β -1,3-glucanase activities as well as stem length and biomass of I. cairica plant only could be significantly improved by F. oxysporum and a mixture of both fungi but not by F. fujikuroi. In addition, as compared to colonization by F. oxysporum and a mixture of both fungi, F. fujikuroi induced significantly higher jasmonic acid (JA) level but significantly lower β -1,3-glucanase activity in leaves of I. cairica plants. Thus, our findings indicated the symbiosis of epiphytic fungiF. fujikuroi and F. oxysporum facilitated the fitness of I. cairicavia the induced systemic resistance of host plant against C. gloeosporioides. F. oxysporum played a dominant role in inducing pathogen resistance of I. cairica. Its presence alleviated the antagonism of the JA signaling on SA-dependentβ -1,3-glucanase activity and enabled I. cairica plantsto maintain relatively higher level of resistance against C. gloeosporioides.The interplay between movement, dispersal and morphology in Tetrahymena ciliateshttps://peerj.com/preprints/265402019-09-032019-09-03Frank PennekampJean ClobertNicolas Schtickzelle
Understanding how and why individual movement translates into dispersal between populations is a long-term goal in ecology. Movement is broadly defined as “any change in the spatial location of an individual”, whereas dispersal is more narrowly defined as a movement that may lead to gene flow. Because the former may create the condition for the latter, behavioural decisions that lead to dispersal may be detectable in underlying movement behaviour. In addition, dispersing individuals also have specific sets of morphological and behavioural traits that help them coping with the costs of movement and dispersal, and traits that mitigate costs should be under selection and evolve if they have a genetic basis. Here we experimentally study the relationships between movement behaviour, morphology and dispersal across 44 genotypes of the actively dispersing unicellular, aquatic model organism Tetrahymena thermophila. We used two-patch populations to quantify individual movement trajectories, as well as activity, morphology and dispersal rate. First, we studied variation in movement behaviour among and within genotypes (i.e. between dispersers and residents) and tested whether this variation can be explained by morphology. Then, we address how much the dispersal rate is driven by differences in the underlying movement behaviour. Genotypes revealed clear differences in terms of movement speed and linearity. We also detected marked movement differences between resident and dispersing individuals, mediated by the genotype. Movement variation was partly explained by morphological properties such as cell size and shape, with larger cells consistently showing higher movement speed and higher linearity. Genetic differences in activity and diffusion rates were positively related to the observed dispersal and jointly explained 47% of the variation in dispersal rate. Our study shows that a detailed understanding of the interplay between morphology, movement and dispersal may have potential to improve dispersal predictions over broader spatio-temporal scales.
Understanding how and why individual movement translates into dispersal between populations is a long-term goal in ecology. Movement is broadly defined as “any change in the spatial location of an individual”, whereas dispersal is more narrowly defined as a movement that may lead to gene flow. Because the former may create the condition for the latter, behavioural decisions that lead to dispersal may be detectable in underlying movement behaviour. In addition, dispersing individuals also have specific sets of morphological and behavioural traits that help them coping with the costs of movement and dispersal, and traits that mitigate costs should be under selection and evolve if they have a genetic basis. Here we experimentally study the relationships between movement behaviour, morphology and dispersal across 44 genotypes of the actively dispersing unicellular, aquatic model organism Tetrahymena thermophila. We used two-patch populations to quantify individual movement trajectories, as well as activity, morphology and dispersal rate. First, we studied variation in movement behaviour among and within genotypes (i.e. between dispersers and residents) and tested whether this variation can be explained by morphology. Then, we address how much the dispersal rate is driven by differences in the underlying movement behaviour. Genotypes revealed clear differences in terms of movement speed and linearity. We also detected marked movement differences between resident and dispersing individuals, mediated by the genotype. Movement variation was partly explained by morphological properties such as cell size and shape, with larger cells consistently showing higher movement speed and higher linearity. Genetic differences in activity and diffusion rates were positively related to the observed dispersal and jointly explained 47% of the variation in dispersal rate. Our study shows that a detailed understanding of the interplay between morphology, movement and dispersal may have potential to improve dispersal predictions over broader spatio-temporal scales.Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termiteshttps://peerj.com/preprints/279292019-08-302019-08-30Vincent HervéPengfei LiuCarsten DietrichDavid Sillam-DussèsPetr StiblikJan ŠobotníkAndreas Brune
“Higher” termites have been able to colonize all tropical and subtropical regions because of their ability to digest lignocellulose with the aid of their prokaryotic gut microbiota. Over the last decade, numerous studies based on 16S rRNA gene amplicon libraries have largely described both the taxonomy and structure of the prokaryotic communities associated with termite guts. Host diet and microenvironmental conditions have emerged as the main factors structuring the microbial assemblages in the different gut compartments. Additionally, these molecular inventories have revealed the existence of termite-specific clusters that indicate coevolutionary processes in numerous prokaryotic lineages. However, for lack of representative isolates, the functional role of most lineages remains unclear. We reconstructed 589 metagenome-assembled genomes (MAGs) from the different gut compartments of eight higher termite species that encompass 17 prokaryotic phyla. By iteratively building genome trees for each clade, we significantly improved the initial automated assignment, frequently up to the genus level. We recovered MAGs from most of the termite-specific clusters in the radiation of, e.g., Planctomycetes, Fibrobacteres, Bacteroidetes, Euryarchaeota, Bathyarchaeota, Spirochaetes, Saccharibacteria, and Firmicutes, which to date contained only few or no representative genomes. Moreover, the MAGs included abundant members of the termite gut microbiota. This dataset represents the largest genomic resource for arthropod-associated microorganisms available to date and contributes substantially to populating the tree of life. More importantly, it provides a backbone for studying the metabolic potential of the termite gut microbiota, including the key members involved in carbon and nitrogen biogeochemical cycles, and important clues that may help cultivating representatives of these understudied clades.
“Higher” termites have been able to colonize all tropical and subtropical regions because of their ability to digest lignocellulose with the aid of their prokaryotic gut microbiota. Over the last decade, numerous studies based on 16S rRNA gene amplicon libraries have largely described both the taxonomy and structure of the prokaryotic communities associated with termite guts. Host diet and microenvironmental conditions have emerged as the main factors structuring the microbial assemblages in the different gut compartments. Additionally, these molecular inventories have revealed the existence of termite-specific clusters that indicate coevolutionary processes in numerous prokaryotic lineages. However, for lack of representative isolates, the functional role of most lineages remains unclear. We reconstructed 589 metagenome-assembled genomes (MAGs) from the different gut compartments of eight higher termite species that encompass 17 prokaryotic phyla. By iteratively building genome trees for each clade, we significantly improved the initial automated assignment, frequently up to the genus level. We recovered MAGs from most of the termite-specific clusters in the radiation of, e.g., Planctomycetes, Fibrobacteres, Bacteroidetes, Euryarchaeota, Bathyarchaeota, Spirochaetes, Saccharibacteria, and Firmicutes, which to date contained only few or no representative genomes. Moreover, the MAGs included abundant members of the termite gut microbiota. This dataset represents the largest genomic resource for arthropod-associated microorganisms available to date and contributes substantially to populating the tree of life. More importantly, it provides a backbone for studying the metabolic potential of the termite gut microbiota, including the key members involved in carbon and nitrogen biogeochemical cycles, and important clues that may help cultivating representatives of these understudied clades.