Nutrient deficiency and an algicidal bacterium improved the lipid profiles of a novel promising oleaginous dinoflagellate, < em > Prorocentrum donghaiense, < /em > for biodiesel production
This study demonstrates the high potential of P. donghaiense, a dominant bloom-causing dinoflagellate, for lipid production. Compared with previously studied oleaginous microalgae, P. donghaiense exhibit greater potential for practical application due to its higher biomass and lipid contents. Nutrient deficiency and the algicidal bacterium Paracoccus sp. Y42 could improve the suitability of the lipid profile of P. donghaiense for biodiesel production. Furthermore, Paracoccus sp. Y42 effectively lyse algal cells, which facilitates the downstream oil extraction process for biodiesel production and results in energy savings t...
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Jiali Gui Shuangshuang Chen Guiying Luo Zixiang Wu Yongxian Fan Luming Yao Hong Xu Source Type: research

Illuminating key microbial players and metabolic processes involved in the remineralization of particulate organic carbon in the ocean's twilight zone by metaproteomics
This study provides insight into the key bacteria and metabolic processes involved in POC remineralization, and niche complementarity and species substitution among bacterial groups are critical for efficient POC remineralization in the twilight zone. IMPORTANCE The Ocean's twilight zone is a critical zone where more than 70% of the sinking particulate organic carbon (POC) are remineralized. Therefore, the twilight zone determines the size of biological carbon storage in the ocean, and regulates the global climate. Prokaryotes are major players that govern remineralization of POC in this region. However, knowledge of micro...
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Ling-Fen Kong Yan-Bin He Zhang-Xian Xie Xing Luo Hao Zhang Sheng-Hui Yi Zhi-Long Lin Shu-Feng Zhang Ke-Qiang Yan Hong-Kai Xu Tao Jin Lin Lin Wei Qin Feng Chen Si-Qi Liu Da-Zhi Wang Source Type: research

Sequence-specific capture of oligonucleotide probes (SCOPE): A simple and rapid microbial rRNA quantification method using molecular weight cut-off membrane
Appl Environ Microbiol. 2021 Jul 28:AEM0116721. doi: 10.1128/AEM.01167-21. Online ahead of print.ABSTRACTA method named sequence-specific capture of oligonucleotide probes (SCOPE) was developed for quantification of microbial rRNA molecules in a multiplex manner. In this method, molecular weight cut-off membrane (MWCOM) was used for the separation of fluorescent-labeled oligonucleotide probes hybridized with rRNA from free unhybridized probes. To demonstrate proof-of-concept, probes targeting bacteria or archaea at different taxonomic levels were prepared and were hybridized with rRNAs. The hybridization stringency was con...
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Yasuyuki Takemura Yuji Sekiguchi Kazuaki Syutsubo Hideki Harada Tatsuo Omura Yu-You Li Kengo Kubota Source Type: research

Anti-biofilm potential of < em > Lavandula < /em > preparations against < em > Campylobacter jejuni < /em >
This study highlights the need for efforts directed towards such innovative approaches and alternative strategies against biofilm formation and maintenance by developing new naturally derived agents with anti-biofilm activities.PMID:34319799 | DOI:10.1128/AEM.01099-21 (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Dina Rami ć Franz Bucar Urban Kunej Iztok Dog ša Anja Klan čnik Sonja Smole Mo žina Source Type: research

Outer membrane vesicles derived from < em > Salmonella < /em > Typhimurium can deliver < em > Shigella flexneri < /em > 2a O-polysaccharide antigen to prevent < em > Shigella flexneri < /em > 2a infection in mice
Appl Environ Microbiol. 2021 Jul 28:AEM0096821. doi: 10.1128/AEM.00968-21. Online ahead of print.ABSTRACTShigellosis has become a serious threat to health in many developing countries due to the severe diarrhea it causes. Shigella flexneri 2a (S. flexneri 2a) is the principal species responsible for this endemic disease. Despite multiple attempts to design a vaccine against shigellosis, no effective vaccine has not yet been developed. Lipopolysaccharide (LPS) is both an essential virulence factor and an antigen protective against Shigella, due to its outer domain, termed O-polysaccharide antigen. In the present study, S. f...
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Huizhen Tian Biaoxian Li Tian Xu Haolin Yu Jingxuan Chen Haiyan Yu Shan Li Lingbing Zeng Xiaotian Huang Qiong Liu Source Type: research

The fish pathogen < em > Aliivibrio salmonicida < /em > LFI1238 can degrade and metabolize chitin despite major gene loss in the chitinolytic pathway
In conclusion, our results show that Al. salmonicida LFI1238 can utilize chitin as a nutrient source and that the GH18 chitinase and the two LPMOs are needed for this ability. IMPORTANCE The ability to utilize chitin as a source of nutrients is important for the survival and spread of marine microbial pathogens in the environment. One such pathogen is Aliivibrio (Vibrio) salmonicida, the causative agent of cold water vibriosis. Due to extensive gene decay, many key enzymes in the chitinolytic pathway have been disrupted, putatively rendering this bacterium incapable of chitin degradation and utilization. In the present stu...
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Anna Sk åne Giusi Minniti Jennifer S M Loose Sophanit Mekasha Bastien Bissaro Geir Mathiesen Magnus Ø Arntzen Gustav Vaaje-Kolstad Source Type: research

Nutrient deficiency and an algicidal bacterium improved the lipid profiles of a novel promising oleaginous dinoflagellate, < em > Prorocentrum donghaiense, < /em > for biodiesel production
This study demonstrates the high potential of P. donghaiense, a dominant bloom-causing dinoflagellate, for lipid production. Compared with previously studied oleaginous microalgae, P. donghaiense exhibit greater potential for practical application due to its higher biomass and lipid contents. Nutrient deficiency and the algicidal bacterium Paracoccus sp. Y42 could improve the suitability of the lipid profile of P. donghaiense for biodiesel production. Furthermore, Paracoccus sp. Y42 effectively lyse algal cells, which facilitates the downstream oil extraction process for biodiesel production and results in energy savings t...
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Jiali Gui Shuangshuang Chen Guiying Luo Zixiang Wu Yongxian Fan Luming Yao Hong Xu Source Type: research

Illuminating key microbial players and metabolic processes involved in the remineralization of particulate organic carbon in the ocean's twilight zone by metaproteomics
This study provides insight into the key bacteria and metabolic processes involved in POC remineralization, and niche complementarity and species substitution among bacterial groups are critical for efficient POC remineralization in the twilight zone. IMPORTANCE The Ocean's twilight zone is a critical zone where more than 70% of the sinking particulate organic carbon (POC) are remineralized. Therefore, the twilight zone determines the size of biological carbon storage in the ocean, and regulates the global climate. Prokaryotes are major players that govern remineralization of POC in this region. However, knowledge of micro...
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Ling-Fen Kong Yan-Bin He Zhang-Xian Xie Xing Luo Hao Zhang Sheng-Hui Yi Zhi-Long Lin Shu-Feng Zhang Ke-Qiang Yan Hong-Kai Xu Tao Jin Lin Lin Wei Qin Feng Chen Si-Qi Liu Da-Zhi Wang Source Type: research

Sequence-specific capture of oligonucleotide probes (SCOPE): A simple and rapid microbial rRNA quantification method using molecular weight cut-off membrane
Appl Environ Microbiol. 2021 Jul 28:AEM0116721. doi: 10.1128/AEM.01167-21. Online ahead of print.ABSTRACTA method named sequence-specific capture of oligonucleotide probes (SCOPE) was developed for quantification of microbial rRNA molecules in a multiplex manner. In this method, molecular weight cut-off membrane (MWCOM) was used for the separation of fluorescent-labeled oligonucleotide probes hybridized with rRNA from free unhybridized probes. To demonstrate proof-of-concept, probes targeting bacteria or archaea at different taxonomic levels were prepared and were hybridized with rRNAs. The hybridization stringency was con...
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Yasuyuki Takemura Yuji Sekiguchi Kazuaki Syutsubo Hideki Harada Tatsuo Omura Yu-You Li Kengo Kubota Source Type: research

Anti-biofilm potential of < em > Lavandula < /em > preparations against < em > Campylobacter jejuni < /em >
This study highlights the need for efforts directed towards such innovative approaches and alternative strategies against biofilm formation and maintenance by developing new naturally derived agents with anti-biofilm activities.PMID:34319799 | DOI:10.1128/AEM.01099-21 (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Dina Rami ć Franz Bucar Urban Kunej Iztok Dog ša Anja Klan čnik Sonja Smole Mo žina Source Type: research

Outer membrane vesicles derived from < em > Salmonella < /em > Typhimurium can deliver < em > Shigella flexneri < /em > 2a O-polysaccharide antigen to prevent < em > Shigella flexneri < /em > 2a infection in mice
Appl Environ Microbiol. 2021 Jul 28:AEM0096821. doi: 10.1128/AEM.00968-21. Online ahead of print.ABSTRACTShigellosis has become a serious threat to health in many developing countries due to the severe diarrhea it causes. Shigella flexneri 2a (S. flexneri 2a) is the principal species responsible for this endemic disease. Despite multiple attempts to design a vaccine against shigellosis, no effective vaccine has not yet been developed. Lipopolysaccharide (LPS) is both an essential virulence factor and an antigen protective against Shigella, due to its outer domain, termed O-polysaccharide antigen. In the present study, S. f...
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Huizhen Tian Biaoxian Li Tian Xu Haolin Yu Jingxuan Chen Haiyan Yu Shan Li Lingbing Zeng Xiaotian Huang Qiong Liu Source Type: research

The fish pathogen < em > Aliivibrio salmonicida < /em > LFI1238 can degrade and metabolize chitin despite major gene loss in the chitinolytic pathway
In conclusion, our results show that Al. salmonicida LFI1238 can utilize chitin as a nutrient source and that the GH18 chitinase and the two LPMOs are needed for this ability. IMPORTANCE The ability to utilize chitin as a source of nutrients is important for the survival and spread of marine microbial pathogens in the environment. One such pathogen is Aliivibrio (Vibrio) salmonicida, the causative agent of cold water vibriosis. Due to extensive gene decay, many key enzymes in the chitinolytic pathway have been disrupted, putatively rendering this bacterium incapable of chitin degradation and utilization. In the present stu...
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Anna Sk åne Giusi Minniti Jennifer S M Loose Sophanit Mekasha Bastien Bissaro Geir Mathiesen Magnus Ø Arntzen Gustav Vaaje-Kolstad Source Type: research

Nutrient deficiency and an algicidal bacterium improved the lipid profiles of a novel promising oleaginous dinoflagellate, < em > Prorocentrum donghaiense, < /em > for biodiesel production
This study demonstrates the high potential of P. donghaiense, a dominant bloom-causing dinoflagellate, for lipid production. Compared with previously studied oleaginous microalgae, P. donghaiense exhibit greater potential for practical application due to its higher biomass and lipid contents. Nutrient deficiency and the algicidal bacterium Paracoccus sp. Y42 could improve the suitability of the lipid profile of P. donghaiense for biodiesel production. Furthermore, Paracoccus sp. Y42 effectively lyse algal cells, which facilitates the downstream oil extraction process for biodiesel production and results in energy savings t...
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Jiali Gui Shuangshuang Chen Guiying Luo Zixiang Wu Yongxian Fan Luming Yao Hong Xu Source Type: research

Illuminating key microbial players and metabolic processes involved in the remineralization of particulate organic carbon in the ocean's twilight zone by metaproteomics
This study provides insight into the key bacteria and metabolic processes involved in POC remineralization, and niche complementarity and species substitution among bacterial groups are critical for efficient POC remineralization in the twilight zone. IMPORTANCE The Ocean's twilight zone is a critical zone where more than 70% of the sinking particulate organic carbon (POC) are remineralized. Therefore, the twilight zone determines the size of biological carbon storage in the ocean, and regulates the global climate. Prokaryotes are major players that govern remineralization of POC in this region. However, knowledge of micro...
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Ling-Fen Kong Yan-Bin He Zhang-Xian Xie Xing Luo Hao Zhang Sheng-Hui Yi Zhi-Long Lin Shu-Feng Zhang Ke-Qiang Yan Hong-Kai Xu Tao Jin Lin Lin Wei Qin Feng Chen Si-Qi Liu Da-Zhi Wang Source Type: research

Sequence-specific capture of oligonucleotide probes (SCOPE): A simple and rapid microbial rRNA quantification method using molecular weight cut-off membrane
Appl Environ Microbiol. 2021 Jul 28:AEM0116721. doi: 10.1128/AEM.01167-21. Online ahead of print.ABSTRACTA method named sequence-specific capture of oligonucleotide probes (SCOPE) was developed for quantification of microbial rRNA molecules in a multiplex manner. In this method, molecular weight cut-off membrane (MWCOM) was used for the separation of fluorescent-labeled oligonucleotide probes hybridized with rRNA from free unhybridized probes. To demonstrate proof-of-concept, probes targeting bacteria or archaea at different taxonomic levels were prepared and were hybridized with rRNAs. The hybridization stringency was con...
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Yasuyuki Takemura Yuji Sekiguchi Kazuaki Syutsubo Hideki Harada Tatsuo Omura Yu-You Li Kengo Kubota Source Type: research

Anti-biofilm potential of < em > Lavandula < /em > preparations against < em > Campylobacter jejuni < /em >
This study highlights the need for efforts directed towards such innovative approaches and alternative strategies against biofilm formation and maintenance by developing new naturally derived agents with anti-biofilm activities.PMID:34319799 | DOI:10.1128/AEM.01099-21 (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Dina Rami ć Franz Bucar Urban Kunej Iztok Dog ša Anja Klan čnik Sonja Smole Mo žina Source Type: research

Outer membrane vesicles derived from < em > Salmonella < /em > Typhimurium can deliver < em > Shigella flexneri < /em > 2a O-polysaccharide antigen to prevent < em > Shigella flexneri < /em > 2a infection in mice
Appl Environ Microbiol. 2021 Jul 28:AEM0096821. doi: 10.1128/AEM.00968-21. Online ahead of print.ABSTRACTShigellosis has become a serious threat to health in many developing countries due to the severe diarrhea it causes. Shigella flexneri 2a (S. flexneri 2a) is the principal species responsible for this endemic disease. Despite multiple attempts to design a vaccine against shigellosis, no effective vaccine has not yet been developed. Lipopolysaccharide (LPS) is both an essential virulence factor and an antigen protective against Shigella, due to its outer domain, termed O-polysaccharide antigen. In the present study, S. f...
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Huizhen Tian Biaoxian Li Tian Xu Haolin Yu Jingxuan Chen Haiyan Yu Shan Li Lingbing Zeng Xiaotian Huang Qiong Liu Source Type: research

The fish pathogen < em > Aliivibrio salmonicida < /em > LFI1238 can degrade and metabolize chitin despite major gene loss in the chitinolytic pathway
In conclusion, our results show that Al. salmonicida LFI1238 can utilize chitin as a nutrient source and that the GH18 chitinase and the two LPMOs are needed for this ability. IMPORTANCE The ability to utilize chitin as a source of nutrients is important for the survival and spread of marine microbial pathogens in the environment. One such pathogen is Aliivibrio (Vibrio) salmonicida, the causative agent of cold water vibriosis. Due to extensive gene decay, many key enzymes in the chitinolytic pathway have been disrupted, putatively rendering this bacterium incapable of chitin degradation and utilization. In the present stu...
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Anna Sk åne Giusi Minniti Jennifer S M Loose Sophanit Mekasha Bastien Bissaro Geir Mathiesen Magnus Ø Arntzen Gustav Vaaje-Kolstad Source Type: research

Nutrient deficiency and an algicidal bacterium improved the lipid profiles of a novel promising oleaginous dinoflagellate, < em > Prorocentrum donghaiense, < /em > for biodiesel production
This study demonstrates the high potential of P. donghaiense, a dominant bloom-causing dinoflagellate, for lipid production. Compared with previously studied oleaginous microalgae, P. donghaiense exhibit greater potential for practical application due to its higher biomass and lipid contents. Nutrient deficiency and the algicidal bacterium Paracoccus sp. Y42 could improve the suitability of the lipid profile of P. donghaiense for biodiesel production. Furthermore, Paracoccus sp. Y42 effectively lyse algal cells, which facilitates the downstream oil extraction process for biodiesel production and results in energy savings t...
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Jiali Gui Shuangshuang Chen Guiying Luo Zixiang Wu Yongxian Fan Luming Yao Hong Xu Source Type: research

Illuminating key microbial players and metabolic processes involved in the remineralization of particulate organic carbon in the ocean's twilight zone by metaproteomics
This study provides insight into the key bacteria and metabolic processes involved in POC remineralization, and niche complementarity and species substitution among bacterial groups are critical for efficient POC remineralization in the twilight zone. IMPORTANCE The Ocean's twilight zone is a critical zone where more than 70% of the sinking particulate organic carbon (POC) are remineralized. Therefore, the twilight zone determines the size of biological carbon storage in the ocean, and regulates the global climate. Prokaryotes are major players that govern remineralization of POC in this region. However, knowledge of micro...
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Ling-Fen Kong Yan-Bin He Zhang-Xian Xie Xing Luo Hao Zhang Sheng-Hui Yi Zhi-Long Lin Shu-Feng Zhang Ke-Qiang Yan Hong-Kai Xu Tao Jin Lin Lin Wei Qin Feng Chen Si-Qi Liu Da-Zhi Wang Source Type: research

Sequence-specific capture of oligonucleotide probes (SCOPE): A simple and rapid microbial rRNA quantification method using molecular weight cut-off membrane
Appl Environ Microbiol. 2021 Jul 28:AEM0116721. doi: 10.1128/AEM.01167-21. Online ahead of print.ABSTRACTA method named sequence-specific capture of oligonucleotide probes (SCOPE) was developed for quantification of microbial rRNA molecules in a multiplex manner. In this method, molecular weight cut-off membrane (MWCOM) was used for the separation of fluorescent-labeled oligonucleotide probes hybridized with rRNA from free unhybridized probes. To demonstrate proof-of-concept, probes targeting bacteria or archaea at different taxonomic levels were prepared and were hybridized with rRNAs. The hybridization stringency was con...
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Yasuyuki Takemura Yuji Sekiguchi Kazuaki Syutsubo Hideki Harada Tatsuo Omura Yu-You Li Kengo Kubota Source Type: research

Anti-biofilm potential of < em > Lavandula < /em > preparations against < em > Campylobacter jejuni < /em >
This study highlights the need for efforts directed towards such innovative approaches and alternative strategies against biofilm formation and maintenance by developing new naturally derived agents with anti-biofilm activities.PMID:34319799 | DOI:10.1128/AEM.01099-21 (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Dina Rami ć Franz Bucar Urban Kunej Iztok Dog ša Anja Klan čnik Sonja Smole Mo žina Source Type: research

Outer membrane vesicles derived from < em > Salmonella < /em > Typhimurium can deliver < em > Shigella flexneri < /em > 2a O-polysaccharide antigen to prevent < em > Shigella flexneri < /em > 2a infection in mice
Appl Environ Microbiol. 2021 Jul 28:AEM0096821. doi: 10.1128/AEM.00968-21. Online ahead of print.ABSTRACTShigellosis has become a serious threat to health in many developing countries due to the severe diarrhea it causes. Shigella flexneri 2a (S. flexneri 2a) is the principal species responsible for this endemic disease. Despite multiple attempts to design a vaccine against shigellosis, no effective vaccine has not yet been developed. Lipopolysaccharide (LPS) is both an essential virulence factor and an antigen protective against Shigella, due to its outer domain, termed O-polysaccharide antigen. In the present study, S. f...
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Huizhen Tian Biaoxian Li Tian Xu Haolin Yu Jingxuan Chen Haiyan Yu Shan Li Lingbing Zeng Xiaotian Huang Qiong Liu Source Type: research

The fish pathogen < em > Aliivibrio salmonicida < /em > LFI1238 can degrade and metabolize chitin despite major gene loss in the chitinolytic pathway
In conclusion, our results show that Al. salmonicida LFI1238 can utilize chitin as a nutrient source and that the GH18 chitinase and the two LPMOs are needed for this ability. IMPORTANCE The ability to utilize chitin as a source of nutrients is important for the survival and spread of marine microbial pathogens in the environment. One such pathogen is Aliivibrio (Vibrio) salmonicida, the causative agent of cold water vibriosis. Due to extensive gene decay, many key enzymes in the chitinolytic pathway have been disrupted, putatively rendering this bacterium incapable of chitin degradation and utilization. In the present stu...
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Anna Sk åne Giusi Minniti Jennifer S M Loose Sophanit Mekasha Bastien Bissaro Geir Mathiesen Magnus Ø Arntzen Gustav Vaaje-Kolstad Source Type: research

Nutrient deficiency and an algicidal bacterium improved the lipid profiles of a novel promising oleaginous dinoflagellate, < em > Prorocentrum donghaiense, < /em > for biodiesel production
This study demonstrates the high potential of P. donghaiense, a dominant bloom-causing dinoflagellate, for lipid production. Compared with previously studied oleaginous microalgae, P. donghaiense exhibit greater potential for practical application due to its higher biomass and lipid contents. Nutrient deficiency and the algicidal bacterium Paracoccus sp. Y42 could improve the suitability of the lipid profile of P. donghaiense for biodiesel production. Furthermore, Paracoccus sp. Y42 effectively lyse algal cells, which facilitates the downstream oil extraction process for biodiesel production and results in energy savings t...
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Jiali Gui Shuangshuang Chen Guiying Luo Zixiang Wu Yongxian Fan Luming Yao Hong Xu Source Type: research

Illuminating key microbial players and metabolic processes involved in the remineralization of particulate organic carbon in the ocean's twilight zone by metaproteomics
This study provides insight into the key bacteria and metabolic processes involved in POC remineralization, and niche complementarity and species substitution among bacterial groups are critical for efficient POC remineralization in the twilight zone. IMPORTANCE The Ocean's twilight zone is a critical zone where more than 70% of the sinking particulate organic carbon (POC) are remineralized. Therefore, the twilight zone determines the size of biological carbon storage in the ocean, and regulates the global climate. Prokaryotes are major players that govern remineralization of POC in this region. However, knowledge of micro...
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Ling-Fen Kong Yan-Bin He Zhang-Xian Xie Xing Luo Hao Zhang Sheng-Hui Yi Zhi-Long Lin Shu-Feng Zhang Ke-Qiang Yan Hong-Kai Xu Tao Jin Lin Lin Wei Qin Feng Chen Si-Qi Liu Da-Zhi Wang Source Type: research

Sequence-specific capture of oligonucleotide probes (SCOPE): A simple and rapid microbial rRNA quantification method using molecular weight cut-off membrane
Appl Environ Microbiol. 2021 Jul 28:AEM0116721. doi: 10.1128/AEM.01167-21. Online ahead of print.ABSTRACTA method named sequence-specific capture of oligonucleotide probes (SCOPE) was developed for quantification of microbial rRNA molecules in a multiplex manner. In this method, molecular weight cut-off membrane (MWCOM) was used for the separation of fluorescent-labeled oligonucleotide probes hybridized with rRNA from free unhybridized probes. To demonstrate proof-of-concept, probes targeting bacteria or archaea at different taxonomic levels were prepared and were hybridized with rRNAs. The hybridization stringency was con...
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Yasuyuki Takemura Yuji Sekiguchi Kazuaki Syutsubo Hideki Harada Tatsuo Omura Yu-You Li Kengo Kubota Source Type: research

Anti-biofilm potential of < em > Lavandula < /em > preparations against < em > Campylobacter jejuni < /em >
This study highlights the need for efforts directed towards such innovative approaches and alternative strategies against biofilm formation and maintenance by developing new naturally derived agents with anti-biofilm activities.PMID:34319799 | DOI:10.1128/AEM.01099-21 (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Dina Rami ć Franz Bucar Urban Kunej Iztok Dog ša Anja Klan čnik Sonja Smole Mo žina Source Type: research

Outer membrane vesicles derived from < em > Salmonella < /em > Typhimurium can deliver < em > Shigella flexneri < /em > 2a O-polysaccharide antigen to prevent < em > Shigella flexneri < /em > 2a infection in mice
Appl Environ Microbiol. 2021 Jul 28:AEM0096821. doi: 10.1128/AEM.00968-21. Online ahead of print.ABSTRACTShigellosis has become a serious threat to health in many developing countries due to the severe diarrhea it causes. Shigella flexneri 2a (S. flexneri 2a) is the principal species responsible for this endemic disease. Despite multiple attempts to design a vaccine against shigellosis, no effective vaccine has not yet been developed. Lipopolysaccharide (LPS) is both an essential virulence factor and an antigen protective against Shigella, due to its outer domain, termed O-polysaccharide antigen. In the present study, S. f...
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Huizhen Tian Biaoxian Li Tian Xu Haolin Yu Jingxuan Chen Haiyan Yu Shan Li Lingbing Zeng Xiaotian Huang Qiong Liu Source Type: research

The fish pathogen < em > Aliivibrio salmonicida < /em > LFI1238 can degrade and metabolize chitin despite major gene loss in the chitinolytic pathway
In conclusion, our results show that Al. salmonicida LFI1238 can utilize chitin as a nutrient source and that the GH18 chitinase and the two LPMOs are needed for this ability. IMPORTANCE The ability to utilize chitin as a source of nutrients is important for the survival and spread of marine microbial pathogens in the environment. One such pathogen is Aliivibrio (Vibrio) salmonicida, the causative agent of cold water vibriosis. Due to extensive gene decay, many key enzymes in the chitinolytic pathway have been disrupted, putatively rendering this bacterium incapable of chitin degradation and utilization. In the present stu...
Source: Applied and Environmental Microbiology - July 28, 2021 Category: Microbiology Authors: Anna Sk åne Giusi Minniti Jennifer S M Loose Sophanit Mekasha Bastien Bissaro Geir Mathiesen Magnus Ø Arntzen Gustav Vaaje-Kolstad Source Type: research

Articles of Significant Interest in This Issue
Appl Environ Microbiol. 2021 Jul 27;87(16):e0118221. doi: 10.1128/AEM.01182-21. Epub 2021 Jul 27.NO ABSTRACTPMID:34313494 | DOI:10.1128/AEM.01182-21 (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - July 27, 2021 Category: Microbiology Source Type: research

Retracted and Republished from: "Substrate-Specific Differential Gene Expression and RNA Editing in the Brown Rot Fungus < em > Fomitopsis pinicola < /em > "
This study provides clues to how wood-decaying fungi may adjust their arsenal of decay enzymes to accommodate different host substrates.PMID:34313495 | DOI:10.1128/AEM.00329-21 (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - July 27, 2021 Category: Microbiology Authors: Baojun Wu Jill Gaskell Benjamin W Held Cristina Toapanta Thu V Vuong Steven Ahrendt Anna Lipzen Jiwei Zhang Jonathan S Schilling Emma Master Igor V Grigoriev Robert A Blanchette Dan Cullen David S Hibbett Source Type: research

Retraction for Wu et al., "Substrate-Specific Differential Gene Expression and RNA Editing in the Brown Rot Fungus < em > Fomitopsis pinicola < /em > "
Appl Environ Microbiol. 2021 Jul 27;87(16):e0033021. doi: 10.1128/AEM.00330-21. Epub 2021 Jul 27.NO ABSTRACTPMID:34313496 | DOI:10.1128/AEM.00330-21 (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - July 27, 2021 Category: Microbiology Authors: Baojun Wu Jill Gaskell Benjamin W Held Cristina Toapanta Thu Vuong Steven Ahrendt Anna Lipzen Jiwei Zhang Jonathan S Schilling Emma Master Igor V Grigoriev Robert A Blanchette Dan Cullen David S Hibbett Source Type: research

Eight metagenome-assembled genomes provide evidence for microbial adaptation in 20,000 to 1,000,000-year-old Siberian permafrost
Appl Environ Microbiol. 2021 Jul 21:AEM0097221. doi: 10.1128/AEM.00972-21. Online ahead of print.ABSTRACTPermafrost microbes may be metabolically active in microscopic layers of liquid brines, even in ancient soil. Metagenomics can help discern whether permafrost microbes show adaptations to this environment. Thirty-three metagenome-assembled genomes (MAGs) were obtained from six depths (3.5 m to 20 m) of freshly-cored permafrost from the Siberia Kolyma-Indigirka Lowland region. These soils have been continuously frozen for ∼20,000 to 1,000,000 years. Eight of these MAGs were ≥80% complete with
Source: Applied and Environmental Microbiology - July 21, 2021 Category: Microbiology Authors: Katie Sipes Abraham Almatari Alexander Eddie Daniel Williams Elena Spirina Elizaveta Rivkina Renxing Liang Tullis C Onstott Tatiana Vishnivetskaya Karen G Lloyd Source Type: research

Genomic evolution of the marine bacterium < em > Phaeobacter inhibens < /em > during biofilm growth
This study aimed to elucidate the genetic basis of these phenotypic changes. Despite the progress made to date in characterizing the dispersal variants in P. inhibens, little is understood about the underlying genetic changes that result in the development of the specific variants. Here, P. inhibens phenotypic variation was linked to single nucleotide polymorphisms (SNPs), in particular in genes affecting the competitive ability of P. inhibens, including genes related to the production of the antibiotic tropodithietic acid (TDA) and bacterial cell-cell communication (e.g. quorum sensing). This work is significant as it rev...
Source: Applied and Environmental Microbiology - July 21, 2021 Category: Microbiology Authors: Marwan E Majzoub Kerensa McElroy Michael Maczka Stefan Schulz Torsten Thomas Suhelen Egan Source Type: research

Heat-treated virus inactivation rate depends strongly on treatment procedure: illustration with SARS-CoV-2
Appl Environ Microbiol. 2021 Jul 21:AEM0031421. doi: 10.1128/AEM.00314-21. Online ahead of print.ABSTRACTDecontamination helps limit environmental transmission of infectious agents. It is required for the safe re-use of contaminated medical, laboratory and personal protective equipment, and for the safe handling of biological samples. Heat treatment is a common decontamination method, notably used for viruses. We show that for liquid specimens (here, solution of SARS-CoV-2 in cell culture medium), virus inactivation rate under heat treatment at 70°C can vary by almost two orders of magnitude depending on the treatment ...
Source: Applied and Environmental Microbiology - July 21, 2021 Category: Microbiology Authors: Amandine Gamble Robert J Fischer Dylan H Morris Kwe Claude Yinda Vincent J Munster James O Lloyd-Smith Source Type: research

The functional expression in yeast of two unusual acidic peroxygenases from < em > Candolleomyces aberdarensis < /em > by adopting evolved secretion mutations
Appl Environ Microbiol. 2021 Jul 21:AEM0087821. doi: 10.1128/AEM.00878-21. Online ahead of print.ABSTRACTFungal unspecific peroxygenases (UPOs) are emergent biocatalysts that perform highly selective C-H oxyfunctionalizations of organic compounds, yet their heterologous production at high levels is required for their practical use in synthetic chemistry. Here, we achieved functional expression in yeast of two new unusual acidic peroxygenases from Candolleomyces (Psathyrella) aberdarensis (PabUPO) and their production at large scale in bioreactor. Our strategy was based on adopting secretion mutations from Agrocybe aegerita...
Source: Applied and Environmental Microbiology - July 21, 2021 Category: Microbiology Authors: Patricia Gomez de Santos Manh Dat Hoang Jan Kiebist Harald Kellner Ren é Ullrich Katrin Scheibner Martin Hofrichter Christiane Liers Miguel Alcalde Source Type: research

Improving mobilization of foreign DNA into < em > Zymomonas mobilis < /em > ZM4 by removal of multiple restriction systems
In this study we have developed an all-purpose strain, devoid of known host restriction systems and free of any antibiotic resistance markers, which dramatically improves the uptake efficiency of heterologous DNA into Z. mobilis ZM4. We also confirmed the role of a previously known restriction system as well as identified a previously unknown Type I RM system on an endogenous plasmid. Elimination of the barriers to DNA uptake as shown here will allow facile genetic engineering of Z. mobilis.PMID:34288704 | DOI:10.1128/AEM.00808-21 (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - July 21, 2021 Category: Microbiology Authors: Piyush Behari Lal Fritz Wells Kevin S Myers Rajdeep Banerjee Adam M Guss Patricia J Kiley Source Type: research

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) is essential for growth of the methanotroph < em > Methylococcus capsulatus < /em > Bath
This study expands the known capacity of methanotrophs to fix CO2 via RubisCO, which may play a more pivotal role in the Earth's biogeochemical carbon cycling and greenhouse gas regulation than previously recognized. Further, M. capsulatus Bath and other CO2-assimilating methanotrophs represent excellent candidates for use in the bioconversion of biogas waste streams that consist of both CH4 and CO2. Importance The importance of RubisCO and CO2 in M. capsulatus Bath metabolism is unclear. In this study, we demonstrated that both CO2 and RubisCO are essential for M. capsulatus Bath growth. 13CO2 tracing experiments supporte...
Source: Applied and Environmental Microbiology - July 21, 2021 Category: Microbiology Authors: Calvin A Henard Chao Wu Wei Xiong Jessica M Henard Brett Davidheiser-Kroll Fabini D Orata Michael T Guarnieri Source Type: research

Comparative Investigation of Fifteen Xenobiotic Metabolizing < em > N < /em > -Acetyltransferase (NAT) Homologs from Bacteria
Appl Environ Microbiol. 2021 Jul 21:AEM0081921. doi: 10.1128/AEM.00819-21. Online ahead of print.ABSTRACTArylamines constitute a large group of industrial chemicals detoxified by certain bacteria through conjugation reactions catalyzed by N-acetyltransferase (NAT) enzymes. NAT homologs, mostly from pathogenic bacteria, have been the subject of individual studies that do not facilitate direct comparisons. By implementing a practicable pipeline, we present comparative investigation of fifteen NAT homologs from ten bacteria, mainly bacilli, streptomycetes, and one alphaproteobacterium. The new homologs were characterized for ...
Source: Applied and Environmental Microbiology - July 21, 2021 Category: Microbiology Authors: Vasiliki Garefalaki Maria-Giusy Papavergi Olga Savvidou Georgia Papanikolaou Tam ás Felföldi K ároly Márialigeti Giannoulis Fakis Sotiria Boukouvala Source Type: research

Assessment of antiviral coatings for high-touch surfaces using human coronaviruses HCoV-229E and SARS-CoV-2
Appl Environ Microbiol. 2021 Jul 21:AEM0109821. doi: 10.1128/AEM.01098-21. Online ahead of print.ABSTRACTA novel and robust approach to evaluate the antiviral activity of coatings was developed, assessing three commercially available leave-on surface coating products for efficacy against human coronaviruses HCoV-229E and SARS-CoV-2. The assessment is based on three criteria that reflect real-life settings, namely (i) immediate antiviral effect, (ii) effect after repeated cleaning of the coated surface, and (iii) antiviral activity in the presence of organic material. The results showed that only a copper compound-based coa...
Source: Applied and Environmental Microbiology - July 21, 2021 Category: Microbiology Authors: S Butot L Baert S Zuber Source Type: research

Exploration of social spreading reveals behavior is prevalent among < em > Pedobacter < /em > and < em > P. fluorescens < /em > isolates, and shows variations in induction of phenotype
Appl Environ Microbiol. 2021 Jul 21:AEM0134421. doi: 10.1128/AEM.01344-21. Online ahead of print.ABSTRACTWithin soil, bacteria are found in multi-species communities, where interactions can lead to emergent community properties. Studying bacteria in a social context is critical for investigation of community-level functions. We previously showed that co-cultured Pseudomonas fluorescens Pf0-1 and Pedobacter sp. V48 engage in interspecies social spreading (ISS) on a hard agar surface, a behavior which required close contact and depended on the nutritional environment. Here, we investigate whether social spreading is widespre...
Source: Applied and Environmental Microbiology - July 21, 2021 Category: Microbiology Authors: Lucy M McCully Jasmine Graslie Alana R McGraw Adam S Bitzer Au ður M Sigurbjörnsdóttir Oddur Vilhelmsson Mark W Silby Source Type: research

Phospholipid < em > N < /em > -methyltransferases produce various methylated phosphatidylethanolamine derivatives in thermophilic bacteria
Appl Environ Microbiol. 2021 Jul 21:AEM0110521. doi: 10.1128/AEM.01105-21. Online ahead of print.ABSTRACTOne of the most common pathways for the biosynthesis of the phospholipid phosphatidylcholine (PC) in bacteria is the successive three-fold N-methylation of phosphatidylethanolamine (PE) catalyzed by phospholipid N-methyltransferases (Pmts). Pmts with different activities have been described in a number of mesophilic bacteria. In the present study, we identified and characterized the substrate and product spectrum of four Pmts from thermophilic bacteria. Three of these enzymes were purified in an active form. The Pmts fr...
Source: Applied and Environmental Microbiology - July 21, 2021 Category: Microbiology Authors: Julia Kleetz Leon Welter Ann-Sophie Mizza Meriyem Aktas Franz Narberhaus Source Type: research

Dipeptidase PEPDA is required for the conidiation pattern shift in < em > Metarhizium acridum < /em >
In this study, we investigated the role of a dipeptidase gene pepdA in conidiation pattern shift in Metarhizium acridum, which is upregulated in MC pattern compared to typical conidiation. Results showed that disruption of the pepdA resulted in a shift of conidiation pattern from MC to typical conidiation. Metabolomic analyses of amino acids showed that the levels of 19 amino acids significantly changed in ΔpepdA mutant. The defect of MC in ΔpepdA can be rescued when nonpolar amino acids, α-alanine, β-alanine or proline, were added into sucrose yeast extract agar (SYA) medium. Digital gene expression...
Source: Applied and Environmental Microbiology - July 21, 2021 Category: Microbiology Authors: Juan Li Xueling Su Yueqing Cao Yuxian Xia Source Type: research

Eight metagenome-assembled genomes provide evidence for microbial adaptation in 20,000 to 1,000,000-year-old Siberian permafrost
Appl Environ Microbiol. 2021 Jul 21:AEM0097221. doi: 10.1128/AEM.00972-21. Online ahead of print.ABSTRACTPermafrost microbes may be metabolically active in microscopic layers of liquid brines, even in ancient soil. Metagenomics can help discern whether permafrost microbes show adaptations to this environment. Thirty-three metagenome-assembled genomes (MAGs) were obtained from six depths (3.5 m to 20 m) of freshly-cored permafrost from the Siberia Kolyma-Indigirka Lowland region. These soils have been continuously frozen for ∼20,000 to 1,000,000 years. Eight of these MAGs were ≥80% complete with
Source: Applied and Environmental Microbiology - July 21, 2021 Category: Microbiology Authors: Katie Sipes Abraham Almatari Alexander Eddie Daniel Williams Elena Spirina Elizaveta Rivkina Renxing Liang Tullis C Onstott Tatiana Vishnivetskaya Karen G Lloyd Source Type: research

Genomic evolution of the marine bacterium < em > Phaeobacter inhibens < /em > during biofilm growth
This study aimed to elucidate the genetic basis of these phenotypic changes. Despite the progress made to date in characterizing the dispersal variants in P. inhibens, little is understood about the underlying genetic changes that result in the development of the specific variants. Here, P. inhibens phenotypic variation was linked to single nucleotide polymorphisms (SNPs), in particular in genes affecting the competitive ability of P. inhibens, including genes related to the production of the antibiotic tropodithietic acid (TDA) and bacterial cell-cell communication (e.g. quorum sensing). This work is significant as it rev...
Source: Applied and Environmental Microbiology - July 21, 2021 Category: Microbiology Authors: Marwan E Majzoub Kerensa McElroy Michael Maczka Stefan Schulz Torsten Thomas Suhelen Egan Source Type: research

Heat-treated virus inactivation rate depends strongly on treatment procedure: illustration with SARS-CoV-2
Appl Environ Microbiol. 2021 Jul 21:AEM0031421. doi: 10.1128/AEM.00314-21. Online ahead of print.ABSTRACTDecontamination helps limit environmental transmission of infectious agents. It is required for the safe re-use of contaminated medical, laboratory and personal protective equipment, and for the safe handling of biological samples. Heat treatment is a common decontamination method, notably used for viruses. We show that for liquid specimens (here, solution of SARS-CoV-2 in cell culture medium), virus inactivation rate under heat treatment at 70°C can vary by almost two orders of magnitude depending on the treatment ...
Source: Applied and Environmental Microbiology - July 21, 2021 Category: Microbiology Authors: Amandine Gamble Robert J Fischer Dylan H Morris Kwe Claude Yinda Vincent J Munster James O Lloyd-Smith Source Type: research

The functional expression in yeast of two unusual acidic peroxygenases from < em > Candolleomyces aberdarensis < /em > by adopting evolved secretion mutations
Appl Environ Microbiol. 2021 Jul 21:AEM0087821. doi: 10.1128/AEM.00878-21. Online ahead of print.ABSTRACTFungal unspecific peroxygenases (UPOs) are emergent biocatalysts that perform highly selective C-H oxyfunctionalizations of organic compounds, yet their heterologous production at high levels is required for their practical use in synthetic chemistry. Here, we achieved functional expression in yeast of two new unusual acidic peroxygenases from Candolleomyces (Psathyrella) aberdarensis (PabUPO) and their production at large scale in bioreactor. Our strategy was based on adopting secretion mutations from Agrocybe aegerita...
Source: Applied and Environmental Microbiology - July 21, 2021 Category: Microbiology Authors: Patricia Gomez de Santos Manh Dat Hoang Jan Kiebist Harald Kellner Ren é Ullrich Katrin Scheibner Martin Hofrichter Christiane Liers Miguel Alcalde Source Type: research

Improving mobilization of foreign DNA into < em > Zymomonas mobilis < /em > ZM4 by removal of multiple restriction systems
In this study we have developed an all-purpose strain, devoid of known host restriction systems and free of any antibiotic resistance markers, which dramatically improves the uptake efficiency of heterologous DNA into Z. mobilis ZM4. We also confirmed the role of a previously known restriction system as well as identified a previously unknown Type I RM system on an endogenous plasmid. Elimination of the barriers to DNA uptake as shown here will allow facile genetic engineering of Z. mobilis.PMID:34288704 | DOI:10.1128/AEM.00808-21 (Source: Applied and Environmental Microbiology)
Source: Applied and Environmental Microbiology - July 21, 2021 Category: Microbiology Authors: Piyush Behari Lal Fritz Wells Kevin S Myers Rajdeep Banerjee Adam M Guss Patricia J Kiley Source Type: research

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) is essential for growth of the methanotroph < em > Methylococcus capsulatus < /em > Bath
This study expands the known capacity of methanotrophs to fix CO2 via RubisCO, which may play a more pivotal role in the Earth's biogeochemical carbon cycling and greenhouse gas regulation than previously recognized. Further, M. capsulatus Bath and other CO2-assimilating methanotrophs represent excellent candidates for use in the bioconversion of biogas waste streams that consist of both CH4 and CO2. Importance The importance of RubisCO and CO2 in M. capsulatus Bath metabolism is unclear. In this study, we demonstrated that both CO2 and RubisCO are essential for M. capsulatus Bath growth. 13CO2 tracing experiments supporte...
Source: Applied and Environmental Microbiology - July 21, 2021 Category: Microbiology Authors: Calvin A Henard Chao Wu Wei Xiong Jessica M Henard Brett Davidheiser-Kroll Fabini D Orata Michael T Guarnieri Source Type: research